Starting phenix.real_space_refine on Wed Feb 21 19:17:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw2_24708/02_2024/7rw2_24708.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw2_24708/02_2024/7rw2_24708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw2_24708/02_2024/7rw2_24708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw2_24708/02_2024/7rw2_24708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw2_24708/02_2024/7rw2_24708.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw2_24708/02_2024/7rw2_24708.pdb" } resolution = 3.5 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= 0.058 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 138 5.16 5 C 20088 2.51 5 N 5184 2.21 5 O 6204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31614 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8406 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 8406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8406 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 8406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8406 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1054 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "G" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1054 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "J" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1054 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 15.32, per 1000 atoms: 0.48 Number of scatterers: 31614 At special positions: 0 Unit cell: (169.06, 172.27, 171.2, 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 138 16.00 O 6204 8.00 N 5184 7.00 C 20088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 17 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 149 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A 709 " " NAG A1313 " - " ASN A 717 " " NAG A1314 " - " ASN A1134 " " NAG A1315 " - " ASN A 603 " " NAG A1316 " - " ASN A 331 " " NAG B1301 " - " ASN B 343 " " NAG B1302 " - " ASN B 17 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B 709 " " NAG B1313 " - " ASN B 717 " " NAG B1314 " - " ASN B1134 " " NAG B1315 " - " ASN B 603 " " NAG B1316 " - " ASN B 331 " " NAG C1301 " - " ASN C 343 " " NAG C1302 " - " ASN C 17 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 149 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C 603 " " NAG C1313 " - " ASN C 717 " " NAG C1314 " - " ASN C1134 " " NAG C1315 " - " ASN C 331 " " NAG C1316 " - " ASN C 709 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 122 " Time building additional restraints: 11.80 Conformation dependent library (CDL) restraints added in 5.8 seconds 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7368 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 69 sheets defined 21.0% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.521A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.233A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.199A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.421A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.608A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 630 through 638 removed outlier: 4.289A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 783 removed outlier: 4.521A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.574A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 Processing helix chain 'A' and resid 945 through 967 removed outlier: 4.058A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.941A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.246A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.910A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.362A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.539A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.678A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.594A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 626 through 629 Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.518A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 748 through 783 removed outlier: 3.610A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.546A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 967 removed outlier: 4.028A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.786A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.243A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.326A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.507A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.611A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.608A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.812A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 626 through 629 removed outlier: 3.527A pdb=" N LEU C 629 " --> pdb=" O ALA C 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 626 through 629' Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.698A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 748 through 783 removed outlier: 4.052A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.607A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.654A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 967 removed outlier: 4.163A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.894A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1029 