Starting phenix.real_space_refine on Sun Mar 17 09:56:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d82_27244/03_2024/8d82_27244.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d82_27244/03_2024/8d82_27244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d82_27244/03_2024/8d82_27244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d82_27244/03_2024/8d82_27244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d82_27244/03_2024/8d82_27244.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d82_27244/03_2024/8d82_27244.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 10970 2.51 5 N 2920 2.21 5 O 3390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 29": "OE1" <-> "OE2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ASP 162": "OD1" <-> "OD2" Residue "D ASP 168": "OD1" <-> "OD2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 602": "OD1" <-> "OD2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G ASP 41": "OD1" <-> "OD2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 111": "OD1" <-> "OD2" Residue "G PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G ARG 287": "NH1" <-> "NH2" Residue "G PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 302": "OE1" <-> "OE2" Residue "G GLU 305": "OE1" <-> "OE2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 58": "NH1" <-> "NH2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 68": "NH1" <-> "NH2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 162": "OD1" <-> "OD2" Residue "H ASP 168": "OD1" <-> "OD2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ASP 185": "OD1" <-> "OD2" Residue "E PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 265": "OD1" <-> "OD2" Residue "E PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 325": "NH1" <-> "NH2" Residue "E ASP 337": "OD1" <-> "OD2" Residue "E TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 365": "OD1" <-> "OD2" Residue "E TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 410": "OD1" <-> "OD2" Residue "E ASP 420": "OD1" <-> "OD2" Residue "E ASP 429": "OD1" <-> "OD2" Residue "E GLU 448": "OE1" <-> "OE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 474": "OD1" <-> "OD2" Residue "E GLU 508": "OE1" <-> "OE2" Residue "E GLU 534": "OE1" <-> "OE2" Residue "E GLU 538": "OE1" <-> "OE2" Residue "E PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 565": "OE1" <-> "OE2" Residue "E GLU 576": "OE1" <-> "OE2" Residue "E TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 602": "OD1" <-> "OD2" Residue "E GLU 605": "OE1" <-> "OE2" Residue "E PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17366 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2340 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 23, 'TRANS': 272} Chain: "D" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1358 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "A" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4719 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 553} Chain: "G" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2340 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 23, 'TRANS': 272} Chain: "H" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1358 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "E" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4719 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 553} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ARG C 101 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG C 101 " occ=0.00 residue: pdb=" N ASN C 155 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN C 155 " occ=0.00 residue: pdb=" N SER C 156 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER C 156 " occ=0.00 residue: pdb=" N ARG G 101 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG G 101 " occ=0.00 residue: pdb=" N ASN G 155 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN G 155 " occ=0.00 residue: pdb=" N SER G 156 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER G 156 " occ=0.00 residue: pdb=" C1 NAG I 2 " occ=0.50 ... (12 atoms not shown) pdb=" O7 NAG I 2 " occ=0.50 residue: pdb=" C1 NAG N 2 " occ=0.50 ... (12 atoms not shown) pdb=" O7 NAG N 2 " occ=0.50 Time building chain proxies: 8.59, per 1000 atoms: 0.49 Number of scatterers: 17366 At special positions: 0 Unit cell: (172.55, 209.95, 166.6, 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 86 16.00 O 3390 8.00 N 2920 7.00 C 10970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 132 " distance=2.03 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 54 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS G 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 47 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS G 132 " distance=2.03 Simple disulfide: pdb=" SG CYS G 165 " - pdb=" SG CYS G 176 " distance=2.03 Simple disulfide: pdb=" SG CYS H 72 " - pdb=" SG CYS H 78 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 111 " distance=2.03 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 54 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 103 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 144 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 458 " - pdb=" SG CYS E 466 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A 801 " - " ASN A 227 " " NAG A 802 " - " ASN A 157 " " NAG A 803 " - " ASN A 383 " " NAG A 804 " - " ASN A 379 " " NAG A 805 " - " ASN A 390 " " NAG A 806 " - " ASN A 564 " " NAG B 1 " - " ASN C 245 " " NAG C 401 " - " ASN C 221 " " NAG C 402 " - " ASN C 55 " " NAG C 403 " - " ASN C 93 " " NAG E 801 " - " ASN E 227 " " NAG E 802 " - " ASN E 157 " " NAG E 803 " - " ASN E 383 " " NAG E 804 " - " ASN E 379 " " NAG E 805 " - " ASN E 390 " " NAG E 806 " - " ASN E 564 " " NAG