Starting phenix.real_space_refine on Tue Feb 20 00:58:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6g_23695/02_2024/7m6g_23695_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6g_23695/02_2024/7m6g_23695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6g_23695/02_2024/7m6g_23695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6g_23695/02_2024/7m6g_23695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6g_23695/02_2024/7m6g_23695_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6g_23695/02_2024/7m6g_23695_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 117 5.16 5 C 16719 2.51 5 N 4316 2.21 5 O 5138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "S GLU 79": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26290 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7393 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 52, 'TRANS': 915} Chain breaks: 11 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 7427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7427 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 53, 'TRANS': 927} Chain breaks: 10 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 308 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 177 Chain: "C" Number of atoms: 7408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7408 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 53, 'TRANS': 931} Chain breaks: 10 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 208 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "R" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "S" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} 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: "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: "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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" 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 Time building chain proxies: 14.35, per 1000 atoms: 0.55 Number of scatterers: 26290 At special positions: 0 Unit cell: (137.302, 135.564, 198.132, 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 117 16.00 O 5138 8.00 N 4316 7.00 C 16719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.05 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 616 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 616 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN C 801 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN C1074 " " NAG O 1 " - " ASN A1074 " " NAG P 1 " - " ASN C 717 " Time building additional restraints: 10.71 Conformation dependent library (CDL) restraints added in 5.4 seconds 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6316 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 54 sheets defined 23.7% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.649A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.087A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.582A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.629A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.681A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.700A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.265A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 976 through 982 removed outlier: 3.628A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.887A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.029A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.970A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.535A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 4.197A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.704A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.752A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.924A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.956A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.769A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.812A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.394A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 984 removed outlier: 3.924A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.463A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing helix chain 'C' and resid 140 through 140 No H-bonds generated for 'chain 'C' and resid 140 through 140' Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.938A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.584A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.839A 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: 3.544A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.930A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.725A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.671A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.033A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 984 removed outlier: 3.923A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.446A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.406A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.505A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 83 through 87 removed outlier: 3.513A pdb=" N THR R 87 " --> pdb=" O SER R 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.058A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 79 through 83 removed outlier: 3.675A pdb=" N PHE S 83 " --> pdb=" O PRO S 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.741A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.634A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.804A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.163A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.728A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 543 removed outlier: 4.763A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.971A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.681A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.600A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.312A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.319A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.577A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.462A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.772A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.781A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.074A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.537A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.585A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.739A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.875A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.875A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.185A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.004A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B1070 