Starting phenix.real_space_refine on Tue Feb 20 23:24:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0g_24105/02_2024/7n0g_24105_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0g_24105/02_2024/7n0g_24105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0g_24105/02_2024/7n0g_24105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0g_24105/02_2024/7n0g_24105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0g_24105/02_2024/7n0g_24105_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0g_24105/02_2024/7n0g_24105_neut.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 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 126 5.16 5 C 18432 2.51 5 N 4788 2.21 5 O 5716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 73": "OD1" <-> "OD2" Residue "X TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29062 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8395 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 57, 'TRANS': 1018} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 8405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8405 Classifications: {'peptide': 1078} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 57, 'TRANS': 1020} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8384 Classifications: {'peptide': 1075} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 57, 'TRANS': 1017} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: "G" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "R" 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: "S" 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: "U" 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: "V" 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: "W" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 14.96, per 1000 atoms: 0.51 Number of scatterers: 29062 At special positions: 0 Unit cell: (163.06, 158.852, 210.4, 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 126 16.00 O 5716 8.00 N 4788 7.00 C 18432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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=2.02 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 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.02 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 X 22 " - pdb=" SG CYS X 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 165 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1312 " - " ASN B 717 " " NAG B1313 " - " ASN B1098 " " NAG B1314 " - " ASN B1134 " " NAG B1315 " - " ASN C 282 " " NAG C1301 " - " ASN A 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 149 " " NAG C1306 " - " ASN C 165 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1074 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN A 122 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN B 61 " " NAG S 1 " - " ASN B 17 " " NAG U 1 " - " ASN C 17 " " NAG V 1 " - " ASN C 122 " " NAG W 1 " - " ASN C 234 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.50 Conformation dependent library (CDL) restraints added in 4.9 seconds 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 61 sheets defined 21.7% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.133A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.585A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.522A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.559A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.539A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.053A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.726A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.710A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.122A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.576A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.748A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.646A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.670A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.742A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.861A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.576A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.278A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.924A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.440A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.590A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.538A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.817A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.695A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.529A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.527A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.509A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.829A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.724A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.842A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.917A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'Y' and resid 87 through 91 removed outlier: 3.501A pdb=" N THR Y 91 " --> pdb=" O PRO Y 88 