F 1 " - " ASN A 83 " " NAG G 401 " - " ASN G 221 " " NAG G 402 " - " ASN G 55 " " NAG G 403 " - " ASN G 93 " " NAG I 1 " - " ASN A 553 " " NAG J 1 " - " ASN A 43 " " NAG K 1 " - " ASN A 131 " " NAG L 1 " - " ASN G 245 " " NAG M 1 " - " ASN E 83 " " NAG N 1 " - " ASN E 553 " " NAG O 1 " - " ASN E 43 " " NAG P 1 " - " ASN E 131 " Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 2.8 seconds 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4028 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 46 sheets defined 13.9% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.528A pdb=" N SER C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 75 removed outlier: 3.740A pdb=" N ILE D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.714A pdb=" N GLY D 100 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 130 removed outlier: 4.517A pdb=" N VAL D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 156 removed outlier: 3.579A pdb=" N ALA D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 143 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 179 removed outlier: 3.540A pdb=" N LEU D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 211 removed outlier: 4.076A pdb=" N GLN D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.289A pdb=" N SER A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.833A pdb=" N ALA A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 4.332A pdb=" N ASN A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.528A pdb=" N SER G 91 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 75 removed outlier: 3.745A pdb=" N ILE H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN H 73 " --> pdb=" O LYS H 69 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.716A pdb=" N GLY H 100 " --> pdb=" O GLU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 130 removed outlier: 4.527A pdb=" N VAL H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR H 125 " --> pdb=" O GLU H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 156 removed outlier: 3.580A pdb=" N ALA H 142 " --> pdb=" O GLU H 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL H 143 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 179 removed outlier: 3.534A pdb=" N LEU H 176 " --> pdb=" O ASN H 172 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 211 removed outlier: 4.087A pdb=" N GLN H 211 " --> pdb=" O ARG H 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 Processing helix chain 'E' and resid 247 through 252 removed outlier: 4.287A pdb=" N SER E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 278 removed outlier: 3.833A pdb=" N ALA E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 548 removed outlier: 4.332A pdb=" N ASN E 548 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 37 removed outlier: 3.819A pdb=" N SER C 37 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.924A pdb=" N VAL C 43 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.660A pdb=" N SER C 120 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP C 134 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 166 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 159 through 163 removed outlier: 3.566A pdb=" N GLU C 159 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 152 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 161 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 150 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 187 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 159 through 163 removed outlier: 3.566A pdb=" N GLU C 159 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 152 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 161 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 150 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 187 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 220 through 226 removed outlier: 5.978A pdb=" N ASN C 221 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN C 239 " --> pdb=" O ASN C 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 266 through 269 Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 88 removed outlier: 7.021A pdb=" N ASP E 26 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.960A pdb=" N ASP A 26 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.598A pdb=" N TYR A 30 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 66 through 68 removed outlier: 6.219A pdb=" N ILE A 105 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASN A 114 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 142 through 147 removed outlier: 6.807A pdb=" N ARG A 143 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS A 134 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU A 145 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 132 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 130 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LYS A 221 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 136 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 172 through 173 removed outlier: 4.029A pdb=" N ASN A 157 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 201 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 195 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 172 through 173 removed outlier: 4.029A pdb=" N ASN A 157 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 201 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 195 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 226 through 231 removed outlier: 4.272A pdb=" N LEU A 228 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR A 243 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 230 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 241 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 