removed outlier: 5.197A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.854A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.510A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 100C through 100J removed outlier: 3.620A pdb=" N TRP H 100F" --> pdb=" O SER H 100C" (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU H 100I" --> pdb=" O TRP H 100F" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.037A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.510A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 100C through 100J removed outlier: 3.619A pdb=" N TRP G 100F" --> pdb=" O SER G 100C" (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU G 100I" --> pdb=" O TRP G 100F" (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.036A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.509A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 100C through 100J removed outlier: 3.620A pdb=" N TRP I 100F" --> pdb=" O SER I 100C" (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU I 100I" --> pdb=" O TRP I 100F" (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.036A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.849A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.821A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 160 removed outlier: 5.506A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.558A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.691A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.518A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.518A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.076A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.728A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 552 through 554 removed outlier: 3.503A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.543A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 659 removed outlier: 5.805A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.448A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.448A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A1101 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.656A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.849A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.834A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 152 through 160 removed outlier: 5.505A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.573A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 651 " --> pdb=" O VAL B 610 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.552A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.552A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.079A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.773A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 539 through 543 removed outlier: 4.155A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 552 through 554 removed outlier: 4.166A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 659 removed outlier: 5.817A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 723 removed outlier: 6.608A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 726 through 727 removed outlier: 3.697A pdb=" N ASN B1098 " --> pdb=" O HIS B1101 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS B1101 " --> pdb=" O ASN B1098 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.235A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.849A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.827A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 152 through 160 removed outlier: 5.506A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.597A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.514A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.897A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.532A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.532A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.150A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.653A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 552 through 554 Processing sheet with id=AF4, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AF5, first strand: chain 'C' and resid 664 through 665 removed outlier: 4.233A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.617A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.617A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C1098 " --> pdb=" O HIS C1101 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS C1101 " --> pdb=" O ASN C1098 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.153A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.936A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.405A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.598A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.564A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.552A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.936A pdb=" N VAL G 5 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.405A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.598A pdb=" N THR J 22 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.564A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.552A pdb=" N TYR J 49 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.935A pdb=" N VAL I 5 " --> pdb=" O LYS I 23 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.404A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.598A pdb=" N THR K 22 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.563A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.552A pdb=" N TYR K 49 " --> pdb=" O THR K 53 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 2961 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: 15.14 Time building geometry restraints manager: 12.