Starting phenix.real_space_refine on Wed Feb 21 21:11:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqy_34039/02_2024/7yqy_34039.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqy_34039/02_2024/7yqy_34039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqy_34039/02_2024/7yqy_34039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqy_34039/02_2024/7yqy_34039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqy_34039/02_2024/7yqy_34039.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqy_34039/02_2024/7yqy_34039.pdb" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.053 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 132 5.16 5 C 20289 2.51 5 N 5271 2.21 5 O 6291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B LEU 441": "CD1" <-> "CD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31983 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8544 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 8544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8544 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 8544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8544 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "J" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 17.78, per 1000 atoms: 0.56 Number of scatterers: 31983 At special positions: 0 Unit cell: (188.32, 160.5, 185.11, 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 132 16.00 O 6291 8.00 N 5271 7.00 C 20289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=11, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " BETA1-6 " NAG M 1 " - " FUC M 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 4 " " NAG U 1 " - " FUC U 4 " NAG-ASN " NAG A1305 " - " ASN A 282 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG A1313 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 74 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 165 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 331 " " NAG B1310 " - " ASN B 603 " " NAG B1311 " - " ASN B 616 " " NAG B1312 " - " ASN B 657 " " NAG B1313 " - " ASN B 709 " " NAG B1314 " - " ASN B1098 " " NAG B1315 " - " ASN B1134 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 74 " " NAG C1305 " - " ASN C 122 " " NAG C1306 " - " ASN C 149 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 657 " " NAG C1313 " - " ASN C 709 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " " NAG C1316 " - " ASN C 331 " " NAG D 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1074 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.44 Conformation dependent library (CDL) restraints added in 6.5 seconds 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7386 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 56 sheets defined 17.4% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 196 through 200 removed outlier: 4.187A pdb=" N GLY A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.572A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.907A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.551A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.531A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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 760 through 782 removed outlier: 3.565A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.657A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 869 through 880 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.820A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.860A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.092A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.795A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.841A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.094A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.563A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.839A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.069A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.748A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.703A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.529A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.933A pdb=" N LYS B 854 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 880 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.507A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.883A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.882A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.953A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1030 removed outlier: 