240 " --> pdb=" O VAL A 286 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 255 through 257 Processing sheet with id=AB8, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AB9, first strand: chain 'A' and resid 332 through 335 removed outlier: 3.740A pdb=" N VAL A 389 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 387 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 376 through 382 removed outlier: 4.044A pdb=" N HIS A 376 " --> pdb=" O ARG A 372 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 370 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 380 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A 365 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 371 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 397 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 430 through 432 removed outlier: 4.256A pdb=" N VAL A 441 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR A 480 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 469 through 474 removed outlier: 4.027A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 458 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 503 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 469 through 474 removed outlier: 4.027A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 458 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 508 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 566 through 571 removed outlier: 3.563A pdb=" N VAL A 568 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 553 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 589 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 594 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 601 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 566 through 571 removed outlier: 3.563A pdb=" N VAL A 568 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 553 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 589 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 606 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 34 through 37 removed outlier: 3.819A pdb=" N SER G 37 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 43 through 44 removed outlier: 3.924A pdb=" N VAL G 43 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.660A pdb=" N SER G 120 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP G 134 " --> pdb=" O PHE G 174 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN G 166 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 159 through 163 removed outlier: 3.563A pdb=" N GLU G 159 " --> pdb=" O LYS G 152 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS G 152 " --> pdb=" O GLU G 159 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G 161 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL G 150 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE G 187 " --> pdb=" O PHE G 153 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 159 through 163 removed outlier: 3.563A pdb=" N GLU G 159 " --> pdb=" O LYS G 152 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS G 152 " --> pdb=" O GLU G 159 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G 161 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL G 150 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE G 187 " --> pdb=" O PHE G 153 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 220 through 226 removed outlier: 5.978A pdb=" N ASN G 221 " --> pdb=" O GLN G 239 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN G 239 " --> pdb=" O ASN G 221 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 266 through 269 Processing sheet with id=AD5, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.587A pdb=" N TYR E 30 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 66 through 68 removed outlier: 6.217A pdb=" N ILE E 105 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASN E 114 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 142 through 147 removed outlier: 6.807A pdb=" N ARG E 143 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS E 134 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU E 145 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU E 132 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS E 130 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS E 221 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL E 136 " --> pdb=" O LYS E 221 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 172 through 173 removed outlier: 4.029A pdb=" N ASN E 157 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU E 201 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU E 195 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 172 through 173 removed outlier: 4.029A pdb=" N ASN E 157 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU E 201 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU E 195 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 226 through 231 removed outlier: 4.272A pdb=" N LEU E 228 " --> pdb=" O THR E 243 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR E 243 " --> pdb=" O LEU E 228 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL E 230 " --> pdb=" O LYS E 241 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS E 241 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU E 240 " --> pdb=" O VAL E 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 255 through 257 Processing sheet with id=AE3, first strand: chain 'E' and resid 270 through 271 Processing sheet with id=AE4, first strand: chain 'E' and resid 332 through 335 removed outlier: 3.740A pdb=" N VAL E 389 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 387 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 376 through 382 removed outlier: 4.044A pdb=" N HIS