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5082 1.29 - 1.43: 8750 1.43 - 1.56: 18325 1.56 - 1.69: 9 1.69 - 1.82: 180 Bond restraints: 32346 Sorted by residual: bond pdb=" C PRO C1079 " pdb=" O PRO C1079 " ideal model delta sigma weight residual 1.238 1.164 0.074 1.24e-02 6.50e+03 3.54e+01 bond pdb=" C ASP B 290 " pdb=" N CYS B 291 " ideal model delta sigma weight residual 1.332 1.399 -0.066 1.29e-02 6.01e+03 2.66e+01 bond pdb=" CA ALA C1080 " pdb=" CB ALA C1080 " ideal model delta sigma weight residual 1.537 1.480 0.057 1.45e-02 4.76e+03 1.52e+01 bond pdb=" CA SER B 711 " pdb=" CB SER B 711 " ideal model delta sigma weight residual 1.533 1.467 0.067 1.72e-02 3.38e+03 1.51e+01 bond pdb=" CA ALA C 892 " pdb=" CB ALA C 892 " ideal model delta sigma weight residual 1.536 1.484 0.053 1.46e-02 4.69e+03 1.30e+01 ... (remaining 32341 not shown) Histogram of bond angle deviations from ideal: 97.42 - 104.79: 597 104.79 - 112.17: 15889 112.17 - 119.54: 10899 119.54 - 126.92: 16292 126.92 - 134.29: 360 Bond angle restraints: 44037 Sorted by residual: angle pdb=" N GLY G 100D" pdb=" CA GLY G 100D" pdb=" C GLY G 100D" ideal model delta sigma weight residual 115.34 101.92 13.42 1.67e+00 3.59e-01 6.46e+01 angle pdb=" N GLY H 100D" pdb=" CA GLY H 100D" pdb=" C GLY H 100D" ideal model delta sigma weight residual 115.34 101.94 13.40 1.67e+00 3.59e-01 6.44e+01 angle pdb=" N GLY I 100D" pdb=" CA GLY I 100D" pdb=" C GLY I 100D" ideal model delta sigma weight residual 115.34 102.00 13.34 1.67e+00 3.59e-01 6.38e+01 angle pdb=" N TYR B 707 " pdb=" CA TYR B 707 " pdb=" C TYR B 707 " ideal model delta sigma weight residual 111.28 103.77 7.51 1.09e+00 8.42e-01 4.75e+01 angle pdb=" N GLY H 55 " pdb=" CA GLY H 55 " pdb=" C GLY H 55 " ideal model delta sigma weight residual 115.21 106.31 8.90 1.30e+00 5.92e-01 4.68e+01 ... (remaining 44032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18041 17.98 - 35.95: 1577 35.95 - 53.93: 292 53.93 - 71.90: 59 71.90 - 89.88: 20 Dihedral angle restraints: 19989 sinusoidal: 8493 harmonic: 11496 Sorted by residual: dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual 93.00 172.72 -79.72 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 167.05 -74.05 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -154.55 68.55 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 19986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.292: 5112 0.292 - 0.583: 23 0.583 - 0.874: 0 0.874 - 1.166: 0 1.166 - 1.457: 1 Chirality restraints: 5136 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.11e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.81e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.20e+01 ... (remaining 5133 not shown) Planarity restraints: 5655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.319 2.00e-02 2.50e+03 2.79e-01 9.73e+02 pdb=" C7 NAG F 2 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.095 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.318 2.00e-02 2.50e+03 2.78e-01 9.69e+02 pdb=" C7 NAG D 2 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.094 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1316 " 0.138 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" C7 NAG C1316 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG C1316 " 0.102 2.00e-02 2.50e+03 pdb=" N2 NAG C1316 " -0.184 2.00e-02 2.50e+03 pdb=" O7 NAG C1316 " -0.021 2.00e-02 2.50e+03 ... (remaining 5652 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6697 2.78 - 3.31: 27427 3.31 - 3.84: 51228 3.84 - 4.37: 58307 4.37 - 4.90: 102362 Nonbonded interactions: 246021 Sorted by model distance: nonbonded pdb=" OE1 GLN A 965 " pdb=" OG SER C 758 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR B 739 " pdb=" ND2 ASN C 317 " model vdw 2.264 2.520 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLN A 52 " pdb=" OG1 THR A 274 " model vdw 2.269 2.440 ... (remaining 246016 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.050 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 81.480 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 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 : 0.005 0.087 32346 Z= 0.356 Angle : 0.971 13.422 44037 Z= 0.575 Chirality : 0.067 1.457 5136 Planarity : 0.009 0.279 5601 Dihedral : 13.472 89.877 12477 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.08 % 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: -1.51 (0.12), residues: 3909 helix: -0.89 (0.18), residues: 696 sheet: -0.08 (0.17), residues: 909 loop : -1.45 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 64 HIS 0.011 0.002 HIS C 207 PHE 0.028 0.002 PHE B 275 TYR 0.030 0.002 TYR C 707 ARG 0.008 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 600 time to evaluate : 3.