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.327A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.327A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.086A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.975A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.382A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.664A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.783A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.764A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.651A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.172A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.889A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.054A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.415A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.847A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.012A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.012A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.956A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.514A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.814A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.417A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.838A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.358A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.786A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.991A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.628A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.703A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.703A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.300A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.505A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.505A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.013A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.488A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.807A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.785A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.735A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.834A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.944A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.510A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.133A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.066A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.335A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'X' and resid 10 through 13 removed outlier: 4.705A pdb=" N LYS X 99 " --> pdb=" O ARG X 33 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG X 33 " --> pdb=" O LYS X 99 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG X 38 " --> pdb=" O TRP X 47 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TRP X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 10 through 13 Processing sheet with id=AG2, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.083A pdb=" N GLY Y 10 " --> pdb=" O THR Y 118 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N SER Y 120 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL Y 12 " --> pdb=" O SER Y 120 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS Y 99 " --> pdb=" O ARG Y 33 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG Y 33 " --> pdb=" O LYS Y 99 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.083A pdb=" N GLY Y 10 " --> pdb=" O THR Y 118 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N SER Y 120 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL Y 12 " --> pdb=" O SER Y 120 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 3 through 8 Processing sheet with id=AG6, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.214A pdb=" N GLY Z 10 " --> pdb=" O THR Z 118 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER Z 120 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL Z 12 " --> pdb=" O SER Z 120 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS Z 99 " --> pdb=" O ARG Z 33 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG Z 33 " --> pdb=" O LYS Z 99 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG Z 38 " --> pdb=" O TRP Z 47 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TRP Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.214A pdb=" N GLY Z 10 " --> pdb=" O THR Z 118 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER Z 120 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL Z 12 " --> pdb=" O SER Z 120 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3258 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: 14.09 Time building geometry restraints manager: 12.