3.584A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.103A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.765A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.595A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.598A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 753 " --> pdb=" O CYS C 749 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 782 removed outlier: 3.997A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.504A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 855 removed outlier: 3.598A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 855' Processing helix chain 'C' and resid 869 through 881 removed outlier: 3.562A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.590A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.985A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.796A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.872A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.660A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.974A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.926A 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: 4.025A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 227 removed outlier: 7.544A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.181A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.422A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.709A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 511 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.983A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.521A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.574A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.574A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.429A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.941A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 101 through 105 removed outlier: 6.293A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.933A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 356 through 357 removed outlier: 3.618A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 538 through 541 removed outlier: 3.836A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.930A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.509A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.131A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 725 through 727 removed outlier: 3.622A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD1, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD4, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.154A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.705A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR C 108 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN C 115 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 205 through 208 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.852A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.594A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 355 through 357 removed outlier: 3.571A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.072A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.736A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.304A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AE7, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AE8, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=AE9, first strand: chain 'F' and resid 45 through 49 removed outlier: 6.636A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 19 through 22 removed outlier: 3.764A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 46 through 49 removed outlier: 6.562A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'H' and resid 45 through 51 removed outlier: 5.684A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'I' and resid 49 through 51 removed outlier: 3.980A pdb=" N GLY I 33 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'J' and resid 49 through 51 removed outlier: 4.505A pdb=" N ASN J 116 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 49 through 51 Processing sheet with id=AG1, first strand: chain 'E' and resid 19 through 22 removed outlier: 3.858A pdb=" N ASP E 71 " --> pdb=" O SER E 68 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 46 through 49 removed outlier: 3.824A pdb=" N ARG E 46 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN E 91 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR E 97 " --> pdb=" O GLN E 91 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.58 Time building geometry restraints manager: 14.