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8443 (p) cc_final: 0.7954 (m) REVERT: A 906 PHE cc_start: 0.7049 (m-10) cc_final: 0.6819 (m-80) REVERT: B 114 THR cc_start: 0.8352 (p) cc_final: 0.7858 (m) REVERT: B 900 MET cc_start: 0.6837 (mpp) cc_final: 0.6599 (mtm) REVERT: C 114 THR cc_start: 0.8124 (p) cc_final: 0.7688 (m) REVERT: C 269 TYR cc_start: 0.7939 (m-80) cc_final: 0.7667 (m-10) REVERT: C 886 TRP cc_start: 0.7395 (p90) cc_final: 0.7194 (p90) REVERT: C 1096 VAL cc_start: 0.7112 (t) cc_final: 0.6898 (m) outliers start: 1 outliers final: 0 residues processed: 601 average time/residue: 0.3987 time to fit residues: 392.4889 Evaluate side-chains 317 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 20.0000 chunk 295 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 305 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 354 optimal weight: 20.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN A1108 ASN B 196 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B1002 GLN C 196 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN G 39 GLN J 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 32346 Z= 0.315 Angle : 0.640 11.442 44037 Z= 0.328 Chirality : 0.047 0.397 5136 Planarity : 0.005 0.051 5601 Dihedral : 7.194 59.903 5526 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.08 % Allowed : 9.48 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 (0.13), residues: 3909 helix: -0.24 (0.19), residues: 729 sheet: -0.20 (0.16), residues: 945 loop : -1.25 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 64 HIS 0.007 0.001 HIS A 66 PHE 0.026 0.002 PHE C 133 TYR 0.029 0.002 TYR C1067 ARG 0.006 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 362 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.7696 (tpp) cc_final: 0.7454 (tpp) REVERT: A 980 ILE cc_start: 0.8860 (pt) cc_final: 0.8547 (pt) REVERT: A 1096 VAL cc_start: 0.7947 (p) cc_final: 0.7601 (t) REVERT: C 503 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8557 (t) REVERT: C 886 TRP cc_start: 0.7380 (p90) cc_final: 0.7075 (p90) REVERT: H 80 MET cc_start: 0.4097 (tmm) cc_final: 0.3600 (tmm) outliers start: 71 outliers final: 57 residues processed: 418 average time/residue: 0.3750 time to fit residues: 270.5015 Evaluate side-chains 358 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 300 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 93 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 chunk 383 optimal weight: 9.9990 chunk 315 optimal weight: 0.7980 chunk 351 optimal weight: 10.0000 chunk 120 optimal weight: 0.1980 chunk 284 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 762 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 49 HIS B 317 ASN B 764 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 317 ASN C 762 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 52 ASN L 38 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 52 ASN K 38 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 32346 Z= 0.210 Angle : 0.561 11.501 44037 Z= 0.286 Chirality : 0.045 0.358 5136 Planarity : 0.004 0.048 5601 Dihedral : 6.477 59.730 5526 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.28 % Allowed : 13.02 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.93 (0.13), residues: 3909 helix: 0.18 (0.20), residues: 729 sheet: -0.16 (0.16), residues: 1005 loop : -1.11 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 64 HIS 0.005 0.001 HIS A1101 PHE 0.020 0.001 PHE B 318 TYR 0.023 0.001 TYR B 707 ARG 0.004 0.000 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 346 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 980 ILE cc_start: 0.8937 (pt) cc_final: 0.8603 (pt) REVERT: A 1096 VAL cc_start: 0.7956 (p) cc_final: 0.7597 (t) REVERT: C 886 TRP cc_start: 0.7546 (p90) cc_final: 0.7210 (p90) REVERT: C 912 THR cc_start: 0.6389 (OUTLIER) cc_final: 0.5989 (p) REVERT: H 80 MET cc_start: 0.4259 (tmm) cc_final: 0.3465 (tmm) REVERT: G 51 ILE cc_start: 0.6025 (OUTLIER) cc_final: 0.5627 (mt) REVERT: I 36 TRP cc_start: 0.5850 (t-100) cc_final: 0.5544 (t-100) REVERT: I 80 MET cc_start: 0.4322 (tmm) cc_final: 0.3072 (tmm) outliers start: 78 outliers final: 51 residues processed: 395 average time/residue: 0.3751 time to fit residues: 254.9904 Evaluate side-chains 337 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 284 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 356 optimal weight: 10.0000 chunk 376 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 337 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 762 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN H 52 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 32346 Z= 0.308 Angle : 0.603 12.061 44037 Z= 0.309 Chirality : 0.046 0.347 5136 Planarity : 0.004 0.048 5601 Dihedral : 6.534 59.231 5526 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.51 % Allowed : 14.25 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 3909 helix: 0.21 (0.20), residues: 729 sheet: -0.10 (0.16), residues: 1020 loop : -1.10 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 64 HIS 0.006 0.001 HIS A 66 PHE 0.030 0.002 PHE B 133 TYR 0.024 0.002 TYR B1067 ARG 0.003 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 316 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7788 (t80) REVERT: A 387 