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.004A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B1070 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.823A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.599A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.811A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 279 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.655A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.688A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.507A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.608A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.780A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.535A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.312A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.348A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.866A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.581A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.581A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.650A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 3 through 6 removed outlier: 3.769A pdb=" N CYS R 22 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA R 78 " --> pdb=" O CYS R 22 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU R 81 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR R 68 " --> pdb=" O GLU R 81 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 10 through 11 removed outlier: 6.258A pdb=" N GLU R 10 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR R 107 " --> pdb=" O TYR R 90 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP R 50 " --> pdb=" O ASN R 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN R 58 " --> pdb=" O TRP R 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.240A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'L' and resid 19 through 28 removed outlier: 12.024A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.809A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.522A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY L 68 " --> pdb=" O VAL L 28 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.547A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.738A pdb=" N LEU S 11 " --> pdb=" O GLU S 105 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR S 102 " --> pdb=" O TYR S 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR S 86 " --> pdb=" O THR S 102 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL S 85 " --> pdb=" O GLN S 38 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU S 33 " --> pdb=" O SER S 49 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER S 49 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN S 37 " --> pdb=" O ARG S 45 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER S 53 " --> pdb=" O SER S 49 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 19 through 24 removed outlier: 3.829A pdb=" N ALA S 19 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE S 75 " --> pdb=" O ALA S 19 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU S 21 " --> pdb=" O LEU S 73 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU S 73 " --> pdb=" O LEU S 21 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE S 71 " --> pdb=" O CYS S 23 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2658 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: 12.04 Time building geometry restraints manager: 11.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8214 1.34 - 1.48: 7251 1.48 - 1.62: 11242 1.62 - 1.76: 8 1.76 - 1.90: 139 Bond restraints: 26854 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.520 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.516 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.516 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.38e+01 bond pdb=" CG PRO C 507 " pdb=" CD PRO C 507 " ideal model delta sigma weight residual 1.503 1.339 0.164 3.40e-02 8.65e+02 2.34e+01 ... (remaining 26849 not shown) Histogram of bond angle deviations from ideal: 90.38 - 101.67: 56 101.67 - 112.96: 13976 112.96 - 124.25: 21686 124.25 - 135.54: 892 135.54 - 146.83: 1 Bond angle restraints: 36611 Sorted by residual: angle pdb=" CA LEU B 948 " pdb=" CB LEU B 948 " pdb=" CG LEU B 948 " ideal model delta sigma weight residual 116.30 146.83 -30.53 3.50e+00 8.16e-02 7.61e+01 angle pdb=" N PRO C 507 " pdb=" CD PRO C 507 " pdb=" CG PRO C 507 " ideal model delta sigma weight residual 103.20 90.38 12.82 1.50e+00 4.44e-01 7.31e+01 angle pdb=" CA PRO A1079 " pdb=" N PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 112.00 100.43 11.57 1.40e+00 5.10e-01 6.84e+01 angle pdb=" CA PRO C1079 " pdb=" N PRO C1079 " pdb=" CD PRO C1079 " ideal model delta sigma weight residual 112.00 100.57 11.43 1.40e+00 5.10e-01 6.67e+01 angle pdb=" N ASN A1098 " pdb=" CA ASN A1098 " pdb=" CB ASN A1098 " ideal model delta sigma weight residual 110.44 98.36 12.08 1.53e+00 4.27e-01 6.24e+01 ... (remaining 36606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 15707 24.43 - 48.86: 714 48.86 - 73.29: 113 73.29 - 97.71: 35 97.71 - 122.14: 14 Dihedral angle restraints: 16583 sinusoidal: 6785 harmonic: 9798 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 3.74 89.26 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -8.20 -77.80 1 1.00e+01 1.00e-02 7.57e+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 -161.78 75.78 1 1.00e+01 1.00e-02 7.24e+01 ... (remaining 16580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 4328 0.304 - 0.608: 45 0.608 - 0.912: 2 0.912 - 1.216: 2 1.216 - 1.520: 1 Chirality restraints: 4378 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.88 -1.52 2.00e-01 2.50e+01 5.77e+01 