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5453 1.32 - 1.45: 9263 1.45 - 1.58: 17834 1.58 - 1.70: 3 1.70 - 1.83: 168 Bond restraints: 32721 Sorted by residual: bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.03e+01 bond pdb=" CG LEU B 441 " pdb=" CD1 LEU B 441 " ideal model delta sigma weight residual 1.521 1.620 -0.099 3.30e-02 9.18e+02 8.99e+00 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.27e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.18e+00 ... (remaining 32716 not shown) Histogram of bond angle deviations from ideal: 97.19 - 104.58: 523 104.58 - 111.97: 16119 111.97 - 119.37: 10671 119.37 - 126.76: 16843 126.76 - 134.15: 379 Bond angle restraints: 44535 Sorted by residual: angle pdb=" C LEU A 984 " pdb=" N ASP A 985 " pdb=" CA ASP A 985 " ideal model delta sigma weight residual 121.61 129.21 -7.60 1.39e+00 5.18e-01 2.99e+01 angle pdb=" CB LEU B 441 " pdb=" CG LEU B 441 " pdb=" CD1 LEU B 441 " ideal model delta sigma weight residual 110.70 126.17 -15.47 3.00e+00 1.11e-01 2.66e+01 angle pdb=" N THR A 333 " pdb=" CA THR A 333 " pdb=" C THR A 333 " ideal model delta sigma weight residual 114.62 108.95 5.67 1.14e+00 7.69e-01 2.47e+01 angle pdb=" CB LEU B 441 " pdb=" CG LEU B 441 " pdb=" CD2 LEU B 441 " ideal model delta sigma weight residual 110.70 123.56 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CA PHE C 329 " pdb=" CB PHE C 329 " pdb=" CG PHE C 329 " ideal model delta sigma weight residual 113.80 117.91 -4.11 1.00e+00 1.00e+00 1.69e+01 ... (remaining 44530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 19127 24.81 - 49.62: 1018 49.62 - 74.43: 145 74.43 - 99.23: 57 99.23 - 124.04: 23 Dihedral angle restraints: 20370 sinusoidal: 8832 harmonic: 11538 Sorted by residual: 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 2.06 -88.06 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -4.02 -81.98 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -23.69 -62.31 1 1.00e+01 1.00e-02 5.14e+01 ... (remaining 20367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.546: 5206 0.546 - 1.092: 1 1.092 - 1.638: 0 1.638 - 2.184: 0 2.184 - 2.730: 1 Chirality restraints: 5208 Sorted by residual: chirality pdb=" CG LEU B 441 " pdb=" CB LEU B 441 " pdb=" CD1 LEU B 441 " pdb=" CD2 LEU B 441 " both_signs ideal model delta sigma weight residual False -2.59 0.14 -2.73 2.00e-01 2.50e+01 1.86e+02 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.77e+00 ... (remaining 5205 not shown) Planarity restraints: 5715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1316 " 0.340 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG C1316 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1316 " 0.122 2.00e-02 2.50e+03 pdb=" N2 NAG C1316 " -0.526 2.00e-02 2.50e+03 pdb=" O7 NAG C1316 " 0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1313 " -0.316 2.00e-02 2.50e+03 2.70e-01 9.14e+02 pdb=" C7 NAG A1313 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A1313 " -0.002 2.00e-02 2.50e+03 pdb=" N2 NAG A1313 " 0.463 2.00e-02 2.50e+03 pdb=" O7 NAG A1313 " -0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.033 2.00e-02 2.50e+03 6.76e-02 5.72e+01 pdb=" C7 NAG B1309 " -0.128 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.059 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.007 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.044 2.00e-02 2.50e+03 ... (remaining 5712 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 252 2.52 - 3.12: 24153 3.12 - 3.71: 46927 3.71 - 4.31: 63868 4.31 - 4.90: 105529 Nonbonded interactions: 240729 Sorted by model distance: nonbonded pdb=" CD2 LEU B 441 " pdb=" O7 NAG B1309 " model vdw 1.925 2.768 nonbonded pdb=" CD1 LEU B 441 " pdb=" O7 NAG B1309 " model vdw 2.051 2.768 nonbonded pdb=" CE1 PHE C 374 " pdb=" O3 NAG U 1 " model vdw 2.135 2.672 nonbonded pdb=" O ALA I 24 " pdb=" OG1 THR I 77 " model vdw 2.160 2.440 nonbonded pdb=" OG SER J 35 " pdb=" OD2 ASP J 99 " model vdw 2.160 2.440 ... (remaining 240724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 25 through 1144 or resid 1301 through 1313)) selection = (chain 'C' and (resid 25 through 1144 or resid 1301 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = (chain 'J' and resid 1 through 123) } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'U' } 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: 2.080 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: 11.180 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 87.440 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 32721 Z= 0.231 Angle : 0.654 15.474 44535 Z= 0.327 Chirality : 0.062 2.730 5208 Planarity : 0.007 0.295 