Starting phenix.real_space_refine on Thu Jul 25 16:06:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn1_36429/07_2024/8jn1_36429.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn1_36429/07_2024/8jn1_36429.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/8jn1_36429/07_2024/8jn1_36429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn1_36429/07_2024/8jn1_36429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn1_36429/07_2024/8jn1_36429.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn1_36429/07_2024/8jn1_36429.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 204 5.16 5 C 19042 2.51 5 N 5062 2.21 5 O 5662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29970 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "V" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1" 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 Time building chain proxies: 15.32, per 1000 atoms: 0.51 Number of scatterers: 29970 At special positions: 0 Unit cell: (160.578, 238.434, 111.918, 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 204 16.00 O 5662 8.00 N 5062 7.00 C 19042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.05 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 30 " distance=2.02 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 121 " distance=2.02 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS E 105 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 116 " distance=2.03 Simple disulfide: pdb=" SG CYS E 300 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS O 3 " - pdb=" SG CYS O 30 " distance=2.03 Simple disulfide: pdb=" SG CYS O 60 " - pdb=" SG CYS O 121 " distance=2.03 Simple disulfide: pdb=" SG CYS O 74 " - pdb=" SG CYS O 105 " distance=2.03 Simple disulfide: pdb=" SG CYS O 92 " - pdb=" SG CYS O 116 " distance=2.04 Simple disulfide: pdb=" SG CYS O 183 " - pdb=" SG CYS O 283 " distance=2.03 Simple disulfide: pdb=" SG CYS O 300 " - pdb=" SG CYS O 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 121 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 74 " - pdb=" SG CYS Q 105 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 92 " - pdb=" SG CYS Q 116 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 183 " - pdb=" SG CYS Q 283 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 300 " - pdb=" SG CYS Q 331 " distance=2.02 Simple disulfide: pdb=" SG CYS S 3 " - pdb=" SG CYS S 30 " distance=2.02 Simple disulfide: pdb=" SG CYS S 60 " - pdb=" SG CYS S 121 " distance=2.02 Simple disulfide: pdb=" SG CYS S 74 " - pdb=" SG CYS S 105 " distance=2.03 Simple disulfide: pdb=" SG CYS S 92 " - pdb=" SG CYS S 116 " distance=2.03 Simple disulfide: pdb=" SG CYS S 300 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 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 Z 2 " - " BMA Z 3 " NAG-ASN " NAG 0 1 " - " ASN S 67 " " NAG 1 1 " - " ASN S 153 " " NAG G 1 " - " ASN A 67 " " NAG I 1 " - " ASN A 153 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN C 153 " " NAG M 1 " - " ASN E 67 " " NAG N 1 " - " ASN E 153 " " NAG W 1 " - " ASN O 67 " " NAG X 1 " - " ASN O 153 " " NAG Y 1 " - " ASN Q 67 " " NAG Z 1 " - " ASN Q 153 " Time building additional restraints: 11.53 Conformation dependent library (CDL) restraints added in 5.4 seconds 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6948 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 72 sheets defined 26.7% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.592A pdb=" N THR A 187 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY A 188 " --> pdb=" O PRO A 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 188' Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.694A pdb=" N PHE A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.697A pdb=" N LEU A 234 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 394 through 414 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 426 through 446 Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.891A pdb=" N ILE A 455 " --> pdb=" O TRP A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 491 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 26 through 39 Processing helix chain 'B' and resid 40 through 52 removed outlier: 4.247A pdb=" N ILE B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 71 Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.905A pdb=" N LEU C 234 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 236 " --> pdb=" O GLU C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 236' Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 394 through 414 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.920A pdb=" N TRP C 418 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 447 Processing helix chain 'C' and resid 450 through 467 Processing helix chain 'C' and resid 470 through 491 Processing helix chain 'D' and resid 20 through 39 removed outlier: 4.113A pdb=" N TRP D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLN D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.727A pdb=" N ILE D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 131 through 135 removed outlier: 3.552A pdb=" N LEU E 135 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 188 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 231 through 234 removed outlier: 3.531A pdb=" N LEU E 234 " --> pdb=" O LYS E 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 231 through 234' Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 394 through 413 Processing helix chain 'E' and resid 414 through 420 removed outlier: 3.874A pdb=" N TRP E 418 " --> pdb=" O ASP E 415 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP E 419 " --> pdb=" O THR E 416 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE E 420 " --> pdb=" O ALA E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 446 removed outlier: 3.507A pdb=" N LEU E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 467 