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-01 2.50e+01 3.42e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.25 -1.15 2.00e-01 2.50e+01 3.28e+01 ... (remaining 4375 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1311 " 0.320 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" C7 NAG B1311 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG B1311 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG B1311 " -0.500 2.00e-02 2.50e+03 pdb=" O7 NAG B1311 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.320 2.00e-02 2.50e+03 2.74e-01 9.40e+02 pdb=" C7 NAG D 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.170 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.483 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.265 2.00e-02 2.50e+03 2.25e-01 6.35e+02 pdb=" C7 NAG A1307 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.388 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.019 2.00e-02 2.50e+03 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2292 2.75 - 3.28: 25088 3.28 - 3.82: 41332 3.82 - 4.36: 47791 4.36 - 4.90: 81941 Nonbonded interactions: 198444 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.208 2.440 nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.220 2.440 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.223 2.440 nonbonded pdb=" O PHE B 106 " pdb=" OG SER B 116 " model vdw 2.228 2.440 ... (remaining 198439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 140 or (resid 157 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 194 or (resid 195 throug \ h 198 and (name N or name CA or name C or name O or name CB )) or resid 199 thro \ ugh 209 or resid 217 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 243 or resid 264 through 331 or \ (resid 332 through 335 and (name N or name CA or name C or name O or name CB )) \ or resid 336 through 350 or (resid 351 through 352 and (name N or name CA or na \ me C or name O or name CB )) or resid 353 through 363 or (resid 364 and (name N \ or name CA or name C or name O or name CB )) or resid 365 through 368 or (resid \ 369 and (name N or name CA or name C or name O or name CB )) or resid 370 throug \ h 373 or (resid 374 and (name N or name CA or name C or name O or name CB )) or \ resid 375 through 407 or (resid 408 and (name N or name CA or name C or name O o \ r name CB )) or resid 409 through 441 or (resid 442 and (name N or name CA or na \ me C or name O or name CB )) or resid 443 or (resid 449 and (name N or name CA o \ r name C or name O or name CB )) or resid 450 through 496 or (resid 497 through \ 498 and (name N or name CA or name C or name O or name CB )) or resid 499 or (re \ sid 500 and (name N or name CA or name C or name O or name CB )) or resid 503 th \ rough 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) \ or resid 510 through 620 or resid 641 through 1146 or resid 1301 through 1307)) \ selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 195 or (resid 196 through 19 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 199 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or re \ sid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) o \ r resid 240 through 289 or (resid 290 and (name N or name CA or name C or name O \ or name CB )) or resid 291 through 443 or resid 449 through 454 or resid 491 th \ rough 500 or resid 503 through 528 or (resid 529 and (name N or name CA or name \ C or name O or name CB )) or resid 530 through 620 or resid 641 through 1146 or \ resid 1301 through 1307)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or resid 81 through 187 or (res \ id 188 and (name N or name CA or name C or name O or name CB )) or resid 189 thr \ ough 209 or resid 217 through 243 or resid 264 through 280 or (resid 281 and (na \ me N or name CA or name C or name O or name CB )) or resid 282 through 443 or re \ sid 449 through 454 or resid 491 through 500 or resid 503 through 1146 or resid \ 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'R' } ncs_group { reference = chain 'L' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 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: 18.030 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 73.280 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 : 0.009 0.164 26854 Z= 0.557 Angle : 1.551 30.530 36611 Z= 0.869 Chirality : 0.096 1.520 4378 Planarity : 0.014 0.279 4666 Dihedral : 14.408 122.143 10147 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 0.47 % Allowed : 1.30 % Favored : 98.23 % Cbeta Deviations : 0.16 % 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 (0.13), residues: 3304 helix: -0.17 (0.18), residues: 672 sheet: 0.96 (0.18), residues: 716 loop : -0.86 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP C 104 HIS 0.037 0.004 HIS A1048 PHE 0.104 0.005 PHE C 392 TYR 0.064 0.004 TYR H 59 ARG 0.047 0.004 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 501 time to evaluate : 3.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7979 (m-80) cc_final: 0.7652 (m-10) REVERT: A 106 PHE cc_start: 0.8739 (m-80) cc_final: 0.8516 (m-80) REVERT: A 298 GLU cc_start: 0.8366 (tp30) cc_final: 0.7949 (mt-10) REVERT: A 611 LEU cc_start: 0.8417 (tp) cc_final: 0.8143 (tt) REVERT: A 671 CYS cc_start: 0.3818 (m) cc_final: 0.2482 (m) REVERT: A 737 ASP cc_start: 0.7528 (p0) cc_final: 0.7112 (p0) REVERT: A 974 SER cc_start: 0.7625 (t) cc_final: 0.7372 (t) REVERT: B 200 TYR cc_start: 0.6556 (m-80) cc_final: 0.6340 (m-10) REVERT: B 290 ASP cc_start: 0.7053 (p0) cc_final: 0.6823 (p0) REVERT: B 731 MET cc_start: 0.7696 (ptm) cc_final: 0.7335 (ptm) REVERT: B 855 PHE cc_start: 0.5247 (m-80) cc_final: 0.5000 (m-80) REVERT: C 443 SER cc_start: 0.8556 (m) cc_final: 0.7877 (m) REVERT: C 918 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: H 59 TYR cc_start: 0.6350 (m-80) cc_final: 0.6021 (m-80) REVERT: H 64 GLN cc_start: 0.8284 (tp40) cc_final: 0.7809 (mm-40) REVERT: H 69 MET cc_start: 0.8175 (mpp) cc_final: 0.7590 (mpp) REVERT: H 99 VAL cc_start: 0.7244 (t) cc_final: 0.7018 (p) REVERT: H 101 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6680 (t70) REVERT: H 102 CYS cc_start: 0.7108 (m) cc_final: 0.6810 (m) REVERT: R 50 TRP cc_start: 