Starting phenix.real_space_refine on Wed Feb 21 07:27:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hec_34687/02_2024/8hec_34687.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hec_34687/02_2024/8hec_34687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hec_34687/02_2024/8hec_34687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hec_34687/02_2024/8hec_34687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hec_34687/02_2024/8hec_34687.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hec_34687/02_2024/8hec_34687.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 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 141 5.16 5 C 18999 2.51 5 N 4894 2.21 5 O 5891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "F TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29925 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8000 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 51, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7992 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 51, 'TRANS': 976} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7985 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 51, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "G" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "H" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.30, per 1000 atoms: 0.51 Number of scatterers: 29925 At special positions: 0 Unit cell: (146.78, 156.62, 223.86, 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 141 16.00 O 5891 8.00 N 4894 7.00 C 18999 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 D 22 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 87 " distance=2.04 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 11.38 Conformation dependent library (CDL) restraints added in 5.2 seconds 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6998 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 66 sheets defined 21.1% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.607A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.179A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.973A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.556A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 removed outlier: 3.642A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.776A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.799A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.178A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.819A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.326A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.647A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.551A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.045A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.659A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.685A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.117A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.090A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.292A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.617A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.164A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.027A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.785A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.705A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.262A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.605A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.189A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.725A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.538A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.528A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.197A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.811A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.653A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.531A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.277A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.799A pdb=" N ALA D 82 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.860A pdb=" N ALA F 82 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 removed outlier: 3.505A pdb=" N ARG G 30 " --> pdb=" O SER G 27 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.678A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.979A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.608A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 142 removed outlier: 10.776A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.451A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.678A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.890A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.882A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.093A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.859A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.641A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.736A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.834A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 132 through 134 removed outlier: 3.689A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.631A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.260A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.095A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.902A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.979A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.476A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.871A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.937A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 