removed outlier: 3.741A pdb=" N ILE E 455 " --> pdb=" O TRP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 491 removed outlier: 4.165A pdb=" N SER E 476 " --> pdb=" O SER E 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 39 removed outlier: 4.329A pdb=" N TRP F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 52 removed outlier: 3.869A pdb=" N ILE F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 75 Proline residue: F 72 - end of helix Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.629A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 188 removed outlier: 3.592A pdb=" N THR O 187 " --> pdb=" O SER O 184 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY O 188 " --> pdb=" O PRO O 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 184 through 188' Processing helix chain 'O' and resid 190 through 194 Processing helix chain 'O' and resid 207 through 212 removed outlier: 3.694A pdb=" N PHE O 211 " --> pdb=" O HIS O 207 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE O 212 " --> pdb=" O ARG O 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 207 through 212' Processing helix chain 'O' and resid 231 through 235 removed outlier: 3.697A pdb=" N LEU O 234 " --> pdb=" O LYS O 231 " (cutoff:3.500A) Processing helix chain 'O' and resid 254 through 262 Processing helix chain 'O' and resid 394 through 414 Processing helix chain 'O' and resid 415 through 420 Processing helix chain 'O' and resid 426 through 446 Processing helix chain 'O' and resid 450 through 467 removed outlier: 3.891A pdb=" N ILE O 455 " --> pdb=" O TRP O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 470 through 491 Processing helix chain 'P' and resid 20 through 25 Processing helix chain 'P' and resid 26 through 39 Processing helix chain 'P' and resid 40 through 52 removed outlier: 4.247A pdb=" N ILE P 44 " --> pdb=" O PRO P 40 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU P 45 " --> pdb=" O GLY P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 71 Processing helix chain 'Q' and resid 190 through 192 No H-bonds generated for 'chain 'Q' and resid 190 through 192' Processing helix chain 'Q' and resid 208 through 214 Processing helix chain 'Q' and resid 231 through 236 removed outlier: 3.905A pdb=" N LEU Q 234 " --> pdb=" O LYS Q 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU Q 235 " --> pdb=" O LYS Q 232 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL Q 236 " --> pdb=" O GLU Q 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 231 through 236' Processing helix chain 'Q' and resid 254 through 262 Processing helix chain 'Q' and resid 394 through 414 Processing helix chain 'Q' and resid 415 through 420 removed outlier: 3.920A pdb=" N TRP Q 418 " --> pdb=" O ASP Q 415 " (cutoff:3.500A) Processing helix chain 'Q' and resid 425 through 447 Processing helix chain 'Q' and resid 450 through 467 Processing helix chain 'Q' and resid 470 through 491 Processing helix chain 'R' and resid 20 through 39 removed outlier: 4.113A pdb=" N TRP R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLN R 28 " --> pdb=" O GLY R 24 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE R 29 " --> pdb=" O ALA R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 52 removed outlier: 3.727A pdb=" N ILE R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 71 Processing helix chain 'S' and resid 82 through 86 Processing helix chain 'S' and resid 131 through 135 removed outlier: 3.552A pdb=" N LEU S 135 " --> pdb=" O HIS S 132 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 188 Processing helix chain 'S' and resid 208 through 213 Processing helix chain 'S' and resid 231 through 234 removed outlier: 3.531A pdb=" N LEU S 234 " --> pdb=" O LYS S 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 231 through 234' Processing helix chain 'S' and resid 254 through 262 Processing helix chain 'S' and resid 394 through 413 Processing helix chain 'S' and resid 414 through 420 removed outlier: 3.874A pdb=" N TRP S 418 " --> pdb=" O ASP S 415 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP S 419 " --> pdb=" O THR S 416 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE S 420 " --> pdb=" O ALA S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 425 through 446 removed outlier: 3.507A pdb=" N LEU S 445 " --> pdb=" O ALA S 441 " (cutoff:3.500A) Processing helix chain 'S' and resid 450 through 467 removed outlier: 3.741A pdb=" N ILE S 455 " --> pdb=" O TRP S 451 " (cutoff:3.500A) Processing helix chain 'S' and resid 470 through 491 removed outlier: 4.165A pdb=" N SER S 476 " --> pdb=" O SER S 472 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 39 removed outlier: 4.329A pdb=" N TRP T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN T 28 " --> pdb=" O GLY T 24 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 52 removed outlier: 3.869A pdb=" N ILE T 44 " --> pdb=" O PRO T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 75 Proline residue: T 72 - end of helix Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'V' and resid 80 through 84 removed outlier: 3.629A pdb=" N GLU V 84 " --> pdb=" O SER V 81 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 11 through 12 removed outlier: 5.404A pdb=" N LEU A 45 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 140 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 20 through 22 removed outlier: 3.897A pdb=" N GLY A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=4, first strand: chain 'A' and resid 53 through 57 removed outlier: 7.451A pdb=" N GLY A 127 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=6, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.530A pdb=" N GLY A 109 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A 115 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS A 93 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 203 through 204 removed