5670 Dihedral : 15.466 124.042 12867 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.98 % Favored : 90.95 % Rotamer: Outliers : 0.18 % Allowed : 0.32 % Favored : 99.50 % 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: -2.25 (0.13), residues: 3954 helix: -1.15 (0.21), residues: 590 sheet: -0.53 (0.19), residues: 754 loop : -1.98 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 47 HIS 0.004 0.001 HIS A 66 PHE 0.036 0.001 PHE C 374 TYR 0.022 0.001 TYR I 100 ARG 0.006 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 243 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7610 (m-80) cc_final: 0.7181 (m-10) REVERT: F 59 ILE cc_start: 0.7027 (mp) cc_final: 0.5902 (mp) REVERT: F 72 PHE cc_start: 0.6192 (m-80) cc_final: 0.5862 (m-80) REVERT: G 46 ARG cc_start: 0.7344 (mpp-170) cc_final: 0.5880 (mmp-170) REVERT: H 80 TYR cc_start: 0.8176 (m-10) cc_final: 0.7897 (m-10) REVERT: I 48 MET cc_start: 0.3151 (ppp) cc_final: 0.2625 (ppp) REVERT: I 70 MET cc_start: 0.2173 (ptt) cc_final: 0.0298 (ptt) REVERT: I 80 TYR cc_start: 0.6414 (m-80) cc_final: 0.5213 (m-80) REVERT: J 57 ASN cc_start: 0.7545 (p0) cc_final: 0.7138 (p0) REVERT: J 70 MET cc_start: 0.5250 (mmp) cc_final: 0.4734 (mpp) outliers start: 6 outliers final: 4 residues processed: 249 average time/residue: 0.4307 time to fit residues: 175.9262 Evaluate side-chains 181 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 3.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 4.9990 chunk 297 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 356 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN F 38 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 32721 Z= 0.311 Angle : 0.674 10.230 44535 Z= 0.336 Chirality : 0.049 0.537 5208 Planarity : 0.005 0.076 5670 Dihedral : 10.379 108.878 5863 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.07 % Favored : 89.91 % Rotamer: Outliers : 0.73 % Allowed : 8.22 % Favored : 91.04 % 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: -2.22 (0.13), residues: 3954 helix: -0.47 (0.21), residues: 632 sheet: -0.75 (0.18), residues: 802 loop : -2.10 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 47 HIS 0.006 0.001 HIS B 505 PHE 0.049 0.002 PHE C 374 TYR 0.025 0.002 TYR A1067 ARG 0.005 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 3.417 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 65 PHE cc_start: 0.7666 (m-80) cc_final: 0.7258 (m-10) REVERT: A 100 ILE cc_start: 0.8466 (mm) cc_final: 0.8221 (mp) REVERT: A 353 TRP cc_start: 0.4871 (OUTLIER) cc_final: 0.2802 (m-90) REVERT: B 1030 SER cc_start: 0.9203 (m) cc_final: 0.8811 (t) REVERT: C 957 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8401 (tm-30) REVERT: C 1107 ARG cc_start: 0.7205 (tpp80) cc_final: 0.6996 (tpp80) REVERT: H 29 PHE cc_start: 0.8652 (t80) cc_final: 0.8448 (t80) REVERT: I 48 MET cc_start: 0.3110 (ppp) cc_final: 0.2674 (ppp) REVERT: I 70 MET cc_start: 0.1195 (ptt) cc_final: 0.0860 (ptt) REVERT: I 80 TYR cc_start: 0.6549 (m-80) cc_final: 0.5470 (m-80) REVERT: I 116 ASN cc_start: 0.5328 (p0) cc_final: 0.5009 (p0) REVERT: J 57 ASN cc_start: 0.7635 (p0) cc_final: 0.7045 (p0) REVERT: J 70 MET cc_start: 0.5340 (mmt) cc_final: 0.4820 (mpp) outliers start: 25 outliers final: 18 residues processed: 213 average time/residue: 0.4491 time to fit residues: 156.4737 Evaluate side-chains 188 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 198 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 297 optimal weight: 0.6980 chunk 243 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 357 optimal weight: 2.9990 chunk 386 optimal weight: 20.0000 chunk 318 optimal weight: 4.9990 chunk 354 optimal weight: 9.9990 chunk 121 optimal weight: 0.0670 chunk 286 optimal weight: 1.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN H 43 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32721 Z= 0.197 Angle : 0.618 10.087 44535 Z= 0.304 Chirality : 0.047 0.498 5208 Planarity : 0.004 0.067 5670 Dihedral : 8.981 103.357 5858 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.16 % Favored : 90.82 % Rotamer: Outliers : 1.32 % Allowed : 11.06 % Favored : 87.62 % 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: -2.11 (0.13), residues: 3954 helix: -0.15 (0.21), residues: 627 sheet: -0.71 (0.18), residues: 808 loop : -2.08 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 47 HIS 0.008 0.001 HIS B 505 PHE 0.030 0.001 PHE C 374 TYR 0.027 0.001 TYR F 50 ARG 0.005 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 195 time to evaluate : 3.