E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 370 " --> pdb=" O GLN E 378 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR E 380 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP E 365 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 371 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU E 397 " --> pdb=" O THR E 371 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 430 through 432 removed outlier: 4.256A pdb=" N VAL E 441 " --> pdb=" O THR E 480 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR E 480 " --> pdb=" O VAL E 441 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 469 through 474 removed outlier: 4.027A pdb=" N LYS E 452 " --> pdb=" O VAL E 499 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS E 458 " --> pdb=" O LEU E 493 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY E 503 " --> pdb=" O TYR E 500 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 469 through 474 removed outlier: 4.027A pdb=" N LYS E 452 " --> pdb=" O VAL E 499 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS E 458 " --> pdb=" O LEU E 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU E 508 " --> pdb=" O VAL E 496 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 566 through 571 removed outlier: 3.563A pdb=" N VAL E 568 " --> pdb=" O ILE E 556 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 553 " --> pdb=" O TYR E 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET E 589 " --> pdb=" O ARG E 559 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA E 594 " --> pdb=" O LYS E 601 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS E 601 " --> pdb=" O ALA E 594 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 566 through 571 removed outlier: 3.563A pdb=" N VAL E 568 " --> pdb=" O ILE E 556 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 553 " --> pdb=" O TYR E 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET E 589 " --> pdb=" O ARG E 559 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE E 606 " --> pdb=" O VAL E 590 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1650 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: 6.35 Time building geometry restraints manager: 6.76 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: 5528 1.34 - 1.46: 4317 1.46 - 1.58: 7827 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 17790 Sorted by residual: bond pdb=" C1 NAG A 804 " pdb=" O5 NAG A 804 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C1 NAG E 804 " pdb=" O5 NAG E 804 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.79e+00 ... (remaining 17785 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.24: 744 107.24 - 113.93: 10241 113.93 - 120.61: 6187 120.61 - 127.30: 6786 127.30 - 133.98: 252 Bond angle restraints: 24210 Sorted by residual: angle pdb=" N VAL A 546 " pdb=" CA VAL A 546 " pdb=" C VAL A 546 " ideal model delta sigma weight residual 113.20 109.77 3.43 9.60e-01 1.09e+00 1.28e+01 angle pdb=" N VAL E 546 " pdb=" CA VAL E 546 " pdb=" C VAL E 546 " ideal model delta sigma weight residual 113.20 109.77 3.43 9.60e-01 1.09e+00 1.28e+01 angle pdb=" C PRO A 434 " pdb=" N LYS A 435 " pdb=" CA LYS A 435 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.06e+00 angle pdb=" C PRO E 434 " pdb=" N LYS E 435 " pdb=" CA LYS E 435 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.06e+00 angle pdb=" N LYS E 76 " pdb=" CA LYS E 76 " pdb=" C LYS E 76 " ideal model delta sigma weight residual 111.30 114.49 -3.19 1.36e+00 5.41e-01 5.50e+00 ... (remaining 24205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 10355 22.00 - 44.00: 575 44.00 - 66.01: 152 66.01 - 88.01: 62 88.01 - 110.01: 110 Dihedral angle restraints: 11254 sinusoidal: 5050 harmonic: 6204 Sorted by residual: dihedral pdb=" CB CYS H 72 " pdb=" SG CYS H 72 " pdb=" SG CYS H 78 " pdb=" CB CYS H 78 " ideal model delta sinusoidal sigma weight residual -86.00 -28.34 -57.66 1 1.00e+01 1.00e-02 4.46e+01 dihedral pdb=" CB CYS D 72 " pdb=" SG CYS D 72 " pdb=" SG CYS D 78 " pdb=" CB CYS D 78 " ideal model delta sinusoidal sigma weight residual -86.00 -28.41 -57.59 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CA ASP E 436 " pdb=" C ASP E 436 " pdb=" N ASN E 437 " pdb=" CA ASN E 437 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 11251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2441 0.059 - 0.118: 338 0.118 - 0.177: 19 0.177 - 0.236: 4 0.236 - 0.295: 2 Chirality restraints: 2804 Sorted by residual: chirality pdb=" C1 NAG E 803 " pdb=" ND2 ASN E 383 " pdb=" C2 NAG E 803 " pdb=" O5 NAG E 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1 NAG A 803 " pdb=" ND2 ASN A 383 " pdb=" C2 NAG A 803 " pdb=" O5 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN G 245 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2801 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 325 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO E 326 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 326 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 326 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 325 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO A 326 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 337 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO E 338 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 338 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 338 " -0.021 5.00e-02 4.00e+02 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2830 2.77 - 3.30: 15548 3.30 - 3.84: 27162 3.84 - 4.37: 30064 4.37 - 4.90: 52907 Nonbonded interactions: 128511 Sorted by model distance: nonbonded pdb=" O LEU E 364 " pdb=" O3 NAG E 803 " model vdw 2.239 2.440 nonbonded pdb=" O LEU A 364 " pdb=" O3 NAG A 803 " model vdw 