outlier: 4.273A pdb=" N ALA A 203 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 268 " --> pdb=" O ALA A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=9, first strand: chain 'A' and resid 304 through 312 removed outlier: 7.525A pdb=" N LYS A 321 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLU A 309 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 319 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 373 through 377 Processing sheet with id=11, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.965A pdb=" N THR C 32 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 142 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR C 138 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR C 48 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS C 136 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 158 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.965A pdb=" N THR C 32 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR C 274 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 20 through 26 removed outlier: 3.944A pdb=" N LYS C 282 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASP C 288 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N THR C 178 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 218 through 219 removed outlier: 5.574A pdb=" N THR C 55 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL C 129 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG C 57 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 127 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 126 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA C 203 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 68 through 72 Processing sheet with id=16, first strand: chain 'C' and resid 68 through 72 removed outlier: 3.548A pdb=" N GLY C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=18, first strand: chain 'C' and resid 304 through 306 removed outlier: 3.773A pdb=" N SER C 311 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 304 through 306 Processing sheet with id=20, first strand: chain 'C' and resid 336 through 339 Processing sheet with id=21, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.564A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N MET E 34 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL E 12 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR E 138 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 20 through 26 removed outlier: 4.562A pdb=" N LYS E 282 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 54 through 72 removed outlier: 5.647A pdb=" N THR E 55 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL E 129 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG E 57 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY E 63 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N CYS E 121 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE E 65 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N PHE E 119 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN E 67 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA E 117 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR E 69 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR E 115 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP E 71 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU E 113 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.503A pdb=" N GLU E 126 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR E 266 " --> pdb=" O MET E 205 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 236 through 241 removed outlier: 4.034A pdb=" N LYS E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 304 through 312 removed outlier: 7.339A pdb=" N LYS E 321 " --> pdb=" O LYS E 307 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU E 309 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU E 319 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 331 through 332 Processing sheet with id=28, first strand: chain 'E' and resid 336 through 338 Processing sheet with id=29, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.680A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=31, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.627A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'H' and resid 33 through 34 Processing sheet with id=33, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=34, first strand: chain 'L' and resid 20 through 23 removed outlier: 3.781A pdb=" N ILE L 20 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'L' and resid 46 through 47 Processing sheet with id=36, first strand: chain 'L' and resid 46 through 47 Processing sheet with id=37, first strand: chain 'O' and resid 11 through 12 removed outlier: 5.404A pdb=" N LEU O 45 " --> pdb=" O ILE O 140 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE O 140 " --> pdb=" O LEU O 45 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'O' and resid 20 through 22 removed outlier: 3.897A pdb=" N GLY O 177 " --> pdb=" O LEU O 173 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'O' and resid 25 through 26 Processing sheet with id=40, first strand: chain 'O' and resid 53 through 57 removed outlier: 7.451A pdb=" N GLY O 127 " --> pdb=" O LEU O 56 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'O' and resid 64 through 66 Processing sheet with id=42, first strand: chain 'O' and resid 64 through 66 removed outlier: 3.530A pdb=" N GLY O 109 " --> pdb=" O ARG O 99 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR O 115 " --> pdb=" O LYS O 93 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS O 93 " --> pdb=" O THR O 115 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'O' and resid 203 through 204 removed outlier: 4.273A pdb=" N ALA O 203 " --> pdb=" O ILE O 268 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE O 268 " --> pdb=" O ALA O 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=43 