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7624 (m-80) cc_final: 0.7229 (m-10) REVERT: A 353 TRP cc_start: 0.5305 (OUTLIER) cc_final: 0.2874 (m-90) REVERT: B 306 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8618 (m-80) REVERT: B 332 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8552 (mm) REVERT: B 1030 SER cc_start: 0.9137 (m) cc_final: 0.8838 (t) REVERT: C 403 ARG cc_start: 0.7640 (tpt170) cc_final: 0.6988 (tpp80) REVERT: C 957 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8292 (tm-30) REVERT: I 80 TYR cc_start: 0.6471 (m-80) cc_final: 0.5394 (m-80) REVERT: I 116 ASN cc_start: 0.4979 (p0) cc_final: 0.4488 (p0) REVERT: J 57 ASN cc_start: 0.7583 (p0) cc_final: 0.6879 (p0) REVERT: J 70 MET cc_start: 0.5270 (mmt) cc_final: 0.4911 (mpp) outliers start: 45 outliers final: 20 residues processed: 228 average time/residue: 0.4204 time to fit residues: 159.2835 Evaluate side-chains 193 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 9.9990 chunk 268 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 170 optimal weight: 0.5980 chunk 240 optimal weight: 0.1980 chunk 358 optimal weight: 8.9990 chunk 379 optimal weight: 30.0000 chunk 187 optimal weight: 0.6980 chunk 340 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN G 39 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32721 Z= 0.164 Angle : 0.589 10.095 44535 Z= 0.289 Chirality : 0.046 0.500 5208 Planarity : 0.004 0.063 5670 Dihedral : 8.025 96.407 5858 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.28 % Favored : 90.69 % Rotamer: Outliers : 1.61 % Allowed : 12.82 % Favored : 85.57 % 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: -1.98 (0.13), residues: 3954 helix: 0.11 (0.21), residues: 633 sheet: -0.62 (0.18), residues: 806 loop : -2.05 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP H 47 HIS 0.007 0.001 HIS B 505 PHE 0.029 0.001 PHE C 374 TYR 0.023 0.001 TYR F 50 ARG 0.005 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 201 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7573 (m-80) cc_final: 0.7211 (m-10) REVERT: A 100 ILE cc_start: 0.8412 (mm) cc_final: 0.8167 (mp) REVERT: A 353 TRP cc_start: 0.5187 (OUTLIER) cc_final: 0.2897 (m-90) REVERT: A 630 THR cc_start: 0.3934 (OUTLIER) cc_final: 0.3705 (t) REVERT: A 855 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.6435 (m-10) REVERT: B 523 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8120 (p) REVERT: C 697 MET cc_start: 0.7302 (mtt) cc_final: 0.7036 (mtt) REVERT: C 957 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8218 (tm-30) REVERT: F 72 PHE cc_start: 0.6639 (m-80) cc_final: 0.6305 (m-80) REVERT: H 122 LEU cc_start: 0.6825 (tt) cc_final: 0.6266 (mt) REVERT: I 80 TYR cc_start: 0.6519 (m-80) cc_final: 0.5400 (m-80) REVERT: I 116 ASN cc_start: 0.4962 (p0) cc_final: 0.4485 (p0) REVERT: J 57 ASN cc_start: 0.7558 (p0) cc_final: 0.6855 (p0) REVERT: J 70 MET cc_start: 0.5369 (mmt) cc_final: 0.5010 (mpp) outliers start: 55 outliers final: 34 residues processed: 241 average time/residue: 0.4777 time to fit residues: 190.0386 Evaluate side-chains 212 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 0.0770 chunk 324 optimal weight: 0.0570 chunk 262 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 0.7980 chunk 340 optimal weight: 30.0000 chunk 95 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 544 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32721 Z= 0.145 Angle : 0.581 10.883 44535 Z= 0.284 Chirality : 0.046 0.493 5208 Planarity : 0.004 0.060 5670 Dihedral : 7.537 89.759 5858 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.75 % Favored : 91.20 % Rotamer: Outliers : 2.14 % Allowed : 13.81 % Favored : 84.05 % 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: -1.88 (0.13), residues: 3954 helix: 0.35 (0.21), residues: 635 sheet: -0.53 (0.18), residues: 827 loop : -2.05 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP I 50 HIS 0.007 0.001 HIS C 505 PHE 0.036 0.001 PHE C 374 TYR 0.018 0.001 TYR F 50 ARG 0.009 0.000 ARG I 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 196 time to evaluate : 3.