2.239 2.440 nonbonded pdb=" OG1 THR A 596 " pdb=" O GLY A 599 " model vdw 2.259 2.440 nonbonded pdb=" OG1 THR E 596 " pdb=" O GLY E 599 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR G 257 " pdb=" OD1 ASP G 281 " model vdw 2.292 2.440 ... (remaining 128506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 20.170 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 44.180 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.170 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 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 0.047 17790 Z= 0.192 Angle : 0.524 6.639 24210 Z= 0.272 Chirality : 0.042 0.295 2804 Planarity : 0.003 0.039 3044 Dihedral : 19.913 110.011 7160 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.95 % Allowed : 9.50 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.16), residues: 2096 helix: -0.32 (0.31), residues: 252 sheet: -1.60 (0.16), residues: 806 loop : -2.19 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP E 333 HIS 0.001 0.000 HIS C 107 PHE 0.009 0.001 PHE E 108 TYR 0.004 0.001 TYR A 334 ARG 0.002 0.000 ARG G 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 253 time to evaluate : 2.076 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: C 77 MET cc_start: 0.3044 (ttt) cc_final: 0.2803 (pmm) REVERT: D 189 MET cc_start: 0.6403 (tpp) cc_final: 0.6064 (tpt) REVERT: A 360 ASN cc_start: 0.5259 (m-40) cc_final: 0.4611 (m110) REVERT: A 458 CYS cc_start: 0.5990 (p) cc_final: 0.5420 (p) REVERT: A 592 MET cc_start: 0.2043 (ptp) cc_final: -0.0051 (ttm) REVERT: G 77 MET cc_start: 0.3050 (ttt) cc_final: 0.2808 (pmm) REVERT: H 189 MET cc_start: 0.6458 (tpp) cc_final: 0.6059 (tpt) REVERT: E 360 ASN cc_start: 0.5260 (m-40) cc_final: 0.4611 (m110) REVERT: E 458 CYS cc_start: 0.5998 (p) cc_final: 0.5428 (p) REVERT: E 592 MET cc_start: 0.2053 (ptp) cc_final: -0.0047 (ttm) outliers start: 18 outliers final: 16 residues processed: 269 average time/residue: 0.3363 time to fit residues: 133.5561 Evaluate side-chains 181 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.0470 chunk 156 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 20.0000 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN C 118 GLN C 206 GLN C 215 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS D 73 ASN D 76 ASN D 131 ASN D 144 GLN D 172 ASN D 211 GLN A 104 ASN A 226 HIS A 342 GLN A 348 GLN A 404 ASN A 437 ASN A 516 GLN A 547 GLN A 548 ASN A 569 ASN A 574 HIS G 87 GLN G 118 GLN G 206 GLN G 215 GLN ** G 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 HIS H 56 GLN H 76 ASN H 131 ASN H 144 GLN H 172 ASN H 211 GLN E 104 ASN E 226 HIS E 342 GLN E 348 GLN E 404 ASN E 437 ASN E 516 GLN E 547 GLN E 548 ASN E 569 ASN E 574 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 17790 Z= 0.619 Angle : 0.898 7.996 24210 Z= 0.453 Chirality : 0.057 0.287 2804 Planarity : 0.007 0.083 3044 Dihedral : 17.983 93.609 3098 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.13 % Rotamer: Outliers : 3.48 % Allowed : 16.05 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.17), residues: 2096 helix: 0.50 (0.32), residues: 248 sheet: -1.14 (0.17), residues: 810 loop : -1.85 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 244 HIS 0.012 0.002 HIS D 192 PHE 0.042 0.004 PHE A 91 TYR 0.027 0.003 TYR D 59 ARG 0.011 0.001 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 170 time to evaluate : 1.965 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: C 269 MET cc_start: 0.8346 (mmt) cc_final: 0.7989 (mmt) REVERT: A 380 TYR cc_start: 0.7198 (t80) cc_final: 0.6980 (t80) REVERT: A 481 TYR cc_start: 0.7537 (p90) cc_final: 0.7324 (p90) REVERT: A 557 PHE cc_start: 0.3574 (OUTLIER) cc_final: 0.2833 (p90) REVERT: G 269 MET cc_start: 0.8338 (mmt) cc_final: 0.7990 (mmt) REVERT: E 380 TYR cc_start: 0.7192 (t80) cc_final: 0.6967 (t80) REVERT: E 481 TYR cc_start: 0.7538 (p90) cc_final: 0.7323 (p90) REVERT: E 557 PHE cc_start: 0.3603 (OUTLIER) cc_final: 0.2852 (p90) outliers start: 66 outliers final: 40 residues processed: 218 average time/residue: 0.2824 time to fit residues: 95.0099 Evaluate side-chains 185 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 143 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN C 239 GLN D 76 ASN G 162 GLN G 239 GLN H 56 GLN H 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17790 Z= 0.207 Angle : 0.635 8.805 24210 Z= 0.307 Chirality : 0.046 0.320 2804 Planarity : 0.004 0.045 3044 Dihedral : 14.845 85.250 3096 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.06 % Allowed : 18.48 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2096 helix: 1.37 (0.34), residues: 244 sheet: -0.92 (0.17), residues: 826 loop : -1.52 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 244 HIS 0.005 0.001 HIS D 192 PHE 0.017 0.002 PHE A 72 TYR 0.013 0.001 TYR H 59 ARG 0.004 0.000 ARG H 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 155 time to evaluate : 2.185 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: D 77 MET cc_start: 0.8225 (mtm) cc_final: 0.8009 (mtt) REVERT: A 189 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7832 (p) REVERT: A 387 LEU cc_start: 0.7409 (tp) cc_final: 0.7208 (tt) REVERT: A 470 TRP cc_start: 0.7340 (p-90) cc_final: 0.7086 (p-90) REVERT: A 557 PHE cc_start: 0.3495 (OUTLIER) cc_final: 0.2743 (p90) REVERT: H 77 MET cc_start: 0.8236 (mtm) cc_final: 0.7940 (mtm) REVERT: E 470 TRP cc_start: 0.7335 (p-90) cc_final: 0.7082 (p-90) REVERT: E 557 PHE cc_start: 0.3507 (OUTLIER) cc_final: 0.2748 (p90) outliers start: 58 outliers final: 38 residues processed: 196 average time/residue: 0.2777 time to fit residues: 84.1072 Evaluate side-chains 184 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 178 