Processing sheet with id=44, first strand: chain 'O' and resid 237 through 239 Processing sheet with id=45, first strand: chain 'O' and resid 304 through 312 removed outlier: 7.525A pdb=" N LYS O 321 " --> pdb=" O LYS O 307 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLU O 309 " --> pdb=" O LEU O 319 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU O 319 " --> pdb=" O GLU O 309 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'O' and resid 373 through 377 Processing sheet with id=47, first strand: chain 'Q' and resid 9 through 12 removed outlier: 3.965A pdb=" N THR Q 32 " --> pdb=" O ASP Q 10 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR Q 142 " --> pdb=" O ASP Q 42 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR Q 138 " --> pdb=" O GLN Q 46 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR Q 48 " --> pdb=" O LYS Q 136 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS Q 136 " --> pdb=" O THR Q 48 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL Q 158 " --> pdb=" O ILE Q 141 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'Q' and resid 9 through 12 removed outlier: 3.965A pdb=" N THR Q 32 " --> pdb=" O ASP Q 10 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR Q 274 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'Q' and resid 20 through 26 removed outlier: 3.944A pdb=" N LYS Q 282 " --> pdb=" O SER Q 184 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASP Q 288 " --> pdb=" O THR Q 178 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N THR Q 178 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'Q' and resid 218 through 219 removed outlier: 5.574A pdb=" N THR Q 55 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL Q 129 " --> pdb=" O THR Q 55 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG Q 57 " --> pdb=" O GLY Q 127 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY Q 127 " --> pdb=" O ARG Q 57 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU Q 126 " --> pdb=" O THR Q 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA Q 203 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'Q' and resid 68 through 72 Processing sheet with id=52, first strand: chain 'Q' and resid 68 through 72 removed outlier: 3.548A pdb=" N GLY Q 109 " --> pdb=" O ARG Q 99 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'Q' and resid 237 through 240 Processing sheet with id=54, first strand: chain 'Q' and resid 304 through 306 removed outlier: 3.773A pdb=" N SER Q 311 " --> pdb=" O LEU Q 319 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'Q' and resid 304 through 306 Processing sheet with id=56, first strand: chain 'Q' and resid 336 through 339 Processing sheet with id=57, first strand: chain 'S' and resid 10 through 13 removed outlier: 6.564A pdb=" N ASP S 10 " --> pdb=" O THR S 32 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N MET S 34 " --> pdb=" O ASP S 10 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL S 12 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR S 138 " --> pdb=" O GLN S 46 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'S' and resid 20 through 26 removed outlier: 4.562A pdb=" N LYS S 282 " --> pdb=" O SER S 184 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY S 177 " --> pdb=" O LEU S 173 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'S' and resid 54 through 72 removed outlier: 5.647A pdb=" N THR S 55 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL S 129 " --> pdb=" O THR S 55 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG S 57 " --> pdb=" O GLY S 127 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY S 63 " --> pdb=" O CYS S 121 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N CYS S 121 " --> pdb=" O GLY S 63 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE S 65 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N PHE S 119 " --> pdb=" O ILE S 65 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN S 67 " --> pdb=" O ALA S 117 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA S 117 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR S 69 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR S 115 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP S 71 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU S 113 " --> pdb=" O ASP S 71 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 90 through 91 removed outlier: 3.503A pdb=" N GLU S 126 " --> pdb=" O THR S 198 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR S 266 " --> pdb=" O MET S 205 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'S' and resid 236 through 241 removed outlier: 4.034A pdb=" N LYS S 245 " --> pdb=" O ALA S 241 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'S' and resid 304 through 312 removed outlier: 7.339A pdb=" N LYS S 321 " --> pdb=" O LYS S 307 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU S 309 " --> pdb=" O LEU S 319 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU S 319 " --> pdb=" O GLU S 309 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'S' and resid 331 through 332 Processing sheet with id=64, first strand: chain 'S' and resid 336 through 338 Processing sheet with id=65, first strand: chain 'U' and resid 3 through 6 removed outlier: 3.680A pdb=" N GLN U 3 " --> pdb=" O SER U 25 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER U 25 " --> pdb=" O GLN U 3 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'U' and resid 10 through 12 Processing sheet with id=67, first strand: chain 'U' and resid 18 through 20 removed outlier: 3.627A pdb=" N VAL U 18 " --> pdb=" O LEU U 83 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'U' and resid 33 through 34 Processing sheet with id=69, first strand: chain 'U' and resid 49 through 51 Processing sheet with id=70, first strand: chain 'V' and resid 20 through 23 removed outlier: 3.781A pdb=" N ILE V 20 " --> pdb=" O LEU V 74 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER V 71 " --> pdb=" O SER V 68 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'V' and resid 46 through 47 Processing sheet with id=72, first strand: chain 'V' and resid 46 through 47 1238 hydrogen bonds defined for protein. 