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7598 (m-80) cc_final: 0.7260 (m-10) REVERT: A 100 ILE cc_start: 0.8346 (mm) cc_final: 0.8085 (mp) REVERT: A 630 THR cc_start: 0.3876 (OUTLIER) cc_final: 0.3651 (t) REVERT: A 855 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.6417 (m-10) REVERT: B 523 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8170 (p) REVERT: C 957 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8177 (tm-30) REVERT: F 72 PHE cc_start: 0.6764 (m-80) cc_final: 0.6464 (m-80) REVERT: G 46 ARG cc_start: 0.7020 (mpp-170) cc_final: 0.5961 (mmp-170) REVERT: H 29 PHE cc_start: 0.8594 (t80) cc_final: 0.8268 (t80) REVERT: H 55 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8159 (p0) REVERT: H 80 TYR cc_start: 0.7963 (m-10) cc_final: 0.7676 (m-10) REVERT: H 102 ARG cc_start: 0.7541 (tpp-160) cc_final: 0.7184 (tpp-160) REVERT: I 48 MET cc_start: 0.2868 (ppp) cc_final: 0.2366 (pmm) REVERT: I 80 TYR cc_start: 0.6539 (m-80) cc_final: 0.5468 (m-80) REVERT: I 116 ASN cc_start: 0.4803 (p0) cc_final: 0.4547 (p0) REVERT: J 57 ASN cc_start: 0.7481 (p0) cc_final: 0.6801 (p0) outliers start: 73 outliers final: 35 residues processed: 252 average time/residue: 0.4138 time to fit residues: 172.3862 Evaluate side-chains 209 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 170 time to evaluate : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 9.9990 chunk 342 optimal weight: 40.0000 chunk 75 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 380 optimal weight: 20.0000 chunk 315 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 199 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32721 Z= 0.220 Angle : 0.598 9.685 44535 Z= 0.294 Chirality : 0.046 0.521 5208 Planarity : 0.004 0.057 5670 Dihedral : 7.432 78.487 5858 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.38 % Favored : 90.57 % Rotamer: Outliers : 2.19 % Allowed : 14.54 % Favored : 83.26 % 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: -1.93 (0.13), residues: 3954 helix: 0.27 (0.21), residues: 642 sheet: -0.60 (0.18), residues: 847 loop : -2.07 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP H 47 HIS 0.005 0.001 HIS B 505 PHE 0.037 0.001 PHE B 643 TYR 0.018 0.001 TYR A1067 ARG 0.005 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 181 time to evaluate : 3.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7598 (m-80) cc_final: 0.7266 (m-10) REVERT: A 100 ILE cc_start: 0.8405 (mm) cc_final: 0.8171 (mp) REVERT: A 630 THR cc_start: 0.3869 (OUTLIER) cc_final: 0.3643 (t) REVERT: A 855 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.6442 (m-10) REVERT: B 523 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8092 (p) REVERT: C 957 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8232 (tm-30) REVERT: H 29 PHE cc_start: 0.8659 (t80) cc_final: 0.8412 (t80) REVERT: H 102 ARG cc_start: 0.7602 (tpp-160) cc_final: 0.7270 (tpp-160) REVERT: I 48 MET cc_start: 0.2710 (ppp) cc_final: 0.2115 (pmm) REVERT: I 80 TYR cc_start: 0.6547 (m-80) cc_final: 0.5460 (m-80) REVERT: I 116 ASN cc_start: 0.4857 (p0) cc_final: 0.4499 (p0) REVERT: J 57 ASN cc_start: 0.7307 (p0) cc_final: 0.6597 (p0) outliers start: 75 outliers final: 50 residues processed: 239 average time/residue: 0.4268 time to fit residues: 168.6916 Evaluate side-chains 228 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 175 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain E residue 27 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 0.4980 chunk 42 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 215 optimal weight: 0.0670 chunk 320 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 378 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32721 Z= 0.183 Angle : 0.589 11.741 44535 Z= 0.287 Chirality : 0.046 0.512 5208 Planarity : 0.004 0.058 5670 Dihedral : 7.223 67.732 5858 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.13 % Favored : 90.82 % Rotamer: Outliers : 2.25 % Allowed : 14.98 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 3954 helix: 0.37 (0.21), residues: 638 sheet: -0.50 (0.18), residues: 810 loop : -2.05 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP H 47 HIS 0.005 0.000 HIS B 505 PHE 0.030 0.001 PHE C 374 TYR 0.027 0.001 TYR B 508 ARG 0.007 0.000 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 180 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7630 (m-80) cc_final: 0.7316 (m-10) REVERT: A 630 THR cc_start: 0.3833 (OUTLIER) cc_final: 0.3603 (t) REVERT: A 855 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.6434 (m-10) REVERT: B 523 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8123 (p) REVERT: B 906 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.7928 (t80) REVERT: B 957 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7534 (tm-30) REVERT: C 957 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8202 (tm-30) REVERT: G 46 ARG cc_start: 0.6421 (mtm-85) cc_final: 0.5527 (mmp-170) REVERT: H 29 PHE cc_start: 0.8711 (t80) cc_final: 0.8495 (t80) REVERT: H 55 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8126 (p0) REVERT: H 102 ARG cc_start: 0.7583 (tpp-160) cc_final: 0.7279 (tpp-160) REVERT: I 3 GLN cc_start: 0.6434 (mm110) cc_final: 0.4275 (tt0) REVERT: I 48 MET cc_start: 0.3002 (ppp) cc_final: 0.2586 (pmm) REVERT: I 70 MET cc_start: 0.1278 (ptt) cc_final: 0.0673 (ptt) REVERT: I 80 TYR cc_start: 0.6470 (m-80) cc_final: 0.5431 (m-80) REVERT: J 57 ASN cc_start: 0.7318 (p0) cc_final: 0.6558 (p0) REVERT: J 70 MET cc_start: 0.5327 (mmp) cc_final: 0.4921 (mpp) outliers start: 77 outliers final: 51 residues processed: 243 average time/residue: 0.4153 time to fit residues: 167.8156 Evaluate side-chains 228 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 172 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 68 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 240 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 32721 Z= 0.378 Angle : 0.696 9.704 44535 Z= 0.345 Chirality : 0.049 0.566 5208 Planarity : 0.004 0.060 5670 Dihedral : 7.507 59.981 5858 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.31 % Favored : 88.67 % Rotamer: Outliers : 2.37 % Allowed : 15.77 % Favored : 81.86 % 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: -2.12 (0.13), residues: 3954 helix: -0.04 (0.21), residues: 644 sheet: -0.74 (0.19), residues: 805 loop : -2.13 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP H 47 HIS 0.004 0.001 HIS C1058 PHE 0.031 0.002 PHE C 374 TYR 0.025 0.002 TYR C 501 ARG 0.006 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 176 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7771 (m-80) cc_final: 0.7427 (m-10) REVERT: A 100 ILE cc_start: 0.8424 (mm) cc_final: 0.8188 (mp) REVERT: A 630 THR cc_start: 0.4220 (OUTLIER) cc_final: 0.3994 (t) REVERT: A 855 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.6625 (m-10) REVERT: B 523 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8139 (p) REVERT: B 878 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8825 (tt) REVERT: B 906 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.7928 (t80) REVERT: C 957 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8246 (tm-30) REVERT: H 55 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8106 (p0) REVERT: I 48 MET cc_start: 0.3062 (ppp) cc_final: 0.2385 (pmm) REVERT: I 80 TYR cc_start: 0.6544 (m-80) cc_final: 0.5598 (m-80) REVERT: J 57 ASN cc_start: 0.7388 (p0) cc_final: 0.6592 (p0) REVERT: J 70 MET cc_start: 0.5409 (mmp) cc_final: 0.4975 (mpp) outliers start: 81 outliers final: 54 residues processed: 243 average time/residue: 0.4224 time to fit residues: 171.5410 Evaluate side-chains 231 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 171 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 81 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 40.0000 chunk 362 optimal weight: 7.9990 chunk 331 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 chunk 153 optimal weight: 0.0980 chunk 277 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 318 optimal weight: 0.9980 chunk 333 optimal weight: 30.0000 chunk 351 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32721 Z= 0.269 Angle : 0.641 12.261 44535 Z= 0.316 Chirality : 0.047 0.535 5208 Planarity : 0.004 0.060 5670 Dihedral : 7.312 59.616 5858 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.04 % Favored : 89.91 % Rotamer: Outliers : 2.22 % Allowed : 16.15 % Favored : 81.62 % 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: -2.08 (0.13), residues: 3954 helix: 0.06 (0.21), residues: 640 sheet: -0.71 (0.19), residues: 785 loop : -2.12 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 50 HIS 0.003 0.001 HIS C 505 PHE 0.033 0.002 PHE C 374 TYR 0.024 0.001 TYR F 50 ARG 0.008 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 174 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7689 (m-80) cc_final: 0.7382 (m-10) REVERT: A 100 ILE cc_start: 0.8402 (mm) cc_final: 0.8156 (mp) REVERT: A 146 HIS cc_start: 0.7120 (m-70) cc_final: 0.6808 (m-70) REVERT: A 855 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.6530 (m-10) REVERT: B 523 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8154 (p) REVERT: B 878 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8787 (tt) REVERT: B 906 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.7927 (t80) REVERT: C 237 ARG cc_start: 0.7028 (ptt-90) cc_final: 0.6652 (ptt-90) REVERT: C 957 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8206 (tm-30) REVERT: H 29 PHE cc_start: 0.8599 (t80) cc_final: 0.8381 (t80) REVERT: H 55 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8312 (p0) REVERT: H 102 