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8928 (tt) REVERT: A 398 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: A 556 ASN cc_start: 0.6213 (OUTLIER) cc_final: 0.5945 (t0) REVERT: A 980 ILE cc_start: 0.9026 (pt) cc_final: 0.8622 (pt) REVERT: B 387 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8796 (tt) REVERT: B 1005 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7819 (tm-30) REVERT: C 398 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: C 886 TRP cc_start: 0.7600 (p90) cc_final: 0.7243 (p90) REVERT: C 912 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.6131 (p) REVERT: H 80 MET cc_start: 0.4816 (tmm) cc_final: 0.4031 (tmm) REVERT: G 69 MET cc_start: 0.6405 (mmt) cc_final: 0.6068 (mmt) REVERT: I 80 MET cc_start: 0.4895 (tmm) cc_final: 0.4665 (tmm) outliers start: 120 outliers final: 89 residues processed: 403 average time/residue: 0.3860 time to fit residues: 269.4112 Evaluate side-chains 389 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 293 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 155 optimal weight: 0.1980 chunk 321 optimal weight: 10.0000 chunk 260 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 338 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 755 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 32346 Z= 0.329 Angle : 0.615 9.737 44037 Z= 0.316 Chirality : 0.047 0.338 5136 Planarity : 0.004 0.048 5601 Dihedral : 6.545 59.409 5526 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.13 % Allowed : 15.39 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 3909 helix: 0.17 (0.20), residues: 729 sheet: -0.06 (0.16), residues: 996 loop : -1.17 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 64 HIS 0.005 0.001 HIS C 66 PHE 0.020 0.002 PHE C 238 TYR 0.023 0.002 TYR B 508 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 321 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7771 (m-80) cc_final: 0.7560 (m-10) REVERT: A 238 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7715 (t80) REVERT: A 387 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8938 (tt) REVERT: A 398 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: A 556 ASN cc_start: 0.6227 (OUTLIER) cc_final: 0.5938 (t0) REVERT: B 115 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: B 306 PHE cc_start: 0.8060 (m-80) cc_final: 0.7838 (m-80) REVERT: B 387 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8825 (tt) REVERT: B 398 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: B 866 THR cc_start: 0.8068 (p) cc_final: 0.7851 (p) REVERT: B 1005 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7794 (tm-30) REVERT: C 398 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: C 886 TRP cc_start: 0.7659 (p90) cc_final: 0.7271 (p90) REVERT: C 912 THR cc_start: 0.6754 (OUTLIER) cc_final: 0.6318 (p) REVERT: H 80 MET cc_start: 0.4872 (tmm) cc_final: 0.4194 (tmm) REVERT: G 69 MET cc_start: 0.6477 (mmt) cc_final: 0.6084 (mmt) outliers start: 141 outliers final: 105 residues processed: 426 average time/residue: 0.3760 time to fit residues: 274.1290 Evaluate side-chains 408 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 294 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 93 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 2.9990 chunk 339 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 377 optimal weight: 9.9990 chunk 313 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 ASN B 755 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 32346 Z= 0.207 Angle : 0.572 12.070 44037 Z= 0.291 Chirality : 0.045 0.336 5136 Planarity : 0.004 0.046 5601 Dihedral : 6.259 59.174 5526 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.28 % Allowed : 17.30 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 3909 helix: 0.34 (0.20), residues: 729 sheet: 0.01 (0.16), residues: 990 loop : -1.07 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 64 HIS 0.004 0.001 HIS A 66 PHE 0.020 0.001 PHE L 71 TYR 0.024 0.001 TYR C 508 ARG 0.008 0.000 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 337 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7739 (m-80) cc_final: 0.7515 (m-10) REVERT: A 238 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7379 (t80) REVERT: A 387 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8909 (tt) REVERT: A 697 MET cc_start: 0.7284 (mmm) cc_final: 0.7042 (tpp) REVERT: A 1029 MET cc_start: 0.7818 (tpp) cc_final: 0.7428 (mmm) REVERT: B 115 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: B 200 TYR cc_start: 0.7683 (m-80) cc_final: 0.7369 (m-10) REVERT: B 398 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7677 (m-30) REVERT: B 1005 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7767 (tm-30) REVERT: C 886 TRP cc_start: 0.7541 (p90) cc_final: 0.7148 (p90) REVERT: C 912 THR cc_start: 0.6655 (OUTLIER) cc_final: 0.6221 (p) REVERT: H 80 MET cc_start: 0.4948 (tmm) cc_final: 0.4179 (tmm) REVERT: G 69 MET cc_start: 0.6531 (mmt) cc_final: 0.6236 (mmt) REVERT: I 34 MET cc_start: 0.7741 (tmm) cc_final: 0.7471 (tmm) REVERT: I 80 MET cc_start: 0.5084 (tmm) cc_final: 0.4005 (tmm) outliers start: 112 outliers final: 93 residues processed: 421 average time/residue: 0.3648 time to fit residues: 261.3588 Evaluate side-chains 397 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 