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9221 1.34 - 1.46: 6815 1.46 - 1.58: 13526 1.58 - 1.70: 1 1.70 - 1.82: 162 Bond restraints: 29725 Sorted by residual: bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.534 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 29720 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.31: 582 105.31 - 112.51: 15454 112.51 - 119.71: 9393 119.71 - 126.90: 14715 126.90 - 134.10: 318 Bond angle restraints: 40462 Sorted by residual: angle pdb=" C ASN B 657 " pdb=" CA ASN B 657 " pdb=" CB ASN B 657 " ideal model delta sigma weight residual 109.07 118.79 -9.72 1.68e+00 3.54e-01 3.35e+01 angle pdb=" C ASN B 616 " pdb=" CA ASN B 616 " pdb=" CB ASN B 616 " ideal model delta sigma weight residual 109.33 117.39 -8.06 1.97e+00 2.58e-01 1.67e+01 angle pdb=" C VAL B 615 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta sigma weight residual 122.81 116.89 5.92 1.57e+00 4.06e-01 1.42e+01 angle pdb=" N ASN B 657 " pdb=" CA ASN B 657 " pdb=" CB ASN B 657 " ideal model delta sigma weight residual 110.67 106.03 4.64 1.39e+00 5.18e-01 1.11e+01 angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 121.54 127.85 -6.31 1.91e+00 2.74e-01 1.09e+01 ... (remaining 40457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.27: 17508 25.27 - 50.55: 765 50.55 - 75.82: 194 75.82 - 101.10: 86 101.10 - 126.37: 64 Dihedral angle restraints: 18617 sinusoidal: 8179 harmonic: 10438 Sorted by residual: 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 93.00 165.19 -72.19 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -156.47 70.47 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CA VAL B 656 " pdb=" C VAL B 656 " pdb=" N ASN B 657 " pdb=" CA ASN B 657 " ideal model delta harmonic sigma weight residual 180.00 -140.80 -39.20 0 5.00e+00 4.00e-02 6.15e+01 ... (remaining 18614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.191: 4725 0.191 - 0.381: 14 0.381 - 0.572: 3 0.572 - 0.763: 1 0.763 - 0.953: 2 Chirality restraints: 4745 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 ... (remaining 4742 not shown) Planarity restraints: 5219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.010 2.00e-02 2.50e+03 6.64e-02 5.51e+01 pdb=" CG ASN B 657 " -0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.080 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.061 2.00e-02 2.50e+03 pdb=" C1 NAG B1310 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.023 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" CG ASN B 657 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.033 2.00e-02 2.50e+03 3.28e-02 1.35e+01 pdb=" CG ASN C1074 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " 0.036 2.00e-02 2.50e+03 ... (remaining 5216 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 865 2.71 - 3.25: 28310 3.25 - 3.80: 46094 3.80 - 4.35: 58364 4.35 - 4.90: 99168 Nonbonded interactions: 232801 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.157 2.440 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.205 2.440 nonbonded pdb=" NH1 ARG A 357 " pdb=" O CYS B 166 " model vdw 2.216 2.520 nonbonded pdb=" NE2 GLN Z 116 " pdb=" OG1 THR Z 118 " model vdw 2.217 2.520 nonbonded pdb=" OG SER B 366 " pdb=" OD1 ASN B 388 " model vdw 2.235 2.440 ... (remaining 232796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 331 or (resid 332 through 333 and (name N or na \ me CA or name C or name O or name CB )) or resid 334 through 620 or resid 641 th \ rough 1146 or resid 1301 through 1308)) selection = (chain 'B' and (resid 14 through 528 or (resid 529 and (name N or name CA or nam \ e C or name O or name CB )) or resid 530 through 620 or resid 641 through 1146 o \ r resid 1301 through 1308)) selection = (chain 'C' and (resid 14 through 1146 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 14.730 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 77.610 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.004 0.128 29725 Z= 0.250 Angle : 0.600 9.720 40462 Z= 0.305 Chirality : 0.053 0.953 4745 Planarity : 0.004 0.060 5165 Dihedral : 17.867 126.372 11801 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.03 % Allowed : 0.32 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.27 (0.14), residues: 3562 helix: 2.28 (0.21), residues: 644 sheet: 0.10 (0.16), residues: 1004 loop : -0.47 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.003 0.000 HIS B 655 PHE 0.017 0.001 PHE B 377 TYR 0.027 0.001 TYR A 904 ARG 0.007 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 3.461 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: B 456 PHE cc_start: 0.9018 (m-80) cc_final: 0.8434 (m-80) REVERT: X 37 TYR cc_start: -0.1331 (m-80) cc_final: -0.1731 (m-10) REVERT: X 60 TYR cc_start: 0.4370 (m-80) cc_final: 0.4016 (m-80) REVERT: X 105 TYR cc_start: -0.0054 (m-10) cc_final: -0.0732 (m-80) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.4235 time to fit residues: 94.6921 Evaluate side-chains 106 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 324 optimal weight: 50.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1002 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1005 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 440 ASN C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 29725 Z= 0.471 Angle : 0.685 12.085 40462 Z= 0.333 Chirality : 0.052 0.550 4745 Planarity : 0.004 0.074 5165 Dihedral : 15.033 108.509 5413 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.32 % Allowed : 6.34 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3562 helix: 2.03 (0.21), residues: 655 sheet: 0.14 (0.16), residues: 997 loop : -0.58 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 111 HIS 0.005 0.001 HIS C1048 PHE 0.017 0.002 PHE B 898 TYR 0.040 0.002 TYR A 904 ARG 0.005 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.9022 (m-80) cc_final: 0.8378 (m-80) REVERT: B 869 MET cc_start: 0.9008 (mtt) cc_final: 0.8791 (mtt) REVERT: C 420 ASP cc_start: 0.8958 (m-30) cc_final: 0.8595 (t0) REVERT: C 460 ASN cc_start: 0.8961 (m-40) cc_final: 0.8465 (m-40) REVERT: X 34 MET cc_start: 0.1450 (OUTLIER) cc_final: 0.1130 (pmm) REVERT: X 37 TYR cc_start: -0.1326 (m-80) cc_final: -0.1641 (m-10) REVERT: X 52 TYR cc_start: 0.1908 (m-80) cc_final: 0.1466 (m-80) REVERT: X 60 TYR cc_start: 0.4471 (m-80) cc_final: 0.4038 (m-80) REVERT: Y 37 TYR cc_start: -0.0004 (m-80) cc_final: -0.0333 (m-10) REVERT: Y 83 MET cc_start: 0.0823 (mmp) cc_final: -0.0402 (mtp) outliers start: 10 outliers final: 5 residues processed: 111 average time/residue: 0.3530 time to fit residues: 68.6183 Evaluate side-chains 104 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain Z residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 324 optimal weight: 50.0000 chunk 350 optimal weight: 20.0000 chunk 289 optimal weight: 0.7980 chunk 322 optimal weight: 50.0000 chunk 110 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 440 ASN C 655 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29725 Z= 0.317 Angle : 0.606 9.803 40462 Z= 0.292 Chirality : 0.049 0.502 4745 Planarity : 0.004 0.076 5165 Dihedral : 12.944 110.440 5413 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.81 % Allowed : 8.12 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3562 helix: 2.18 (0.21), residues: 648 sheet: 0.21 (0.16), residues: 994 loop : -0.61 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 111 HIS 0.003 0.001 HIS B 655 PHE 0.015 0.001 PHE C 898 TYR 0.033 0.001 TYR A 904 ARG 0.009 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.5810 (mmt) cc_final: -0.6257 (mtt) REVERT: B 456 PHE cc_start: 0.9010 (m-80) cc_final: 0.8425 (m-80) REVERT: C 177 MET cc_start: -0.4439 (OUTLIER) cc_final: -0.4886 (ttt) REVERT: X 37 TYR cc_start: -0.1321 (m-80) cc_final: -0.1602 (m-10) REVERT: X 52 TYR cc_start: 0.1729 (m-80) cc_final: 0.1342 (m-10) REVERT: X 60 TYR cc_start: 0.4460 (m-80) cc_final: 0.4015 (m-80) REVERT: Y 37 TYR cc_start: -0.0175 (m-80) cc_final: -0.0461 (m-10) REVERT: Y 83 MET cc_start: 0.1047 (mmp) cc_final: -0.0113 (mtp) outliers start: 25 outliers final: 8 residues processed: 120 average time/residue: 0.3855 time to fit residues: 80.1002 Evaluate side-chains 107 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain Z residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 6.9990 chunk 244 optimal weight: 0.4980 chunk 168 optimal weight: 1.9990 chunk 35 optimal weight: 0.0060 chunk 154 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 325 optimal weight: 30.0000 chunk 345 optimal weight: 20.0000 chunk 170 optimal weight: 0.8980 chunk 308 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 29725 Z= 0.214 Angle : 0.570 9.831 40462 Z= 0.272 Chirality : 0.048 0.481 4745 Planarity : 0.003 0.051 5165 Dihedral : 11.622 110.136 5413 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.74 % Allowed : 9.82 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3562 helix: 2.42 (0.21), residues: 636 sheet: 0.28 (0.16), residues: 1009 loop : -0.56 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 152 HIS 0.003 0.000 HIS B 655 PHE 0.015 0.001 PHE B 490 TYR 0.028 0.001 TYR A 904 ARG 0.003 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.5809 (mmt) cc_final: -0.6283 (mtt) REVERT: B 456 PHE cc_start: 0.8968 (m-80) cc_final: 0.8370 (m-80) REVERT: C 177 MET cc_start: -0.4928 (OUTLIER) cc_final: -0.5354 (ttt) REVERT: X 34 MET cc_start: 0.1433 (pmm) cc_final: 0.1196 (pmm) REVERT: X 37 TYR cc_start: -0.1427 (m-80) cc_final: -0.1699 (m-10) REVERT: X 52 TYR cc_start: 0.1774 (m-80) cc_final: 0.1252 (m-10) REVERT: X 60 TYR cc_start: 0.4463 (m-80) cc_final: 0.4014 (m-80) REVERT: Y 83 MET cc_start: 0.1484 (mmp) cc_final: 0.0413 (mtp) REVERT: Y 95 TYR cc_start: 0.6704 (m-80) cc_final: 0.6387 (t80) outliers start: 23 outliers final: 10 residues processed: 121 average time/residue: 0.3744 time to fit residues: 79.9127 Evaluate side-chains 108 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 256 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 294 optimal weight: 0.5980 chunk 238 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 176 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29725 Z= 0.221 Angle : 0.563 10.239 40462 Z= 0.269 Chirality : 0.047 0.470 4745 Planarity : 0.003 0.051 5165 Dihedral : 10.854 110.172 5413 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.16 % Allowed : 10.47 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3562 helix: 2.41 (0.21), residues: 643 sheet: 0.34 (0.16), residues: 997 loop : -0.52 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 111 HIS 0.002 0.000 HIS B 655 PHE 0.014 0.001 PHE C 898 TYR 0.026 0.001 TYR A 904 ARG 0.003 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 99 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.5788 (mmt) cc_final: -0.6275 (mtt) REVERT: B 456 PHE cc_start: 0.8978 (m-80) cc_final: 0.8410 (m-80) REVERT: C 152 TRP cc_start: 0.5541 (m100) cc_final: 0.5305 (m100) REVERT: C 177 MET cc_start: -0.5052 (OUTLIER) cc_final: -0.5441 (ttt) REVERT: C 449 TYR