ARG cc_start: 0.7638 (tpp-160) cc_final: 0.6988 (tpm170) REVERT: I 3 GLN cc_start: 0.6485 (mm110) cc_final: 0.4321 (tt0) REVERT: I 48 MET cc_start: 0.3091 (OUTLIER) cc_final: 0.2742 (pmm) REVERT: I 80 TYR cc_start: 0.6488 (m-80) cc_final: 0.5465 (m-80) REVERT: J 70 MET cc_start: 0.5377 (mmp) cc_final: 0.4942 (mpp) outliers start: 76 outliers final: 57 residues processed: 236 average time/residue: 0.4197 time to fit residues: 164.2625 Evaluate side-chains 234 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 171 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 48 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 3.9990 chunk 373 optimal weight: 0.0270 chunk 227 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 chunk 391 optimal weight: 20.0000 chunk 360 optimal weight: 40.0000 chunk 311 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 240 optimal weight: 0.0030 chunk 191 optimal weight: 3.9990 overall best weight: 1.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32721 Z= 0.193 Angle : 0.625 12.813 44535 Z= 0.305 Chirality : 0.047 0.527 5208 Planarity : 0.004 0.063 5670 Dihedral : 7.409 59.823 5858 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.76 % Favored : 90.19 % Rotamer: Outliers : 1.87 % Allowed : 16.65 % Favored : 81.47 % 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: -2.02 (0.13), residues: 3954 helix: 0.22 (0.21), residues: 636 sheet: -0.70 (0.19), residues: 797 loop : -2.10 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 47 HIS 0.003 0.000 HIS C 505 PHE 0.035 0.001 PHE C 374 TYR 0.034 0.001 TYR C 501 ARG 0.013 0.000 ARG C 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 178 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7659 (m-80) cc_final: 0.7372 (m-10) REVERT: A 100 ILE cc_start: 0.8416 (mm) cc_final: 0.8187 (mp) REVERT: A 146 HIS cc_start: 0.7110 (m-70) cc_final: 0.6805 (m-70) REVERT: A 855 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.6548 (m-10) REVERT: B 523 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8172 (p) REVERT: B 878 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8750 (tt) REVERT: B 906 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.7925 (t80) REVERT: B 957 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7561 (tm-30) REVERT: C 237 ARG cc_start: 0.7085 (ptt-90) cc_final: 0.6705 (ptt-90) REVERT: C 957 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8143 (tm-30) REVERT: H 55 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8361 (p0) REVERT: H 102 ARG cc_start: 0.7634 (tpp-160) cc_final: 0.7262 (tpp-160) REVERT: I 3 GLN cc_start: 0.6569 (mm110) cc_final: 0.4392 (tt0) REVERT: I 48 MET cc_start: 0.3149 (OUTLIER) cc_final: 0.2436 (pmm) REVERT: I 80 TYR cc_start: 0.6452 (m-80) cc_final: 0.5467 (m-80) REVERT: J 70 MET cc_start: 0.5369 (mmt) cc_final: 0.4937 (mpp) outliers start: 64 outliers final: 52 residues processed: 229 average time/residue: 0.4132 time to fit residues: 156.9522 Evaluate side-chains 230 residues out of total 3441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 172 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 48 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 247 optimal weight: 2.9990 chunk 332 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 130 optimal weight: 0.0870 chunk 320 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 chunk 57 optimal weight: 5.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 185 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.140959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.094024 restraints weight = 85921.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093457 restraints weight = 59824.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093200 restraints weight = 48772.084| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32721 Z= 0.165 Angle : 0.602 13.358 44535 Z= 0.294 Chirality : 0.046 0.507 5208 Planarity : 0.004 0.063 5670 Dihedral : 6.838 58.168 5858 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.36 % Favored : 90.59 % Rotamer: Outliers : 1.87 % Allowed : 16.74 % Favored : 81.39 % 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: -1.91 (0.13), residues: 3954 helix: 0.48 (0.22), residues: 632 sheet: -0.60 (0.18), residues: 826 loop : -2.09 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP H 47 HIS 0.003 0.000 HIS C 505 PHE 0.034 0.001 PHE C 374 TYR 0.030 0.001 TYR C 501 ARG 0.008 0.000 ARG C 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5545.38 seconds wall clock time: 103 minutes 18.27 seconds (6198.27 seconds total)