299 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 69 MET Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 93 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 275 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 375 optimal weight: 20.0000 chunk 235 optimal weight: 0.9990 chunk 229 optimal weight: 0.9980 chunk 173 optimal weight: 0.0270 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN A 965 GLN A 978 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 32346 Z= 0.332 Angle : 0.626 10.345 44037 Z= 0.320 Chirality : 0.047 0.335 5136 Planarity : 0.004 0.049 5601 Dihedral : 6.490 59.080 5526 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.16 % Allowed : 17.53 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 3909 helix: 0.22 (0.20), residues: 729 sheet: -0.08 (0.16), residues: 1014 loop : -1.14 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 64 HIS 0.004 0.001 HIS A 66 PHE 0.021 0.002 PHE C 238 TYR 0.032 0.002 TYR C 508 ARG 0.006 0.001 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 324 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7544 (t80) REVERT: A 387 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8947 (tt) REVERT: A 398 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: A 556 ASN cc_start: 0.6261 (OUTLIER) cc_final: 0.6021 (t0) REVERT: A 1029 MET cc_start: 0.7909 (tpp) cc_final: 0.7524 (mmm) REVERT: B 115 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7530 (mt0) REVERT: B 200 TYR cc_start: 0.7846 (m-80) cc_final: 0.7607 (m-10) REVERT: B 387 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8813 (tt) REVERT: B 398 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7709 (m-30) REVERT: B 866 THR cc_start: 0.8083 (p) cc_final: 0.7881 (p) REVERT: B 878 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7430 (mt) REVERT: B 900 MET cc_start: 0.7806 (mpp) cc_final: 0.7142 (mtm) REVERT: B 1005 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 398 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: C 886 TRP cc_start: 0.7688 (p90) cc_final: 0.7319 (p90) REVERT: C 1049 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7053 (mt) REVERT: H 80 MET cc_start: 0.5218 (tmm) cc_final: 0.4445 (tmm) REVERT: G 69 MET cc_start: 0.6640 (mmt) cc_final: 0.6397 (mmt) REVERT: J 22 THR cc_start: 0.5937 (t) cc_final: 0.5495 (t) REVERT: I 34 MET cc_start: 0.7593 (tmm) cc_final: 0.7009 (tmm) outliers start: 142 outliers final: 114 residues processed: 432 average time/residue: 0.3640 time to fit residues: 269.9714 Evaluate side-chains 410 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 286 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.172 32346 Z= 0.375 Angle : 0.659 9.589 44037 Z= 0.338 Chirality : 0.047 0.332 5136 Planarity : 0.005 0.049 5601 Dihedral : 6.780 59.779 5526 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.62 % Allowed : 17.71 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 3909 helix: 0.11 (0.20), residues: 711 sheet: -0.19 (0.17), residues: 993 loop : -1.21 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 64 HIS 0.005 0.001 HIS H 99 PHE 0.025 0.002 PHE K 71 TYR 0.033 0.002 TYR B 508 ARG 0.006 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 306 time to evaluate : 3.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 387 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8984 (tt) REVERT: A 398 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: A 818 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8190 (pt) REVERT: A 866 THR cc_start: 0.8426 (p) cc_final: 0.8187 (p) REVERT: A 1029 MET cc_start: 0.7942 (tpp) cc_final: 0.7521 (mmm) REVERT: B 115 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: B 387 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8775 (tt) REVERT: B 489 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: B 866 THR cc_start: 0.8095 (p) cc_final: 0.7883 (p) REVERT: B 878 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7509 (mt) REVERT: B 1005 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7708 (tm-30) REVERT: C 398 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: C 508 TYR cc_start: 0.8216 (m-80) cc_final: 0.8013 (m-80) REVERT: C 731 MET cc_start: 0.7846 (ttt) cc_final: 0.7577 (ttt) REVERT: C 886 TRP cc_start: 0.7843 (p90) cc_final: 0.7464 (p90) REVERT: C 1135 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7675 (p0) REVERT: G 69 MET cc_start: 0.7085 (mmt) cc_final: 0.6823 (mmt) REVERT: I 34 MET cc_start: 0.7977 (tmm) cc_final: 0.7598 (tmm) outliers start: 158 outliers final: 126 residues processed: 435 average time/residue: 0.3796 time to fit residues: 284.7096 Evaluate side-chains 411 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 275 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 93 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 6.9990 chunk 360 optimal weight: 10.0000 chunk 328 optimal weight: 7.9990 chunk 350 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 316 optimal weight: 0.0770 chunk 331 optimal weight: 0.6980 chunk 349 optimal weight: 4.9990 overall best weight: 3.