cc_start: 0.8164 (m-80) cc_final: 0.7119 (m-80) REVERT: X 34 MET cc_start: 0.1410 (pmm) cc_final: 0.1181 (pmm) REVERT: X 37 TYR cc_start: -0.1528 (m-80) cc_final: -0.1816 (m-10) REVERT: X 52 TYR cc_start: 0.1573 (m-80) cc_final: 0.0959 (m-10) REVERT: X 60 TYR cc_start: 0.4407 (m-80) cc_final: 0.3960 (m-80) REVERT: Y 37 TYR cc_start: 0.0318 (m-10) cc_final: 0.0051 (m-80) REVERT: Y 83 MET cc_start: 0.1437 (mmp) cc_final: 0.0426 (mtp) outliers start: 36 outliers final: 19 residues processed: 130 average time/residue: 0.3673 time to fit residues: 84.0887 Evaluate side-chains 117 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 345 optimal weight: 20.0000 chunk 286 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29725 Z= 0.260 Angle : 0.574 11.285 40462 Z= 0.274 Chirality : 0.048 0.468 4745 Planarity : 0.003 0.052 5165 Dihedral : 10.106 109.492 5413 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.22 % Allowed : 11.14 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3562 helix: 2.38 (0.21), residues: 641 sheet: 0.34 (0.16), residues: 991 loop : -0.51 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.005 0.001 HIS A 655 PHE 0.015 0.001 PHE C 898 TYR 0.028 0.001 TYR A 904 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 99 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.6022 (mmt) cc_final: -0.6428 (mtt) REVERT: B 456 PHE cc_start: 0.8968 (m-80) cc_final: 0.8423 (m-80) REVERT: C 177 MET cc_start: -0.4956 (OUTLIER) cc_final: -0.5357 (ttt) REVERT: C 387 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8579 (mm) REVERT: C 449 TYR cc_start: 0.8332 (m-80) cc_final: 0.7383 (m-80) REVERT: X 34 MET cc_start: 0.1403 (pmm) cc_final: 0.1178 (pmm) REVERT: X 52 TYR cc_start: 0.1549 (OUTLIER) cc_final: 0.1042 (m-10) REVERT: X 60 TYR cc_start: 0.4249 (m-80) cc_final: 0.3828 (m-80) REVERT: Y 37 TYR cc_start: 0.0254 (m-80) cc_final: -0.0250 (m-80) REVERT: Y 83 MET cc_start: 0.1653 (mmp) cc_final: 0.0751 (mtp) outliers start: 38 outliers final: 23 residues processed: 131 average time/residue: 0.3556 time to fit residues: 81.8994 Evaluate side-chains 123 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain X residue 52 TYR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 50.0000 chunk 38 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 290 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 344 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 209 optimal weight: 0.0060 chunk 158 optimal weight: 2.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 103 HIS ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29725 Z= 0.246 Angle : 0.568 10.400 40462 Z= 0.272 Chirality : 0.047 0.463 4745 Planarity : 0.003 0.051 5165 Dihedral : 9.625 108.989 5413 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.29 % Allowed : 11.50 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3562 helix: 2.41 (0.21), residues: 641 sheet: 0.34 (0.16), residues: 985 loop : -0.49 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP X 111 HIS 0.002 0.000 HIS B 655 PHE 0.015 0.001 PHE B 490 TYR 0.026 0.001 TYR A 904 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 95 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.6006 (mmt) cc_final: -0.6409 (mtt) REVERT: A 948 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8928 (mp) REVERT: B 456 PHE cc_start: 0.8976 (m-80) cc_final: 0.8439 (m-80) REVERT: C 177 MET cc_start: -0.4920 (OUTLIER) cc_final: -0.5300 (ttt) REVERT: C 387 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8570 (mm) REVERT: C 449 TYR cc_start: 0.8316 (m-80) cc_final: 0.7334 (m-80) REVERT: X 52 TYR cc_start: 0.1536 (OUTLIER) cc_final: 0.1050 (m-10) REVERT: X 60 TYR cc_start: 0.4234 (m-80) cc_final: 0.3816 (m-80) REVERT: Y 37 TYR cc_start: 0.0319 (m-80) cc_final: -0.0136 (m-80) REVERT: Y 83 MET cc_start: 0.1580 (mmp) cc_final: 0.0712 (mtp) outliers start: 40 outliers final: 28 residues processed: 128 average time/residue: 0.3492 time to fit residues: 78.8613 Evaluate side-chains 127 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain X residue 52 TYR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 205 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 234 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 270 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29725 Z= 0.155 Angle : 0.542 11.231 40462 Z= 0.260 Chirality : 0.047 0.513 4745 Planarity : 0.003 0.050 5165 Dihedral : 9.181 108.747 5413 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.00 % Allowed : 12.05 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3562 helix: 2.63 (0.21), residues: 632 sheet: 0.34 (0.16), residues: 983 loop : -0.47 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Y 111 HIS 0.002 0.000 HIS B 655 PHE 0.013 0.001 PHE B 490 TYR 0.041 0.001 TYR Y 95 ARG 0.002 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.6032 (mmt) cc_final: -0.6422 (mtt) REVERT: B 456 PHE cc_start: 0.8968 (m-80) cc_final: 0.8439 (m-80) REVERT: C 177 MET cc_start: -0.4978 (OUTLIER) cc_final: -0.5354 (ttt) REVERT: C 387 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8574 (mm) REVERT: C 449 TYR cc_start: 0.8327 (m-80) cc_final: 0.7358 (m-80) REVERT: X 52 TYR cc_start: 0.1534 (OUTLIER) cc_final: 0.1123 (m-10) REVERT: X 60 TYR cc_start: 0.4158 (m-80) cc_final: 0.3695 (m-80) REVERT: Y 37 TYR cc_start: 0.0615 (m-80) cc_final: 0.0241 (m-80) REVERT: Y 83 MET cc_start: 0.1485 (mmp) cc_final: 0.0632 (mtp) outliers start: 31 outliers final: 22 residues processed: 123 average time/residue: 0.3679 time to fit residues: 80.1342 Evaluate side-chains 116 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain X residue 52 TYR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 2.9990 chunk 329 optimal weight: 0.8980 chunk 300 optimal weight: 0.7980 chunk 320 optimal weight: 0.0040 chunk 192 optimal weight: 1.9990 chunk 139 optimal weight: 30.0000 chunk 251 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 303 optimal weight: 3.9990 chunk 319 optimal weight: 0.0170 overall best weight: 0.7432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29725 Z= 0.166 Angle : 0.536 11.690 40462 Z= 0.256 Chirality : 0.047 0.513 4745 Planarity : 0.003 0.049 5165 Dihedral : 8.783 107.876 5413 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.03 % Allowed : 12.14 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3562 helix: 2.68 (0.21), residues: 633 sheet: 0.31 (0.16), residues: 1005 loop : -0.43 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 152 HIS 0.002 0.000 HIS C 245 PHE 0.017 0.001 PHE B 490 TYR 0.028 0.001 TYR Y 95 ARG 0.003 0.000 ARG X 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.6042 (mmt) cc_final: -0.6442 (mtt) REVERT: B 456 PHE cc_start: 0.8962 (m-80) cc_final: 0.8444 (m-80) REVERT: C 177 MET cc_start: -0.4945 (OUTLIER) cc_final: -0.5327 (ttt) REVERT: C 387 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8596 (mm) REVERT: C 449 TYR cc_start: 0.8349 (m-80) cc_final: 0.7392 (m-80) REVERT: X 52 TYR cc_start: 0.1429 (OUTLIER) cc_final: 0.1059 (m-10) REVERT: X 60 TYR cc_start: 0.4038 (m-80) cc_final: 0.3589 (m-80) REVERT: Y 37 TYR cc_start: 0.0578 (m-80) cc_final: 0.0173 (m-80) REVERT: Y 83 MET cc_start: 0.1618 (mmp) cc_final: 0.0798 (mtp) outliers start: 32 outliers final: 25 residues processed: 122 average time/residue: 0.3837 time to fit residues: 82.0063 Evaluate side-chains 123 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain X residue 52 TYR Chi-restraints excluded: chain Y residue 95 TYR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 0.9990 chunk 339 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 355 optimal weight: 20.0000 chunk 327 optimal weight: 20.0000 chunk 283 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 chunk 218 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Y 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29725 Z= 0.195 Angle : 0.539 9.859 40462 Z= 0.259 Chirality : 0.047 0.444 4745 Planarity : 0.003 0.049 5165 Dihedral : 8.425 106.869 5413 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.16 % Allowed : 12.14 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3562 helix: 2.68 (0.21), residues: 632 sheet: 0.32 (0.16), residues: 988 loop : -0.43 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 111 HIS 0.002 0.000 HIS B 655 PHE 0.019 0.001 PHE B 490 TYR 0.029 0.001 TYR Y 95 ARG 0.003 0.000 ARG C1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 95 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.6024 (mmt) cc_final: -0.6439 (mtt) REVERT: B 456 PHE cc_start: 0.8976 (m-80) cc_final: 0.8463 (m-80) REVERT: C 177 MET cc_start: -0.4918 (OUTLIER) cc_final: -0.5298 (ttt) REVERT: C 449 TYR cc_start: 0.8368 (m-80) cc_final: 0.7413 (m-80) REVERT: X 52 TYR cc_start: 0.1418 (OUTLIER) cc_final: 0.1019 (m-10) REVERT: X 60 TYR cc_start: 0.3985 (m-80) cc_final: 0.3578 (m-80) REVERT: Y 37 TYR cc_start: 0.0519 (m-80) cc_final: 0.0210 (m-80) REVERT: Y 83 MET cc_start: 0.1712 (mmp) cc_final: 0.0898 (mtp) outliers start: 36 outliers final: 27 residues processed: 125 average time/residue: 0.3753 time to fit residues: 83.4236 Evaluate side-chains 123 residues out of total 3117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain X residue 52 TYR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 5.9990 chunk 301 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 291 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.151744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096545 restraints weight = 77397.418| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.45 r_work: 0.2966 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 29725 Z= 0.357 Angle : 0.590 9.948 40462 Z= 0.287 Chirality : 0.048 0.454 4745 Planarity : 0.003 0.051 5165 Dihedral : 8.349 104.442 5413 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.13 % Allowed : 12.11 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3562 helix: 2.37 (0.21), residues: 651 sheet: 0.27 (0.16), residues: 977 loop : -0.47 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 111 HIS 0.003 0.001 HIS C1048 PHE 0.018 0.001 PHE B 490 TYR 0.029 0.001 TYR A 904 ARG 0.005 0.000 ARG C1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5552.57 seconds wall clock time: 103 minutes 12.98 seconds (6192.98 seconds total)