0.6014 (p-90) cc_final: 0.5012 (p-90) REVERT: R 91 TYR cc_start: 0.5945 (m-80) cc_final: 0.5722 (m-80) REVERT: R 101 ASP cc_start: 0.8407 (m-30) cc_final: 0.7791 (m-30) REVERT: R 105 GLN cc_start: 0.4053 (OUTLIER) cc_final: 0.3753 (pm20) REVERT: L 33 LEU cc_start: 0.8680 (mt) cc_final: 0.8455 (mt) REVERT: L 39 LYS cc_start: 0.7449 (tptt) cc_final: 0.7111 (mmtm) REVERT: L 89 GLN cc_start: 0.6631 (tm-30) cc_final: 0.4735 (tp-100) REVERT: L 91 TYR cc_start: 0.7687 (p90) cc_final: 0.7154 (p90) REVERT: S 47 LEU cc_start: 0.8916 (mp) cc_final: 0.8096 (pp) REVERT: S 103 LYS cc_start: 0.4556 (tptp) cc_final: 0.4344 (mmmt) outliers start: 13 outliers final: 2 residues processed: 511 average time/residue: 0.3326 time to fit residues: 279.0945 Evaluate side-chains 335 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 330 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain R residue 105 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN A1005 GLN B 207 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS C1088 HIS R 105 GLN S 6 GLN ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26854 Z= 0.295 Angle : 0.775 12.757 36611 Z= 0.395 Chirality : 0.053 0.592 4378 Planarity : 0.006 0.092 4666 Dihedral : 10.098 114.094 4598 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 2.28 % Allowed : 10.67 % Favored : 87.06 % 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: -0.25 (0.14), residues: 3304 helix: 0.23 (0.19), residues: 679 sheet: 0.65 (0.17), residues: 774 loop : -0.64 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 103 HIS 0.009 0.002 HIS C 655 PHE 0.027 0.002 PHE C 643 TYR 0.023 0.002 TYR B1067 ARG 0.006 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 345 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8694 (ptp) cc_final: 0.8464 (ptm) REVERT: A 902 MET cc_start: 0.8110 (tpt) cc_final: 0.7734 (tpt) REVERT: A 974 SER cc_start: 0.8293 (t) cc_final: 0.8014 (t) REVERT: B 200 TYR cc_start: 0.6774 (m-80) cc_final: 0.6047 (m-10) REVERT: B 290 ASP cc_start: 0.7216 (p0) cc_final: 0.6905 (p0) REVERT: B 338 PHE cc_start: 0.6746 (m-80) cc_final: 0.6510 (m-10) REVERT: B 399 SER cc_start: 0.8920 (m) cc_final: 0.8660 (p) REVERT: B 983 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7374 (ttp-170) REVERT: C 43 PHE cc_start: 0.7094 (t80) cc_final: 0.6678 (t80) REVERT: C 315 THR cc_start: 0.8257 (p) cc_final: 0.8012 (t) REVERT: C 574 ASP cc_start: 0.6444 (m-30) cc_final: 0.6162 (m-30) REVERT: C 918 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: H 59 TYR cc_start: 0.6521 (m-80) cc_final: 0.6116 (m-80) REVERT: H 64 GLN cc_start: 0.8204 (tp40) cc_final: 0.7827 (mm-40) REVERT: H 69 MET cc_start: 0.8081 (mpp) cc_final: 0.7735 (mpp) REVERT: R 50 TRP cc_start: 0.5912 (p-90) cc_final: 0.5683 (p-90) REVERT: R 80 MET cc_start: 0.5468 (ttt) cc_final: 0.4395 (tmm) REVERT: R 101 ASP cc_start: 0.8103 (m-30) cc_final: 0.7637 (m-30) REVERT: L 39 LYS cc_start: 0.7923 (tptt) cc_final: 0.7492 (mptt) REVERT: L 90 GLN cc_start: 0.8431 (pp30) cc_final: 0.7994 (pp30) REVERT: S 54 ARG cc_start: 0.6135 (ptp90) cc_final: 0.5510 (ptp-170) REVERT: S 79 GLU cc_start: 0.7613 (tp30) cc_final: 0.7286 (tp30) REVERT: S 81 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7454 (mp0) outliers start: 63 outliers final: 35 residues processed: 385 average time/residue: 0.3349 time to fit residues: 213.8660 Evaluate side-chains 327 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 289 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 81 GLU Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 168 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 303 optimal weight: 10.0000 chunk 328 optimal weight: 0.0980 chunk 270 optimal weight: 0.8980 chunk 301 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 895 GLN A1002 GLN B 134 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS R 6 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26854 Z= 0.200 Angle : 0.672 15.635 36611 Z= 0.339 Chirality : 0.049 0.500 4378 Planarity : 0.005 0.067 4666 Dihedral : 9.155 112.724 4593 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.07 % Allowed : 13.27 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3304 helix: 0.20 (0.19), residues: 684 sheet: 0.64 (0.17), residues: 777 loop : -0.54 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP H 103 HIS 0.008 0.001 HIS B 49 PHE 0.032 0.002 PHE C 86 TYR 0.024 0.002 TYR B 38 ARG 0.005 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 319 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8626 (ptp) cc_final: 0.8300 (ptp) REVERT: A 974 SER cc_start: 0.8459 (t) cc_final: 0.8200 (t) REVERT: B 129 LYS cc_start: 0.7292 (tptm) cc_final: 0.7005 (tptm) REVERT: B 200 TYR cc_start: 0.6754 (m-80) cc_final: 0.5993 (m-10) REVERT: B 290 ASP cc_start: 0.6959 (p0) cc_final: 0.6633 (p0) REVERT: B 298 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6743 (mm-30) REVERT: B 983 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7501 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8446 (tp-100) cc_final: 0.8181 (tp40) REVERT: C 86 PHE cc_start: 0.6326 (t80) cc_final: 0.6072 (t80) REVERT: C 223 LEU cc_start: 0.6449 (tp) cc_final: 0.6229 (tp) REVERT: C 265 TYR cc_start: 0.5420 (p90) cc_final: 0.4955 (p90) REVERT: C 315 THR cc_start: 0.8332 (p) cc_final: 0.8109 (t) REVERT: C 574 ASP cc_start: 0.6313 (m-30) cc_final: 0.6041 (m-30) REVERT: C 765 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8556 (ttp80) REVERT: C 780 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: C 918 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: C 1050 MET cc_start: 0.6760 (ptm) cc_final: 0.6010 (ptt) REVERT: H 59 TYR cc_start: 0.6509 (m-80) cc_final: 0.5967 (m-80) REVERT: H 64 GLN cc_start: 0.8191 (tp40) cc_final: 0.7788 (mm-40) REVERT: H 79 TYR cc_start: 0.7726 (m-80) cc_final: 0.7496 (m-80) REVERT: H 103 TRP cc_start: 0.7120 (m100) cc_final: 0.6409 (m100) REVERT: R 80 MET cc_start: 0.5848 (ttt) cc_final: 0.4531 (tmm) REVERT: L 39 LYS cc_start: 0.7950 (tptt) cc_final: 0.7498 (mptt) REVERT: L 87 TYR cc_start: 0.2197 (m-10) cc_final: 0.1843 (m-10) REVERT: L 91 TYR cc_start: 0.7899 (p90) cc_final: 0.7073 (p90) REVERT: S 47 LEU cc_start: 0.8950 (mt) cc_final: 0.7851 (tp) outliers start: 85 outliers final: 55 residues processed: 379 average time/residue: 0.3388 time to fit residues: 214.5393 Evaluate side-chains 342 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 283 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 300 optimal weight: 20.0000 chunk 228 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 204 optimal weight: 30.0000 chunk 304 optimal weight: 9.9990 chunk 322 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 289 optimal weight: 0.0270 chunk 87 optimal weight: 3.