132 through 135 removed outlier: 4.180A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.947A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.269A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.691A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 540 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 659 removed outlier: 6.077A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.612A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 719 removed outlier: 6.458A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 717 through 719 removed outlier: 6.458A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.428A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.836A pdb=" N HIS D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.682A pdb=" N VAL D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 12 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 110 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 47 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.682A pdb=" N VAL D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 12 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 110 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY D 89 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA D 100 " --> pdb=" O GLY D 89 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.866A pdb=" N LEU E 17 " --> pdb=" O MET E 79 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.938A pdb=" N MET E 33 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TRP E 35 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.869A pdb=" N PHE E 106 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.719A pdb=" N HIS F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.830A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.830A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY F 89 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 100 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AG5, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.596A pdb=" N LEU G 17 " --> pdb=" O MET G 79 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 10 through 11 removed outlier: 7.157A pdb=" N MET G 33 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.724A pdb=" N HIS H 69 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.650A pdb=" N VAL H 108 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 12 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS H 110 " --> pdb=" O ALA H 12 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.650A pdb=" N VAL H 108 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 12 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS H 110 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY H 89 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA H 100 " --> pdb=" O GLY H 89 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AH2, first strand: chain 'I' and resid 2 through 6 Processing sheet with id=AH3, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.643A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3042 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.37 Time building geometry restraints manager: 12.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9523 1.35 - 1.47: 7843 1.47 - 1.59: 13039 1.59 - 1.71: 0 1.71 - 1.83: 177 Bond restraints: 30582 Sorted by residual: bond pdb=" N GLY D 96 " pdb=" CA GLY D 96 " ideal model delta sigma weight residual 1.451 1.479 -0.029 8.60e-03 1.35e+04 1.10e+01 bond pdb=" N ASP D 97 " pdb=" CA ASP D 97 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.55e+00 bond pdb=" N SER F 94 " pdb=" CA SER F 94 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.16e+00 bond pdb=" N SER H 95 " pdb=" CA SER H 95 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.72e+00 bond pdb=" N SER F 95 " pdb=" CA SER F 95 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.23e-02 6.61e+03 5.52e+00 ... (remaining 30577 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.17: 539 105.17 - 112.39: 15922 112.39 - 119.62: 9514 119.62 - 126.85: 15337 126.85 - 134.07: 330 Bond angle restraints: 41642 Sorted by residual: angle pdb=" N ILE D 28 " pdb=" CA ILE D 28 " pdb=" C ILE D 28 " ideal model delta sigma weight residual 113.53 109.12 4.41 9.80e-01 1.04e+00 2.02e+01 angle pdb=" C SER F 92 " pdb=" CA SER F 92 " pdb=" CB SER F 92 " ideal model delta sigma weight residual 116.54 111.70 4.84 1.15e+00 7.56e-01 1.77e+01 angle pdb=" CA GLY D 96 " pdb=" C GLY D 96 " pdb=" O GLY D 96 " ideal model delta sigma weight residual 121.78 118.12 3.66 9.10e-01 1.21e+00 1.61e+01 angle pdb=" C SER H 92 " pdb=" CA SER H 92 " pdb=" CB SER H 92 " ideal model delta sigma weight residual 116.63 112.04 4.59 1.16e+00 7.43e-01 1.56e+01 angle pdb=" C SER D 92 " pdb=" N CYS D 93 " pdb=" CA CYS D 93 " ideal model delta sigma weight residual 121.54 114.03 7.51 1.91e+00 2.74e-01 1.55e+01 ... (remaining 41637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 16631 17.64 - 35.27: 1735 35.27 - 52.91: 410 52.91 - 70.54: 70 70.54 - 88.18: 34 Dihedral angle restraints: 18880 sinusoidal: 7985 harmonic: 10895 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 175.26 -82.26 1 1.00e+01 1.00e-02 