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 965 GLN B 23 GLN B 66 HIS B 99 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN K 55 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.233 32346 Z= 0.561 Angle : 0.789 13.015 44037 Z= 0.404 Chirality : 0.051 0.337 5136 Planarity : 0.005 0.059 5601 Dihedral : 7.395 59.969 5526 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.93 % Favored : 92.99 % Rotamer: Outliers : 4.65 % Allowed : 18.26 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 3909 helix: -0.31 (0.19), residues: 711 sheet: -0.51 (0.16), residues: 993 loop : -1.47 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 353 HIS 0.007 0.001 HIS H 35 PHE 0.033 0.003 PHE C 133 TYR 0.044 0.003 TYR B 508 ARG 0.006 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 294 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9017 (tt) REVERT: A 866 THR cc_start: 0.8427 (p) cc_final: 0.8212 (p) REVERT: A 1029 MET cc_start: 0.8041 (tpp) cc_final: 0.7615 (mmm) REVERT: B 387 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8882 (tt) REVERT: B 489 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7556 (m-80) REVERT: B 740 MET cc_start: 0.7912 (mmt) cc_final: 0.7681 (mmt) REVERT: B 900 MET cc_start: 0.7706 (mpp) cc_final: 0.7202 (mtm) REVERT: B 1005 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7770 (tm-30) REVERT: C 886 TRP cc_start: 0.7928 (p90) cc_final: 0.7534 (p90) REVERT: H 29 PHE cc_start: 0.6924 (t80) cc_final: 0.6632 (t80) REVERT: H 52 PRO cc_start: 0.7844 (Cg_endo) cc_final: 0.7613 (Cg_exo) REVERT: L 94 TYR cc_start: 0.8487 (m-10) cc_final: 0.8262 (m-10) REVERT: G 69 MET cc_start: 0.7203 (mmt) cc_final: 0.6860 (mmt) REVERT: I 34 MET cc_start: 0.7934 (tmm) cc_final: 0.7632 (tmm) REVERT: I 81 GLU cc_start: 0.5977 (mp0) cc_final: 0.5682 (mp0) outliers start: 159 outliers final: 137 residues processed: 429 average time/residue: 0.3712 time to fit residues: 276.2027 Evaluate side-chains 420 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 280 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 0.9990 chunk 370 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 257 optimal weight: 0.7980 chunk 388 optimal weight: 6.9990 chunk 357 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 32346 Z= 0.227 Angle : 0.640 12.152 44037 Z= 0.325 Chirality : 0.047 0.338 5136 Planarity : 0.004 0.048 5601 Dihedral : 6.751 58.911 5526 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.84 % Allowed : 19.90 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.13), residues: 3909 helix: 0.15 (0.20), residues: 711 sheet: -0.41 (0.16), residues: 987 loop : -1.22 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 64 HIS 0.005 0.001 HIS A1101 PHE 0.032 0.002 PHE L 71 TYR 0.025 0.001 TYR G 100O ARG 0.006 0.000 ARG I 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 296 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7271 (t80) REVERT: A 387 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8959 (tt) REVERT: A 508 TYR cc_start: 0.7805 (m-80) cc_final: 0.7508 (m-80) REVERT: A 866 THR cc_start: 0.8351 (p) cc_final: 0.8129 (p) REVERT: A 902 MET cc_start: 0.8628 (tpp) cc_final: 0.8424 (tpp) REVERT: A 1029 MET cc_start: 0.7892 (tpp) cc_final: 0.7490 (mmm) REVERT: B 861 LEU cc_start: 0.8491 (mt) cc_final: 0.8143 (mp) REVERT: B 900 MET cc_start: 0.7556 (mpp) cc_final: 0.7017 (mtm) REVERT: B 1005 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7728 (tm-30) REVERT: C 886 TRP cc_start: 0.7739 (p90) cc_final: 0.7346 (p90) REVERT: H 29 PHE cc_start: 0.6838 (t80) cc_final: 0.6558 (t80) REVERT: H 52 PRO cc_start: 0.7785 (Cg_endo) cc_final: 0.7452 (Cg_exo) REVERT: G 29 PHE cc_start: 0.6500 (t80) cc_final: 0.6245 (t80) REVERT: G 36 TRP cc_start: 0.6289 (t-100) cc_final: 0.5995 (m-90) REVERT: J 71 PHE cc_start: 0.6460 (m-10) cc_final: 0.6233 (m-10) outliers start: 97 outliers final: 87 residues processed: 383 average time/residue: 0.3576 time to fit residues: 237.6979 Evaluate side-chains 369 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 280 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 3.9990 chunk 329 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 285 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 309 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 318 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 965 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.167262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.139555 restraints weight = 54287.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.139574 restraints weight = 77601.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.141262 restraints weight = 65557.541| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 32346 Z= 0.218 Angle : 0.623 13.037 44037 Z= 0.315 Chirality : 0.046 0.334 5136 Planarity : 0.004 0.047 5601 Dihedral : 6.416 59.797 5526 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.96 % Allowed : 19.75 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.99 (0.13), residues: 3909 helix: 0.30 (0.19), residues: 726 sheet: -0.32 (0.17), residues: 909 loop : -1.12 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 36 HIS 0.004 0.001 HIS A1101 PHE 0.032 0.001 PHE L 71 TYR 0.029 0.001 TYR C 508 ARG 0.007 0.000 ARG H 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6007.54 seconds wall clock time: 112 minutes 9.25 seconds (6729.25 seconds total)