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN A 547 GLN ** G 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN E 547 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17790 Z= 0.271 Angle : 0.641 7.762 24210 Z= 0.309 Chirality : 0.046 0.321 2804 Planarity : 0.004 0.039 3044 Dihedral : 12.305 74.816 3096 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.22 % Allowed : 19.80 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 2096 helix: 1.52 (0.34), residues: 246 sheet: -0.76 (0.17), residues: 828 loop : -1.35 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 269 HIS 0.007 0.001 HIS G 242 PHE 0.017 0.002 PHE A 91 TYR 0.014 0.001 TYR D 59 ARG 0.003 0.000 ARG E 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 155 time to evaluate : 1.845 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: D 77 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8034 (mtt) REVERT: A 470 TRP cc_start: 0.7479 (p-90) cc_final: 0.7120 (p-90) REVERT: A 472 GLN cc_start: 0.7040 (tt0) cc_final: 0.6623 (mt0) REVERT: A 474 ASP cc_start: 0.6711 (t0) cc_final: 0.6162 (p0) REVERT: A 557 PHE cc_start: 0.3586 (OUTLIER) cc_final: 0.2855 (p90) REVERT: A 568 VAL cc_start: 0.3267 (OUTLIER) cc_final: 0.2722 (p) REVERT: H 77 MET cc_start: 0.8233 (mtm) cc_final: 0.7957 (mtt) REVERT: E 189 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7888 (p) REVERT: E 470 TRP cc_start: 0.7472 (p-90) cc_final: 0.7164 (p-90) REVERT: E 474 ASP cc_start: 0.6712 (t0) cc_final: 0.6159 (p0) REVERT: E 557 PHE cc_start: 0.3601 (OUTLIER) cc_final: 0.2862 (p90) REVERT: E 568 VAL cc_start: 0.3264 (OUTLIER) cc_final: 0.2729 (p) outliers start: 80 outliers final: 59 residues processed: 215 average time/residue: 0.2613 time to fit residues: 88.9116 Evaluate side-chains 211 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 146 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 478 HIS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 586 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN G 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17790 Z= 0.304 Angle : 0.650 7.849 24210 Z= 0.318 Chirality : 0.046 0.299 2804 Planarity : 0.004 0.038 3044 Dihedral : 11.097 67.083 3094 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.49 % Allowed : 20.33 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2096 helix: 1.23 (0.34), residues: 258 sheet: -0.71 (0.17), residues: 822 loop : -1.39 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 333 HIS 0.005 0.001 HIS H 192 PHE 0.018 0.002 PHE A 292 TYR 0.019 0.001 TYR E 513 ARG 0.003 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 156 time to evaluate : 1.860 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: D 77 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: A 189 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7929 (p) REVERT: A 269 TRP cc_start: 0.7791 (OUTLIER) cc_final: 0.6089 (m-90) REVERT: A 470 TRP cc_start: 0.7402 (p-90) cc_final: 0.7056 (p-90) REVERT: A 472 GLN cc_start: 0.7005 (tt0) cc_final: 0.6555 (mt0) REVERT: A 474 ASP cc_start: 0.6738 (t0) cc_final: 0.6208 (p0) REVERT: A 557 PHE cc_start: 0.3729 (OUTLIER) cc_final: 0.2903 (p90) REVERT: E 189 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7931 (p) REVERT: E 269 TRP cc_start: 0.7785 (OUTLIER) cc_final: 0.6079 (m-90) REVERT: E 470 TRP cc_start: 0.7396 (p-90) cc_final: 0.7048 (p-90) REVERT: E 472 GLN cc_start: 0.7007 (tt0) cc_final: 0.6557 (mt0) REVERT: E 474 ASP cc_start: 0.6741 (t0) cc_final: 0.6215 (p0) REVERT: E 557 PHE cc_start: 0.3745 (OUTLIER) cc_final: 0.2914 (p90) outliers start: 85 outliers final: 61 residues processed: 224 average time/residue: 0.2577 time to fit residues: 90.2177 Evaluate side-chains 217 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 149 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 TRP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 269 TRP Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Chi-restraints excluded: chain E residue 586 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 2.9990 chunk 179 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 104 optimal weight: 50.0000 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN E 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17790 Z= 0.166 Angle : 0.580 8.460 24210 Z= 0.281 Chirality : 0.044 0.308 2804 Planarity : 0.004 0.042 3044 Dihedral : 9.775 58.958 3092 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.17 % Allowed : 22.12 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.18), residues: 2096 helix: 1.48 (0.34), residues: 258 sheet: -0.46 (0.18), residues: 800 loop : -1.31 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 333 HIS 0.004 0.000 HIS G 107 PHE 0.015 0.001 PHE A 292 TYR 0.008 0.001 TYR H 59 ARG 0.003 0.000 ARG H 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 156 time to evaluate : 2.005 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: C 201 LYS cc_start: 0.7991 (mptt) cc_final: 0.7778 (mmtp) REVERT: D 77 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7809 (mtm) REVERT: A 189 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7784 (p) REVERT: A 462 ASP cc_start: 0.4202 (OUTLIER) cc_final: 0.3312 (p0) REVERT: A 470 TRP cc_start: 0.7373 (p-90) cc_final: 0.6951 (p-90) REVERT: A 472 GLN cc_start: 0.7055 (tt0) cc_final: 0.6480 (mt0) REVERT: A 474 ASP cc_start: 0.6716 (t0) cc_final: 0.6158 (p0) REVERT: A 557 PHE cc_start: 0.3612 (OUTLIER) cc_final: 0.2822 (p90) REVERT: G 201 LYS cc_start: 0.7997 (mptt) cc_final: 0.7784 (mmtp) REVERT: E 189 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7760 (p) REVERT: E 386 LYS cc_start: 0.8069 (mmmm) cc_final: 0.7315 (mmtm) REVERT: E 462 ASP cc_start: 0.4199 (OUTLIER) cc_final: 0.3308 (p0) REVERT: E 470 TRP