8.31e+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 -5.10 -80.90 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -163.45 77.45 1 1.00e+01 1.00e-02 7.51e+01 ... (remaining 18877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 4923 0.169 - 0.338: 9 0.338 - 0.506: 1 0.506 - 0.675: 0 0.675 - 0.844: 1 Chirality restraints: 4934 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.78e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 4931 not shown) Planarity restraints: 5338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 81 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C ASN C 81 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN C 81 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO C 82 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 92 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C SER D 92 " -0.041 2.00e-02 2.50e+03 pdb=" O SER D 92 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS D 93 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 614 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ASP C 614 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP C 614 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL C 615 " 0.012 2.00e-02 2.50e+03 ... (remaining 5335 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2730 2.74 - 3.28: 28994 3.28 - 3.82: 47777 3.82 - 4.36: 53254 4.36 - 4.90: 95296 Nonbonded interactions: 228051 Sorted by model distance: nonbonded pdb=" N GLU B 583 " pdb=" OE1 GLU B 583 " model vdw 2.203 2.520 nonbonded pdb=" OD1 ASP A 663 " pdb=" OG SER A 673 " model vdw 2.211 2.440 nonbonded pdb=" O PHE A 329 " pdb=" NE2 GLN A 580 " model vdw 2.224 2.520 nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.226 2.440 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.227 2.440 ... (remaining 228046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 518 or (resid 519 through 520 and (name N or na \ me CA or name C or name O or name CB )) or resid 521 through 527 or (resid 528 a \ nd (name N or name CA or name C or name O or name CB )) or resid 529 through 555 \ or (resid 556 and (name N or name CA or name C or name O or name CB )) or resid \ 557 through 827 or resid 854 through 1147 or resid 1301 through 1309)) selection = (chain 'B' and (resid 15 through 527 or (resid 528 and (name N or name CA or nam \ e C or name O or name CB )) or resid 529 through 555 or (resid 556 and (name N o \ r name CA or name C or name O or name CB )) or resid 557 or (resid 558 through 5 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 560 through \ 785 or (resid 786 and (name N or name CA or name C or name O or name CB )) or r \ esid 787 through 827 or (resid 854 and (name N or name CA or name C or name O or \ name CB )) or resid 855 through 903 or (resid 904 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 905 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 15 through 557 or (resid 558 through 559 and (name N or na \ me CA or name C or name O or name CB )) or resid 560 through 827 or resid 854 th \ rough 903 or (resid 904 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid \ 905 through 1147 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 10.690 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: 30.310 Check model and map are aligned: 0.450 Set scattering table: 0.260 Process input model: 78.370 Find NCS groups from input model: 2.260 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 0.045 30582 Z= 0.241 Angle : 0.598 10.132 41642 Z= 0.309 Chirality : 0.047 0.844 4934 Planarity : 0.003 0.048 5294 Dihedral : 14.799 88.180 11753 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.75 % Favored : 95.15 % Rotamer: Outliers : 0.12 % Allowed : 18.48 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3709 helix: 2.02 (0.22), residues: 643 sheet: 0.51 (0.17), residues: 963 loop : -1.30 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 353 HIS 0.003 0.001 HIS E 55 PHE 0.016 0.001 PHE D 91 TYR 0.015 0.001 TYR B1067 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 3.636 Fit side-chains REVERT: E 33 MET cc_start: 0.6239 (tpt) cc_final: 0.6013 (tpt) REVERT: H 74 MET cc_start: 0.0934 (pmm) cc_final: -0.1723 (ttp) outliers start: 4 outliers final: 2 residues processed: 142 average time/residue: 0.4179 time to fit residues: 100.4869 Evaluate side-chains 116 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 6.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 40.0000 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 292 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 338 optimal weight: 0.0470 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30582 Z= 0.166 Angle : 0.513 13.031 41642 Z= 0.263 Chirality : 0.044 0.495 4934 Planarity : 0.003 0.047 5294 Dihedral : 6.735 58.668 5315 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.58 % Rotamer: Outliers : 2.77 % Allowed : 18.01 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3709 helix: 2.29 (0.22), residues: 648 sheet: 0.52 (0.17), residues: 953 loop : -1.19 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.003 0.001 HIS B1088 PHE 0.016 0.001 PHE B 157 TYR 0.016 0.001 TYR A1067 ARG 0.005 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 135 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4959 (tmm) cc_final: 0.4379 (tmm) REVERT: B 727 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9192 (pp) REVERT: G 33 MET cc_start: 0.1301 (mmm) cc_final: 0.0405 (mmt) outliers start: 89 outliers final: 49 residues processed: 211 average time/residue: 0.3728 time to fit residues: 139.2284 Evaluate side-chains 174 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 124 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 69 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 339 optimal weight: 0.8980 chunk 366 optimal weight: 30.0000 chunk 302 optimal weight: 3.9990 chunk 336 optimal weight: 40.0000 chunk 115 optimal weight: 10.0000 chunk 272 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30582 Z= 0.260 Angle : 0.529 9.655 41642 Z= 0.270 Chirality : 0.044 0.489 4934 Planarity : 0.003 0.044 5294 Dihedral : 6.203 59.352 5312 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.69 % Rotamer: Outliers : 3.40 % Allowed : 18.39 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3709 helix: 2.13 (0.21), residues: 666 sheet: 0.48 (0.17), residues: 964 loop : -1.26 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.002 0.001 HIS E 55 PHE 0.017 0.001 PHE E 106 TYR 0.017 0.001 TYR C1067 ARG 0.005 0.000 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 128 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4953 (tmm) cc_final: 0.4619 (tmm) REVERT: A 733 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8038 (ttpt) REVERT: B 726 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9036 (tp) REVERT: B 727 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9331 (pp) REVERT: I 33 MET cc_start: 0.3606 (mmp) cc_final: 0.2431 (ppp) outliers start: 109 outliers final: 74 residues processed: 224 average time/residue: 0.3426 time to fit residues: 134.4335 Evaluate side-chains 194 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 117 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 69 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 30.0000 chunk 255 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 340 optimal weight: 9.9990 chunk 360 optimal weight: 30.0000 chunk 177 optimal weight: 0.6980 chunk 322 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30582 Z= 0.290 Angle : 0.540 10.459 41642 Z= 0.276 Chirality : 0.044 0.485 4934 Planarity : 0.003 0.044 5294 Dihedral : 5.872 58.670 5312 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.53 % Favored : 94.45 % Rotamer: Outliers : 4.21 % Allowed : 19.01 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3709 helix: 2.05 (0.21), residues: 667 sheet: 0.47 (0.17), residues: 988 loop : -1.32 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.003 0.001 HIS B1088 PHE 0.021 0.001 PHE C 855 TYR 0.016 0.001 TYR C1067 ARG 0.006 0.000 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 121 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8138 (ttpt) REVERT: B 726 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9040 (tp) REVERT: B 727 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9353 (pp) REVERT: I 33 MET cc_start: 0.3523 (mmp) cc_final: 0.2532 (ppp) outliers start: 135 outliers final: 99 residues processed: 244 average time/residue: 0.3573 time to fit residues: 153.4196 Evaluate side-chains 219 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 117 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 69 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 268 optimal weight: 0.4980 chunk 148 optimal weight: 0.9990 chunk 307 optimal weight: 7.9990 chunk 249 optimal weight: 50.0000 chunk 0 optimal weight: 30.0000 chunk 184 optimal weight: 4.9990 chunk 323 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30582 Z= 0.270 Angle : 0.531 10.474 41642 Z= 0.271 Chirality : 0.044 0.473 4934 Planarity : 0.003 0.044 5294 Dihedral : 5.638 57.894 5312 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 4.52 % Allowed : 19.38 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3709 helix: 2.06 (0.21), residues: 667 sheet: 0.39 (0.17), residues: 974 loop : -1.30 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.003 0.001 HIS B1088 PHE 0.016 0.001 PHE B 157 TYR 0.016 0.001 TYR C1067 ARG 0.006 0.000 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 122 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4886 (tmm) cc_final: 0.4236 (tmm) REVERT: A 271 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8284 (mp10) REVERT: A 733 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8142 (ttpt) REVERT: A 1125 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8176 (p0) REVERT: B 726 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9037 (tp) REVERT: B 727 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9352 (pp) REVERT: G 33 MET cc_start: 0.1186 (OUTLIER) cc_final: 0.0719 (mmm) REVERT: H 74 MET cc_start: 0.1096 (OUTLIER) cc_final: 0.0782 (pmm) REVERT: I 33 MET cc_start: 0.3384 (mmp) cc_final: 0.2568 (ppp) outliers start: 145 outliers final: 107 residues processed: 255 average time/residue: 0.3466 time to fit residues: 155.4135 Evaluate side-chains 228 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 114 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 33 MET Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 71 optimal weight: 0.0470 chunk 211 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 360 optimal weight: 40.0000 chunk 299 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30582 Z= 0.215 Angle : 0.511 9.893 41642 Z= 0.260 Chirality : 0.044 0.463 4934 Planarity : 0.003 0.044 5294 Dihedral : 5.346 58.053 