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1058 HIS R 105 GLN ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26854 Z= 0.295 Angle : 0.680 15.300 36611 Z= 0.347 Chirality : 0.049 0.454 4378 Planarity : 0.005 0.061 4666 Dihedral : 8.571 111.277 4591 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.23 % Allowed : 14.14 % Favored : 81.63 % 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: -0.36 (0.14), residues: 3304 helix: 0.09 (0.19), residues: 689 sheet: 0.44 (0.17), residues: 799 loop : -0.64 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 103 HIS 0.006 0.001 HIS A1101 PHE 0.028 0.002 PHE R 100A TYR 0.021 0.002 TYR B 917 ARG 0.007 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 301 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8379 (mm110) REVERT: A 220 PHE cc_start: 0.7711 (t80) cc_final: 0.7288 (t80) REVERT: A 731 MET cc_start: 0.8618 (ptp) cc_final: 0.8306 (ptp) REVERT: A 740 MET cc_start: 0.7991 (mmm) cc_final: 0.7351 (mpp) REVERT: A 894 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8079 (pp) REVERT: B 290 ASP cc_start: 0.7102 (p0) cc_final: 0.6637 (p0) REVERT: B 298 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6968 (mm-30) REVERT: B 409 GLN cc_start: 0.8507 (mt0) cc_final: 0.8200 (tt0) REVERT: B 584 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7558 (pt) REVERT: B 1050 MET cc_start: 0.7174 (ptm) cc_final: 0.6945 (ptm) REVERT: C 223 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6642 (tp) REVERT: C 265 TYR cc_start: 0.6038 (p90) cc_final: 0.5636 (p90) REVERT: C 574 ASP cc_start: 0.6455 (m-30) cc_final: 0.6120 (m-30) REVERT: C 578 ASP cc_start: 0.7270 (p0) cc_final: 0.6895 (p0) REVERT: C 780 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: C 918 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: C 1050 MET cc_start: 0.6975 (ptm) cc_final: 0.6374 (ptt) REVERT: H 59 TYR cc_start: 0.6674 (m-80) cc_final: 0.5909 (m-80) REVERT: H 64 GLN cc_start: 0.8162 (tp40) cc_final: 0.7771 (mm-40) REVERT: H 69 MET cc_start: 0.7816 (mpp) cc_final: 0.7428 (mpp) REVERT: H 79 TYR cc_start: 0.7812 (m-80) cc_final: 0.7531 (m-80) REVERT: R 80 MET cc_start: 0.6022 (ttt) cc_final: 0.4748 (tmm) REVERT: R 96 TYR cc_start: 0.7778 (t80) cc_final: 0.7484 (t80) REVERT: R 101 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: L 39 LYS cc_start: 0.7961 (tptt) cc_final: 0.7541 (mmtp) REVERT: S 54 ARG cc_start: 0.5980 (ptp90) cc_final: 0.5310 (ptp-170) REVERT: S 79 GLU cc_start: 0.7818 (tp30) cc_final: 0.7567 (tp30) outliers start: 117 outliers final: 78 residues processed: 393 average time/residue: 0.3249 time to fit residues: 215.1890 Evaluate side-chains 356 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 270 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 36 TYR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 81 GLU Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 268 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 275 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C1058 HIS ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 26854 Z= 0.339 Angle : 0.699 16.075 36611 Z= 0.355 Chirality : 0.049 0.485 4378 Planarity : 0.005 0.069 4666 Dihedral : 8.112 109.196 4591 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.56 % Allowed : 15.55 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3304 helix: 0.11 (0.20), residues: 681 sheet: 0.31 (0.18), residues: 764 loop : -0.80 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 103 HIS 0.005 0.001 HIS A1048 PHE 0.037 0.002 PHE C 86 TYR 0.031 0.002 TYR B 904 ARG 0.008 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 293 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8606 (ptp) cc_final: 0.8368 (ptp) REVERT: A 740 MET cc_start: 0.7866 (mmm) cc_final: 0.7303 (mpp) REVERT: A 742 ILE cc_start: 0.9522 (mm) cc_final: 0.9224 (tt) REVERT: A 759 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8210 (t80) REVERT: A 894 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8210 (pp) REVERT: B 129 LYS cc_start: 0.7077 (tptm) cc_final: 0.6744 (tptm) REVERT: B 204 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.5621 (m-80) REVERT: B 290 ASP cc_start: 0.6939 (p0) cc_final: 0.6489 (p0) REVERT: B 298 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: B 409 GLN cc_start: 0.8484 (mt0) cc_final: 0.8129 (tt0) REVERT: B 583 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7168 (tm-30) REVERT: B 584 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7429 (pt) REVERT: B 983 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7425 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8651 (tp-100) cc_final: 0.7677 (tp-100) REVERT: C 223 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6587 (tp) REVERT: C 265 TYR cc_start: 0.6549 (p90) cc_final: 0.6261 (p90) REVERT: C 712 ILE cc_start: 0.7921 (tp) cc_final: 0.7572 (tp) REVERT: C 780 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: C 918 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: H 50 TRP cc_start: 0.5145 (t60) cc_final: 0.4606 (t60) REVERT: H 59 TYR cc_start: 0.6567 (m-80) cc_final: 0.5749 (m-80) REVERT: H 64 GLN cc_start: 0.8157 (tp40) cc_final: 0.7794 (mm-40) REVERT: H 69 MET cc_start: 0.7823 (mpp) cc_final: 0.7527 (mpp) REVERT: H 79 TYR cc_start: 0.7866 (m-80) cc_final: 0.7528 (m-80) REVERT: H 103 TRP cc_start: 0.6845 (m100) cc_final: 0.6301 (m100) REVERT: R 80 MET cc_start: 0.6187 (ttt) cc_final: 0.4908 (tmm) REVERT: R 82 ARG cc_start: 0.6975 (ptp-170) cc_final: 0.6632 (mtm180) REVERT: R 89 ILE cc_start: 0.2807 (mm) cc_final: 0.2538 (mm) REVERT: R 91 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.5311 (m-80) REVERT: R 101 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: R 103 TRP cc_start: 0.6002 (m100) cc_final: 0.5559 (m100) REVERT: L 39 LYS cc_start: 0.7990 (tptt) cc_final: 0.7533 (mmtp) REVERT: L 71 PHE cc_start: 0.7805 (m-80) cc_final: 0.7576 (m-10) REVERT: L 91 TYR cc_start: 0.7943 (p90) cc_final: 0.7722 (p90) REVERT: S 54 ARG cc_start: 0.6107 (ptp90) cc_final: 0.5436 (ptp-170) outliers start: 126 outliers final: 95 residues processed: 394 average time/residue: 0.3110 time to fit residues: 205.8743 Evaluate side-chains 372 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 266 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 32 PHE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 108 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 323 optimal weight: 8.9990 chunk 268 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 30.0000 chunk 169 optimal weight: 0.3980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C1058 HIS ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26854 Z= 0.286 Angle : 0.676 15.717 36611 Z= 0.343 Chirality : 0.049 0.463 4378 Planarity : 0.005 0.060 4666 Dihedral : 7.862 109.213 4591 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.77 % Allowed : 17.72 % Favored : 77.51 % 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: -0.61 (0.14), residues: 3304 helix: 0.15 (0.20), residues: 681 sheet: 0.23 (0.18), residues: 763 loop : -0.88 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 103 HIS 0.006 0.001 HIS A1048 PHE 0.022 0.002 PHE B 201 TYR 0.029 0.002 TYR B 904 ARG 0.004 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 289 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7810 (t80) cc_final: 0.7306 (t80) REVERT: A 731 MET cc_start: 0.8571 (ptp) cc_final: 0.8371 (ptp) REVERT: A 740 MET cc_start: 0.7848 (mmm) cc_final: 0.7359 (mpp) REVERT: A 759 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.8143 (t80) REVERT: A 894 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8190 (pp) REVERT: B 129 LYS cc_start: 0.7119 (tptm) cc_final: 0.6919 (tptm) REVERT: B 134 GLN cc_start: 0.7652 (tp40) cc_final: 0.6886 (tp40) REVERT: B 189 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8258 (mm) REVERT: B 204 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.5713 (m-80) REVERT: B 290 ASP cc_start: 0.6732 (p0) cc_final: 0.6358 (p0) REVERT: B 409 GLN cc_start: 0.8468 (mt0) cc_final: 0.7964 (tt0) REVERT: B 421 TYR cc_start: 0.4682 (OUTLIER) cc_final: 0.3677 (m-80) REVERT: B 583 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7098 (tm-30) REVERT: B 584 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7312 (pt) REVERT: B 983 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7397 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8710 (tp-100) cc_final: 0.7800 (tp-100) REVERT: B 1050 MET cc_start: 0.7386 (ptm) cc_final: 0.7172 (ptm) REVERT: C 223 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6683 (tp) REVERT: C 918 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: H 50 TRP cc_start: 0.5178 (t60) cc_final: 0.4628 (t60) REVERT: H 59 TYR cc_start: 0.6633 (m-80) cc_final: 0.5801 (m-80) REVERT: H 64 GLN cc_start: 0.8114 (tp40) cc_final: 0.7824 (mm-40) REVERT: H 69 MET cc_start: 0.7795 (mpp) cc_final: 0.7560 (mpp) REVERT: H 79 TYR cc_start: 0.7863 (m-80) cc_final: 0.7556 (m-80) REVERT: H 103 TRP cc_start: 0.6605 (m100) cc_final: 0.6219 (m100) REVERT: R 80 MET cc_start: 0.6005 (ttt) cc_final: 0.4943 (tmm) REVERT: R 82 ARG cc_start: 0.6974 (ptp-170) cc_final: 0.6736 (mtm180) REVERT: R 100 PHE cc_start: 0.7253 (p90) cc_final: 0.7014 (p90) REVERT: R 101 ASP cc_start: 0.7737 (m-30) cc_final: 0.7294 (m-30) REVERT: R 103 TRP cc_start: 0.6126 (m100) cc_final: 0.5757 (m100) REVERT: L 36 TYR cc_start: 0.8126 (m-10) cc_final: 0.7834 (m-10) REVERT: L 39 LYS cc_start: 0.8022 (tptt) cc_final: 0.7553 (mmtp) REVERT: L 71 PHE cc_start: 0.7746 (m-80) cc_final: 0.7539 (m-10) REVERT: S 54 ARG cc_start: 0.6004 (ptp90) cc_final: 0.5294 (ptp-170) outliers start: 132 outliers final: 99 residues processed: 398 average time/residue: 0.3390 time to fit residues: 225.0220 Evaluate side-chains 368 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 260 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 81 GLU Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 311 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 235 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 272 optimal weight: 0.0030 chunk 180 optimal weight: 0.7980 chunk 321 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 overall best weight: 1.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26854 Z= 0.266 Angle : 0.667 16.517 36611 Z= 0.338 Chirality : 0.049 0.443 4378 Planarity : 0.005 0.063 4666 Dihedral : 7.686 109.165 4591 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.77 % Allowed : 19.09 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3304 helix: 0.17 (0.20), residues: 683 sheet: 0.18 (0.18), residues: 773 loop : -0.84 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 103 HIS 0.006 0.001 HIS A1048 PHE 0.028 0.002 PHE B 168 TYR 0.028 0.002 TYR B 904 ARG 0.004 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 282 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7778 (t80) cc_final: 0.7317 (t80) REVERT: A 731 MET cc_start: 0.8568 (ptp) cc_final: 0.8367 (ptp) REVERT: A 740 MET cc_start: 0.7835 (mmm) cc_final: 0.7335 (mpp) REVERT: A 742 ILE cc_start: 0.9497 (mm) cc_final: 0.9201 (tt) REVERT: A 759 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8162 (t80) REVERT: A 894 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8184 (pp) REVERT: B 134 GLN cc_start: 0.7683 (tp40) cc_final: 0.6917 (tp40) REVERT: B 189 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8205 (mm) REVERT: B 204 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.5714 (m-80) REVERT: B 290 ASP cc_start: 0.6636 (p0) cc_final: 0.6219 (p0) REVERT: B 409 GLN cc_start: 0.8453 (mt0) cc_final: 0.7984 (tt0) REVERT: B 421 TYR cc_start: 0.4755 (OUTLIER) cc_final: 0.3780 (m-80) REVERT: B 583 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7022 (tm-30) REVERT: B 584 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7258 (pt) REVERT: B 983 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7398 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8705 (tp-100) cc_final: 0.7808 (tp-100) REVERT: B 1050 MET cc_start: 0.7411 (ptm) cc_final: 0.7193 (ptm) REVERT: C 223 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6698 (tp) REVERT: C 452 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7476 (mp) REVERT: C 918 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: H 50 TRP cc_start: 0.5187 (t60) cc_final: 0.4872 (t60) REVERT: H 59 TYR cc_start: 0.6556 (m-80) cc_final: 0.5667 (m-80) REVERT: H 64 GLN cc_start: 0.8097 (tp40) cc_final: 0.7801 (mm-40) REVERT: H 69 MET cc_start: 0.7808 (mpp) cc_final: 0.7592 (mpp) REVERT: H 79 TYR cc_start: 0.7879 (m-80) cc_final: 0.7573 (m-80) REVERT: R 80 MET cc_start: 0.5990 (ttt) cc_final: 0.4967 (tmm) REVERT: R 82 ARG cc_start: 0.6934 (ptp-170) cc_final: 0.6623 (mtm180) REVERT: R 91 TYR cc_start: 0.6124 (OUTLIER) cc_final: 0.4983 (m-80) REVERT: R 96 TYR cc_start: 0.7768 (t80) cc_final: 0.7476 (t80) REVERT: R 101 ASP cc_start: 0.7680 (m-30) cc_final: 0.7299 (m-30) REVERT: R 103 TRP cc_start: 0.6038 (m100) cc_final: 0.5798 (m100) REVERT: L 39 LYS cc_start: 0.8058 (tptt) cc_final: 0.7574 (mmtp) outliers start: 132 outliers final: 105 residues processed: 394 average time/residue: 0.3395 time to fit residues: 221.7834 Evaluate side-chains 376 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 260 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 905 ARG Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 199 optimal weight: 10.0000 chunk 128 optimal weight: 0.3980 chunk 192 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 204 optimal weight: 30.0000 chunk 219 optimal weight: 0.2980 chunk 159 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 253 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26854 Z= 0.182 Angle : 0.637 15.510 36611 Z= 0.321 Chirality : 0.048 0.406 4378 Planarity : 0.005 0.065 4666 Dihedral : 7.340 107.842 4591 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.16 % Allowed : 20.25 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3304 helix: 0.26 (0.20), residues: 681 sheet: 0.27 (0.18), residues: 772 loop : -0.74 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP H 103 HIS 0.008 0.001 HIS A1048 PHE 0.026 0.002 PHE B 888 TYR 0.026 0.001 TYR B 904 ARG 0.003 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 291 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASN cc_start: 0.6805 (m110) cc_final: 0.6408 (t0) REVERT: A 220 PHE cc_start: 0.7764 (t80) cc_final: 0.7389 (t80) REVERT: A 731 MET cc_start: 0.8492 (ptp) cc_final: 0.8283 (ptp) REVERT: A 740 MET cc_start: 0.7762 (mmm) cc_final: 0.7262 (mpp) REVERT: A 742 ILE cc_start: 0.9457 (mm) cc_final: 0.9214 (tt) REVERT: A 759 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.8025 (t80) REVERT: A 894 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8105 (pp) REVERT: B 58 PHE cc_start: 0.8110 (m-80) cc_final: 0.7881 (m-80) REVERT: B 129 LYS cc_start: 0.7220 (tptm) cc_final: 0.6917 (tptm) REVERT: B 134 GLN cc_start: 0.7670 (tp40) cc_final: 0.6905 (tp40) REVERT: B 290 ASP cc_start: 0.6443 (p0) cc_final: 0.6060 (p0) REVERT: B 298 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: B 409 GLN cc_start: 0.8446 (mt0) cc_final: 0.8021 (tt0) REVERT: B 421 TYR cc_start: 0.4709 (OUTLIER) cc_final: 0.3735 (m-80) REVERT: B 583 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7022 (tm-30) REVERT: B 584 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7306 (pt) REVERT: B 983 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7496 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8029 (tp40) REVERT: C 223 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6629 (tp) REVERT: C 918 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: H 50 TRP cc_start: 0.5025 (t60) cc_final: 0.4474 (t60) REVERT: H 59 TYR cc_start: 0.6536 (m-80) cc_final: 0.5745 (m-80) REVERT: H 64 GLN cc_start: 0.8035 (tp40) cc_final: 0.7773 (mm-40) REVERT: H 69 MET cc_start: 0.7794 (mpp) cc_final: 0.7552 (mpp) REVERT: H 79 TYR cc_start: 0.7801 (m-80) cc_final: 0.7514 (m-80) REVERT: H 103 TRP cc_start: 0.6379 (m100) cc_final: 0.6060 (m100) REVERT: R 80 MET cc_start: 0.6020 (ttt) cc_final: 0.5026 (tmm) REVERT: R 82 ARG cc_start: 0.6944 (ptp-170) cc_final: 0.6680 (mtm180) REVERT: L 39 LYS cc_start: 0.8055 (tptt) cc_final: 0.7579 (mmtp) REVERT: L 93 SER cc_start: 0.7223 (OUTLIER) cc_final: 0.6967 (t) outliers start: 115 outliers final: 84 residues processed: 379 average time/residue: 0.3308 time to fit residues: 206.7720 Evaluate side-chains 369 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 276 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain L residue 32 PHE Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 292 optimal weight: 6.9990 chunk 308 optimal weight: 0.4980 chunk 281 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 chunk 283 optimal weight: 0.0570 chunk 298 optimal weight: 4.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26854 Z= 0.220 Angle : 0.644 13.592 36611 Z= 0.325 Chirality : 0.048 0.394 4378 Planarity : 0.005 0.063 4666 Dihedral : 7.207 108.376 4590 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.87 % Allowed : 20.93 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3304 helix: 0.30 (0.20), residues: 682 sheet: 0.23 (0.18), residues: 784 loop : -0.73 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 103 HIS 0.007 0.001 HIS A1048 PHE 0.032 0.002 PHE B 888 TYR 0.044 0.001 TYR B 707 ARG 0.019 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 280 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7768 (t80) cc_final: 0.7379 (t80) REVERT: A 731 MET cc_start: 0.8519 (ptp) cc_final: 0.8311 (ptp) REVERT: A 740 MET cc_start: 0.7779 (mmm) cc_final: 0.7300 (mpp) REVERT: A 759 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8080 (t80) REVERT: A 894 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8151 (pp) REVERT: B 129 LYS cc_start: 0.7274 (tptm) cc_final: 0.6960 (tptm) REVERT: B 134 GLN cc_start: 0.7703 (tp40) cc_final: 0.6928 (tp40) REVERT: B 204 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.5689 (m-80) REVERT: B 290 ASP cc_start: 0.6465 (p0) cc_final: 0.5676 (p0) REVERT: B 298 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: B 409 GLN cc_start: 0.8459 (mt0) cc_final: 0.8042 (tt0) REVERT: B 421 TYR cc_start: 0.4745 (OUTLIER) cc_final: 0.3767 (m-80) REVERT: B 583 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 584 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7288 (pt) REVERT: B 983 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7375 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8667 (tp-100) cc_final: 0.7774 (tp-100) REVERT: B 1050 MET cc_start: 0.7591 (ptm) cc_final: 0.7159 (ptm) REVERT: C 223 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6759 (tp) REVERT: C 918 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: H 50 TRP cc_start: 0.5081 (t60) cc_final: 0.4740 (t60) REVERT: H 59 TYR cc_start: 0.6592 (m-80) cc_final: 0.5802 (m-80) REVERT: H 64 GLN cc_start: 0.8051 (tp40) cc_final: 0.7762 (mm-40) REVERT: H 79 TYR cc_start: 0.7766 (m-80) cc_final: 0.7487 (m-80) REVERT: R 48 MET cc_start: 0.6868 (mpp) cc_final: 0.6659 (mpp) REVERT: R 80 MET cc_start: 0.6078 (ttt) cc_final: 0.5120 (tmm) REVERT: R 82 ARG cc_start: 0.6915 (ptp-170) cc_final: 0.6632 (mtm180) REVERT: R 96 TYR cc_start: 0.7843 (t80) cc_final: 0.7571 (t80) REVERT: L 39 LYS cc_start: 0.8063 (tptt) cc_final: 0.7580 (mmtp) REVERT: S 46 LEU cc_start: 0.8947 (tt) cc_final: 0.8704 (mt) REVERT: S 79 GLU cc_start: 0.8098 (tp30) cc_final: 0.7842 (tp30) outliers start: 107 outliers final: 83 residues processed: 367 average time/residue: 0.3370 time to fit residues: 205.4901 Evaluate side-chains 361 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 269 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 196 optimal weight: 0.9990 chunk 317 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 332 optimal weight: 8.9990 chunk 306 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26854 Z= 0.255 Angle : 0.659 14.249 36611 Z= 0.334 Chirality : 0.048 0.394 4378 Planarity : 0.005 0.064 4666 Dihedral : 7.274 109.011 4590 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.65 % Allowed : 21.19 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3304 helix: 0.18 (0.20), residues: 696 sheet: 0.17 (0.18), residues: 784 loop : -0.75 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 103 HIS 0.007 0.001 HIS A1048 PHE 0.031 0.002 PHE B 888 TYR 0.033 0.002 TYR B 707 ARG 0.010 0.001 ARG C 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 277 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7767 (t80) cc_final: 0.7357 (t80) REVERT: A 737 ASP cc_start: 0.7675 (p0) cc_final: 0.7285 (p0) REVERT: A 740 MET cc_start: 0.7796 (mmm) cc_final: 0.7311 (mpp) REVERT: A 742 ILE cc_start: 0.9494 (mm) cc_final: 0.9261 (tt) REVERT: A 759 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.8124 (t80) REVERT: A 894 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8214 (pp) REVERT: B 58 PHE cc_start: 0.8194 (m-80) cc_final: 0.7990 (m-80) REVERT: B 129 LYS cc_start: 0.7276 (tptm) cc_final: 0.6956 (tptm) REVERT: B 134 GLN cc_start: 0.7789 (tp40) cc_final: 0.7032 (tp40) REVERT: B 204 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.5716 (m-80) REVERT: B 290 ASP cc_start: 0.6447 (p0) cc_final: 0.6069 (p0) REVERT: B 409 GLN cc_start: 0.8451 (mt0) cc_final: 0.8040 (tt0) REVERT: B 421 TYR cc_start: 0.4795 (OUTLIER) cc_final: 0.3807 (m-80) REVERT: B 505 TYR cc_start: 0.5972 (t80) cc_final: 0.5742 (t80) REVERT: B 583 GLU cc_start: 0.7465 (tm-30) cc_final: 0.6874 (tm-30) REVERT: B 983 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7387 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8703 (tp-100) cc_final: 0.7784 (tp-100) REVERT: B 1050 MET cc_start: 0.7663 (ptm) cc_final: 0.7290 (ptm) REVERT: C 223 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6826 (tp) REVERT: C 918 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: H 50 TRP cc_start: 0.5123 (t60) cc_final: 0.4808 (t60) REVERT: H 59 TYR cc_start: 0.6458 (m-80) cc_final: 0.5837 (m-80) REVERT: H 64 GLN cc_start: 0.8020 (tp40) cc_final: 0.7764 (mm-40) REVERT: H 79 TYR cc_start: 0.7720 (m-80) cc_final: 0.7466 (m-80) REVERT: H 103 TRP cc_start: 0.6239 (m100) cc_final: 0.5948 (m100) REVERT: R 80 MET cc_start: 0.6115 (ttt) cc_final: 0.5163 (tmm) REVERT: R 82 ARG cc_start: 0.6948 (ptp-170) cc_final: 0.6670 (mtm180) REVERT: R 96 TYR cc_start: 0.7829 (t80) cc_final: 0.7563 (t80) REVERT: L 33 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8149 (mt) REVERT: L 39 LYS cc_start: 0.8088 (tptt) cc_final: 0.7590 (mmtp) REVERT: S 46 LEU cc_start: 0.8956 (tt) cc_final: 0.8711 (mt) outliers start: 101 outliers final: 89 residues processed: 361 average time/residue: 0.3436 time to fit residues: 205.0036 Evaluate side-chains 363 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 266 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 210 optimal weight: 1.9990 chunk 282 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 265 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 272 optimal weight: 0.7980 chunk 33 optimal weight: 0.0470 chunk 48 optimal weight: 3.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C1058 HIS ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.134144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.102126 restraints weight = 67808.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105725 restraints weight = 39806.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.106363 restraints weight = 22192.257| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26854 Z= 0.184 Angle : 0.632 14.493 36611 Z= 0.319 Chirality : 0.047 0.385 4378 Planarity : 0.005 0.064 4666 Dihedral : 7.085 108.064 4590 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.29 % Allowed : 21.87 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3304 helix: 0.23 (0.20), residues: 692 sheet: 0.22 (0.18), residues: 786 loop : -0.69 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 103 HIS 0.008 0.001 HIS A1048 PHE 0.032 0.002 PHE B 888 TYR 0.035 0.001 TYR B 707 ARG 0.011 0.001 ARG B1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5360.39 seconds wall clock time: 98 minutes 55.29 seconds (5935.29 seconds total)