cc_start: 0.7373 (p-90) cc_final: 0.6945 (p-90) REVERT: E 472 GLN cc_start: 0.7048 (tt0) cc_final: 0.6532 (mt0) REVERT: E 474 ASP cc_start: 0.6743 (t0) cc_final: 0.6194 (p0) REVERT: E 557 PHE cc_start: 0.3632 (OUTLIER) cc_final: 0.2839 (p90) outliers start: 60 outliers final: 42 residues processed: 201 average time/residue: 0.2767 time to fit residues: 87.3449 Evaluate side-chains 199 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 150 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Chi-restraints excluded: chain E residue 586 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17790 Z= 0.271 Angle : 0.617 8.458 24210 Z= 0.302 Chirality : 0.044 0.293 2804 Planarity : 0.004 0.041 3044 Dihedral : 8.980 58.651 3090 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.01 % Allowed : 22.07 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2096 helix: 1.51 (0.34), residues: 258 sheet: -0.51 (0.18), residues: 820 loop : -1.30 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 333 HIS 0.006 0.001 HIS H 192 PHE 0.017 0.002 PHE E 292 TYR 0.011 0.001 TYR H 59 ARG 0.002 0.000 ARG E 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 147 time to evaluate : 2.139 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: C 201 LYS cc_start: 0.8040 (mptt) cc_final: 0.7813 (mmtp) REVERT: D 77 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7865 (mtt) REVERT: A 189 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7927 (p) REVERT: A 269 TRP cc_start: 0.7795 (OUTLIER) cc_final: 0.6098 (m-90) REVERT: A 462 ASP cc_start: 0.4243 (OUTLIER) cc_final: 0.3369 (p0) REVERT: A 470 TRP cc_start: 0.7360 (p-90) cc_final: 0.7004 (p-90) REVERT: A 472 GLN cc_start: 0.6980 (tt0) cc_final: 0.6518 (mt0) REVERT: A 474 ASP cc_start: 0.6716 (t0) cc_final: 0.6169 (p0) REVERT: A 557 PHE cc_start: 0.3669 (OUTLIER) cc_final: 0.2842 (p90) REVERT: G 201 LYS cc_start: 0.8043 (mptt) cc_final: 0.7816 (mmtp) REVERT: E 189 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7870 (p) REVERT: E 269 TRP cc_start: 0.7788 (OUTLIER) cc_final: 0.6090 (m-90) REVERT: E 386 LYS cc_start: 0.8119 (mmmm) cc_final: 0.7339 (mmtm) REVERT: E 462 ASP cc_start: 0.4245 (OUTLIER) cc_final: 0.3367 (p0) REVERT: E 470 TRP cc_start: 0.7350 (p-90) cc_final: 0.6979 (p-90) REVERT: E 472 GLN cc_start: 0.7016 (tt0) cc_final: 0.6526 (mt0) REVERT: E 474 ASP cc_start: 0.6775 (t0) cc_final: 0.6242 (p0) REVERT: E 557 PHE cc_start: 0.3681 (OUTLIER) cc_final: 0.2852 (p90) outliers start: 76 outliers final: 60 residues processed: 210 average time/residue: 0.2723 time to fit residues: 89.5101 Evaluate side-chains 215 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 146 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 TRP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 269 TRP Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 344 TYR Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Chi-restraints excluded: chain E residue 586 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.0020 chunk 79 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 98 optimal weight: 40.0000 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17790 Z= 0.196 Angle : 0.579 9.198 24210 Z= 0.283 Chirality : 0.043 0.297 2804 Planarity : 0.004 0.044 3044 Dihedral : 8.336 57.750 3090 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.85 % Allowed : 22.60 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2096 helix: 1.63 (0.34), residues: 258 sheet: -0.45 (0.18), residues: 822 loop : -1.26 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 333 HIS 0.004 0.001 HIS H 192 PHE 0.022 0.001 PHE A 292 TYR 0.013 0.001 TYR A 513 ARG 0.002 0.000 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 153 time to evaluate : 1.985 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: C 201 LYS cc_start: 0.8012 (mptt) cc_final: 0.7779 (mmtp) REVERT: D 77 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7816 (mtm) REVERT: A 189 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7858 (p) REVERT: A 457 TRP cc_start: 0.7606 (p90) cc_final: 0.7272 (p90) REVERT: A 462 ASP cc_start: 0.4150 (OUTLIER) cc_final: 0.3281 (p0) REVERT: A 470 TRP cc_start: 0.7298 (p-90) cc_final: 0.6908 (p-90) REVERT: A 472 GLN cc_start: 0.7000 (tt0) cc_final: 0.6523 (mt0) REVERT: A 474 ASP cc_start: 0.6744 (t0) cc_final: 0.6192 (p0) REVERT: A 557 PHE cc_start: 0.3605 (OUTLIER) cc_final: 0.2819 (p90) REVERT: G 201 LYS cc_start: 0.8020 (mptt) cc_final: 0.7786 (mmtp) REVERT: E 189 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7848 (p) REVERT: E 386 LYS cc_start: 0.8117 (mmmm) cc_final: 0.7392 (mmtm) REVERT: E 457 TRP cc_start: 0.7607 (p90) cc_final: 0.7294 (p90) REVERT: E 462 ASP cc_start: 0.4148 (OUTLIER) cc_final: 0.3275 (p0) REVERT: E 470 TRP cc_start: 0.7248 (p-90) cc_final: 0.6865 (p-90) REVERT: E 472 GLN cc_start: 0.7020 (tt0) cc_final: 0.6531 (mt0) REVERT: E 474 ASP cc_start: 0.6774 (t0) cc_final: 0.6235 (p0) REVERT: E 557 PHE cc_start: 0.3615 (OUTLIER) cc_final: 0.2825 (p90) outliers start: 73 outliers final: 62 residues processed: 211 average time/residue: 0.2809 time to fit residues: 91.8397 Evaluate side-chains 218 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 149 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 344 TYR Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Chi-restraints excluded: chain E residue 586 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 80 optimal weight: 0.2980 chunk 145 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN E 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17790 Z= 0.245 Angle : 0.597 9.782 24210 Z= 0.296 Chirality : 0.044 0.296 2804 Planarity : 0.004 0.045 3044 Dihedral : 7.889 58.135 3090 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.85 % Allowed : 22.23 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.18), residues: 2096 helix: 1.63 (0.34), residues: 258 sheet: -0.46 (0.18), residues: 824 loop : -1.31 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 333 HIS 0.005 0.001 HIS H 192 PHE 0.028 0.002 PHE A 292 TYR 0.014 0.001 TYR E 513 ARG 0.002 0.000 ARG G 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 152 time to evaluate : 2.063 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: C 201 LYS cc_start: 0.8033 (mptt) cc_final: 0.7804 (mmtp) REVERT: D 77 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7844 (mtm) REVERT: A 189 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7886 (p) REVERT: A 332 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.5986 (t80) REVERT: A 387 LEU cc_start: 0.7275 (tp) cc_final: 0.7073 (tp) REVERT: A 457 TRP cc_start: 0.7641 (p90) cc_final: 0.7348 (p90) REVERT: A 462 ASP cc_start: 0.4123 (OUTLIER) cc_final: 0.3277 (p0) REVERT: A 470 TRP cc_start: 0.7257 (p-90) cc_final: 0.6888 (p-90) REVERT: A 472 GLN cc_start: 0.7006 (tt0) cc_final: 0.6496 (mt0) REVERT: A 474 ASP cc_start: 0.6778 (t0) cc_final: 0.6216 (p0) REVERT: G 201 LYS cc_start: 0.8035 (mptt) cc_final: 0.7806 (mmtp) REVERT: E 189 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7875 (p) REVERT: E 386 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7389 (mmtm) REVERT: E 457 TRP cc_start: 0.7622 (p90) cc_final: 0.7324 (p90) REVERT: E 462 ASP cc_start: 0.4127 (OUTLIER) cc_final: 0.3279 (p0) REVERT: E 470 TRP cc_start: 0.7253 (p-90) cc_final: 0.6867 (p-90) REVERT: E 472 GLN cc_start: 0.7031 (tt0) cc_final: 0.6521 (mt0) REVERT: E 474 ASP cc_start: 0.6765 (t0) cc_final: 0.6199 (p0) outliers start: 73 outliers final: 65 residues processed: 210 average time/residue: 0.2918 time to fit residues: 93.8973 Evaluate side-chains 221 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 150 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 344 TYR Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Chi-restraints excluded: chain E residue 586 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 119 optimal weight: 0.4980 chunk 92 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17790 Z= 0.412 Angle : 0.685 9.488 24210 Z= 0.347 Chirality : 0.047 0.297 2804 Planarity : 0.005 0.049 3044 Dihedral : 7.892 58.963 3090 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.12 % Allowed : 22.18 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2096 helix: 1.30 (0.33), residues: 258 sheet: -0.60 (0.18), residues: 822 loop : -1.39 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 333 HIS 0.008 0.001 HIS H 192 PHE 0.028 0.002 PHE A 292 TYR 0.011 0.001 TYR D 59 ARG 0.005 0.001 ARG G 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 153 time to evaluate : 2.202 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: C 201 LYS cc_start: 0.8132 (mptt) cc_final: 0.7846 (mmtp) REVERT: D 77 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7932 (mtt) REVERT: A 189 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7989 (p) REVERT: A 332 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6080 (t80) REVERT: A 457 TRP cc_start: 0.7674 (p90) cc_final: 0.7407 (p90) REVERT: A 462 ASP cc_start: 0.4038 (OUTLIER) cc_final: 0.3334 (p0) REVERT: A 470 TRP cc_start: 0.7323 (p-90) cc_final: 0.6900 (p-90) REVERT: A 472 GLN cc_start: 0.7026 (tt0) cc_final: 0.6517 (mt0) REVERT: A 474 ASP cc_start: 0.6900 (t0) cc_final: 0.6271 (p0) REVERT: A 557 PHE cc_start: 0.3687 (OUTLIER) cc_final: 0.2988 (p90) REVERT: G 201 LYS cc_start: 0.8132 (mptt) cc_final: 0.7846 (mmtp) REVERT: E 189 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7984 (p) REVERT: E 386 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7362 (mmtm) REVERT: E 457 TRP cc_start: 0.7661 (p90) cc_final: 0.7382 (p90) REVERT: E 462 ASP cc_start: 0.4042 (OUTLIER) cc_final: 0.3337 (p0) REVERT: E 470 TRP cc_start: 0.7305 (p-90) cc_final: 0.6858 (p-90) REVERT: E 472 GLN cc_start: 0.7133 (tt0) cc_final: 0.6635 (mt0) REVERT: E 474 ASP cc_start: 0.6895 (t0) cc_final: 0.6270 (p0) REVERT: E 557 PHE cc_start: 0.3689 (OUTLIER) cc_final: 0.2991 (p90) outliers start: 78 outliers final: 66 residues processed: 217 average time/residue: 0.2761 time to fit residues: 92.6889 Evaluate side-chains 224 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 150 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 344 TYR Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Chi-restraints excluded: chain E residue 586 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 0.8980 chunk 174 optimal weight: 0.0870 chunk 50 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 168 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.186003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.135162 restraints weight = 28366.964| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.63 r_work: 0.3502 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 542 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 544 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17790 Z= 0.161 Angle : 0.571 9.524 24210 Z= 0.289 Chirality : 0.042 0.298 2804 Planarity : 0.004 0.051 3044 Dihedral : 7.248 57.819 3090 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.54 % Allowed : 22.70 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2096 helix: 1.68 (0.34), residues: 258 sheet: -0.43 (0.18), residues: 802 loop : -1.24 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 333 HIS 0.004 0.001 HIS H 192 PHE 0.029 0.002 PHE A 292 TYR 0.015 0.001 TYR A 513 ARG 0.004 0.000 ARG G 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4175.09 seconds wall clock time: 76 minutes 10.04 seconds (4570.04 seconds total)