5312 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 4.14 % Allowed : 20.13 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3709 helix: 2.17 (0.21), residues: 660 sheet: 0.44 (0.17), residues: 978 loop : -1.26 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.003 0.000 HIS B1048 PHE 0.015 0.001 PHE B 157 TYR 0.015 0.001 TYR C1067 ARG 0.004 0.000 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 127 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4986 (tmm) cc_final: 0.4408 (tmm) REVERT: A 271 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8275 (mp10) REVERT: A 733 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8110 (ttpt) REVERT: A 1029 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.7861 (ttp) REVERT: A 1125 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8139 (p0) REVERT: B 726 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.9000 (tp) REVERT: B 727 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9327 (pp) REVERT: C 614 ASP cc_start: 0.7828 (t0) cc_final: 0.7443 (t0) REVERT: G 33 MET cc_start: 0.1152 (OUTLIER) cc_final: 0.0736 (mmm) REVERT: H 74 MET cc_start: 0.1048 (OUTLIER) cc_final: 0.0426 (pmm) REVERT: I 33 MET cc_start: 0.3304 (mmp) cc_final: 0.2602 (ppp) outliers start: 133 outliers final: 109 residues processed: 245 average time/residue: 0.3463 time to fit residues: 147.6672 Evaluate side-chains 237 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 120 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 33 MET Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 205 optimal weight: 20.0000 chunk 263 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 303 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 359 optimal weight: 20.0000 chunk 224 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30582 Z= 0.299 Angle : 0.548 10.943 41642 Z= 0.278 Chirality : 0.044 0.495 4934 Planarity : 0.003 0.043 5294 Dihedral : 5.356 57.961 5312 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.26 % Rotamer: Outliers : 4.89 % Allowed : 19.79 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3709 helix: 2.07 (0.21), residues: 665 sheet: 0.39 (0.17), residues: 988 loop : -1.33 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.003 0.001 HIS B1083 PHE 0.015 0.001 PHE C 888 TYR 0.016 0.001 TYR C1067 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 117 time to evaluate : 3.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8427 (t70) cc_final: 0.8205 (t70) REVERT: A 153 MET cc_start: 0.4982 (tmm) cc_final: 0.4463 (tmm) REVERT: A 271 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8312 (mp10) REVERT: A 733 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8122 (ttpt) REVERT: A 1029 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.7933 (ttp) REVERT: B 726 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9002 (tp) REVERT: B 727 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9369 (pp) REVERT: C 614 ASP cc_start: 0.7873 (t0) cc_final: 0.7386 (t0) REVERT: G 33 MET cc_start: 0.1212 (OUTLIER) cc_final: 0.0764 (mmm) REVERT: H 74 MET cc_start: 0.0653 (OUTLIER) cc_final: 0.0391 (pmm) REVERT: I 33 MET cc_start: 0.3452 (mmp) cc_final: 0.2697 (ppp) outliers start: 157 outliers final: 118 residues processed: 259 average time/residue: 0.3672 time to fit residues: 164.9170 Evaluate side-chains 237 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 112 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 33 MET Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 214 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 69 optimal weight: 0.0770 chunk 228 optimal weight: 0.8980 chunk 244 optimal weight: 30.0000 chunk 177 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30582 Z= 0.163 Angle : 0.503 9.587 41642 Z= 0.256 Chirality : 0.044 0.591 4934 Planarity : 0.003 0.043 5294 Dihedral : 5.037 56.786 5312 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.61 % Allowed : 21.10 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3709 helix: 2.22 (0.22), residues: 666 sheet: 0.45 (0.17), residues: 987 loop : -1.22 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 353 HIS 0.003 0.000 HIS B1048 PHE 0.015 0.001 PHE A 347 TYR 0.015 0.001 TYR A1067 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 124 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8415 (t70) cc_final: 0.8184 (t70) REVERT: A 153 MET cc_start: 0.5029 (tmm) cc_final: 0.4539 (tmm) REVERT: A 271 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: A 733 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8067 (ttpt) REVERT: A 1029 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.7829 (ttp) REVERT: B 726 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8999 (tp) REVERT: B 727 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9309 (pp) REVERT: B 988 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8210 (tm-30) REVERT: C 614 ASP cc_start: 0.7796 (t0) cc_final: 0.7333 (t0) REVERT: C 948 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8830 (mp) REVERT: G 33 MET cc_start: 0.1207 (OUTLIER) cc_final: 0.0858 (mmm) REVERT: H 74 MET cc_start: 0.0600 (OUTLIER) cc_final: 0.0370 (pmm) REVERT: I 33 MET cc_start: 0.3604 (mmp) cc_final: 0.2816 (ppp) outliers start: 116 outliers final: 95 residues processed: 228 average time/residue: 0.3631 time to fit residues: 143.3499 Evaluate side-chains 225 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 122 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 33 MET Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 20.0000 chunk 344 optimal weight: 6.9990 chunk 314 optimal weight: 30.0000 chunk 335 optimal weight: 20.0000 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 263 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 316 optimal weight: 30.0000 chunk 333 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30582 Z= 0.328 Angle : 0.567 10.827 41642 Z= 0.288 Chirality : 0.045 0.638 4934 Planarity : 0.003 0.045 5294 Dihedral : 5.210 58.363 5312 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.83 % Allowed : 21.28 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3709 helix: 2.04 (0.21), residues: 671 sheet: 0.33 (0.17), residues: 1009 loop : -1.34 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 353 HIS 0.003 0.001 HIS B1048 PHE 0.017 0.001 PHE C 888 TYR 0.015 0.001 TYR C1067 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 119 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8432 (t70) cc_final: 0.8200 (t70) REVERT: A 271 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8313 (mp10) REVERT: A 733 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8120 (ttpt) REVERT: A 1029 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.7953 (ttp) REVERT: B 726 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.9018 (tp) REVERT: B 727 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9375 (pp) REVERT: B 988 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8283 (tm-30) REVERT: C 614 ASP cc_start: 0.7854 (t0) cc_final: 0.7401 (t0) REVERT: C 948 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8813 (mp) REVERT: G 33 MET cc_start: 0.1232 (OUTLIER) cc_final: 0.0792 (mmm) REVERT: H 74 MET cc_start: 0.0466 (OUTLIER) cc_final: 0.0259 (pmm) REVERT: I 33 MET cc_start: 0.3473 (mmp) cc_final: 0.2690 (ppp) outliers start: 123 outliers final: 105 residues processed: 229 average time/residue: 0.4071 time to fit residues: 162.7428 Evaluate side-chains 230 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 117 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 33 MET Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 371 optimal weight: 30.0000 chunk 342 optimal weight: 6.9990 chunk 295 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 0.036 30582 Z= 0.173 Angle : 0.514 9.936 41642 Z= 0.260 Chirality : 0.044 0.578 4934 Planarity : 0.003 0.044 5294 Dihedral : 4.948 57.198 5312 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.52 % Allowed : 21.56 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3709 helix: 2.26 (0.22), residues: 661 sheet: 0.44 (0.17), residues: 995 loop : -1.23 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 353 HIS 0.002 0.000 HIS B1048 PHE 0.013 0.001 PHE B 157 TYR 0.015 0.001 TYR B1067 ARG 0.006 0.000 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 119 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8406 (t70) cc_final: 0.8167 (t70) REVERT: A 153 MET cc_start: 0.5362 (tmm) cc_final: 0.5022 (tmm) REVERT: A 271 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8265 (mp10) REVERT: A 733 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8077 (ttpt) REVERT: A 1029 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.7909 (ttp) REVERT: B 726 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8991 (tp) REVERT: B 727 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9286 (pp) REVERT: B 988 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8256 (tm-30) REVERT: C 614 ASP cc_start: 0.7794 (t0) cc_final: 0.7341 (t0) REVERT: C 948 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8828 (mp) REVERT: G 33 MET cc_start: 0.1285 (OUTLIER) cc_final: 0.0931 (mmm) REVERT: I 33 MET cc_start: 0.3674 (mmp) cc_final: 0.2855 (ppp) outliers start: 113 outliers final: 100 residues processed: 218 average time/residue: 0.3559 time to fit residues: 136.8333 Evaluate side-chains 226 residues out of total 3255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 119 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 33 MET Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 5.9990 chunk 315 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 296 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 304 optimal weight: 0.5980 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 0.0870 overall best weight: 1.2760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.131285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.077183 restraints weight = 88949.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078561 restraints weight = 37452.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079867 restraints weight = 23100.197| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30582 Z= 0.188 Angle : 0.510 9.394 41642 Z= 0.258 Chirality : 0.044 0.568 4934 Planarity : 0.003 0.044 5294 Dihedral : 4.776 58.668 5312 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.77 % Allowed : 21.44 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3709 helix: 2.29 (0.22), residues: 663 sheet: 0.44 (0.17), residues: 978 loop : -1.21 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 353 HIS 0.002 0.000 HIS B1048 PHE 0.015 0.001 PHE B 157 TYR 0.014 0.001 TYR B1067 ARG 0.006 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6056.07 seconds wall clock time: 112 minutes 17.11 seconds (6737.11 seconds total)