3354 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: 10.97 Time building geometry restraints manager: 12.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9592 1.35 - 1.48: 7436 1.48 - 1.60: 13222 1.60 - 1.73: 0 1.73 - 1.85: 322 Bond restraints: 30572 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG 1 2 " pdb=" O5 NAG 1 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" N MET O 199 " pdb=" CA MET O 199 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.02e+00 bond pdb=" N MET A 199 " pdb=" CA MET A 199 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.02e+00 bond pdb=" C ASN Q 353 " pdb=" N PRO Q 354 " ideal model delta sigma weight residual 1.335 1.323 0.012 8.70e-03 1.32e+04 1.91e+00 ... (remaining 30567 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.82: 556 105.82 - 112.88: 17272 112.88 - 119.95: 9618 119.95 - 127.02: 13546 127.02 - 134.09: 426 Bond angle restraints: 41418 Sorted by residual: angle pdb=" C LYS S 358 " pdb=" N LYS S 359 " pdb=" CA LYS S 359 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C LYS E 358 " pdb=" N LYS E 359 " pdb=" CA LYS E 359 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" N ILE A 61 " pdb=" CA ILE A 61 " pdb=" CB ILE A 61 " ideal model delta sigma weight residual 111.90 106.80 5.10 1.37e+00 5.33e-01 1.39e+01 angle pdb=" N ILE O 61 " pdb=" CA ILE O 61 " pdb=" CB ILE O 61 " ideal model delta sigma weight residual 111.90 106.80 5.10 1.37e+00 5.33e-01 1.39e+01 angle pdb=" CA GLY S 109 " pdb=" C GLY S 109 " pdb=" N LYS S 110 " ideal model delta sigma weight residual 114.23 117.23 -3.00 8.80e-01 1.29e+00 1.16e+01 ... (remaining 41413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 17292 21.63 - 43.25: 972 43.25 - 64.88: 136 64.88 - 86.50: 72 86.50 - 108.13: 20 Dihedral angle restraints: 18492 sinusoidal: 7608 harmonic: 10884 Sorted by residual: dihedral pdb=" CB CYS O 60 " pdb=" SG CYS O 60 " pdb=" SG CYS O 121 " pdb=" CB CYS O 121 " ideal model delta sinusoidal sigma weight residual -86.00 2.69 -88.69 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 2.69 -88.69 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS A 300 " pdb=" SG CYS A 300 " pdb=" SG CYS A 331 " pdb=" CB CYS A 331 " ideal model delta sinusoidal sigma weight residual -86.00 -163.80 77.80 1 1.00e+01 1.00e-02 7.57e+01 ... (remaining 18489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3988 0.057 - 0.114: 760 0.114 - 0.170: 86 0.170 - 0.227: 8 0.227 - 0.284: 6 Chirality restraints: 4848 Sorted by residual: chirality pdb=" C5 BMA Z 3 " pdb=" C4 BMA Z 3 " pdb=" C6 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 4845 not shown) Planarity restraints: 5174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 420 " -0.015 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE C 420 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE C 420 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 420 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 420 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 420 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 420 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 420 " 0.015 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE Q 420 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 420 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 420 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 420 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 420 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE Q 420 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 176 " 0.011 2.00e-02 2.50e+03 1.02e-02 2.08e+00 pdb=" CG TYR S 176 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR S 176 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR S 176 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 176 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR S 176 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR S 176 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR S 176 " 0.005 2.00e-02 2.50e+03 ... (remaining 5171 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1204 2.71 - 3.26: 29952 3.26 - 3.81: 48087 3.81 - 4.35: 58204 4.35 - 4.90: 102739 Nonbonded interactions: 240186 Sorted by model distance: nonbonded pdb=" OG SER B 73 " pdb=" OG SER P 73 " model vdw 2.168 2.440 nonbonded pdb=" OH TYR A 324 " pdb=" OD1 ASP A 328 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR O 324 " pdb=" OD1 ASP O 328 " model vdw 2.202 2.440 nonbonded pdb=" ND2 ASN O 302 " pdb=" O LYS O 325 " model vdw 2.209 2.520 nonbonded pdb=" ND2 ASN A 302 " pdb=" O LYS A 325 " model vdw 2.209 2.520 ... (remaining 240181 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 '0' selection = chain 'K' selection = chain 'M' selection = chain 'Z' } ncs_group { reference = chain '1' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'V' } 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 77.260 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.190 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 0.044 30572 Z= 0.278 Angle : 0.696 9.502 41418 Z= 0.382 Chirality : 0.046 0.284 4848 Planarity : 0.003 0.036 5162 Dihedral : 14.360 108.125 11430 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3838 helix: 1.34 (0.18), residues: 870 sheet: -1.51 (0.14), residues: 1226 loop : -1.35 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 451 HIS 0.009 0.001 HIS S 144 PHE 0.024 0.001 PHE Q 420 TYR 0.022 0.002 TYR E 176 ARG 0.005 0.001 ARG Q 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 744 time to evaluate : 3.338 Fit side-chains REVERT: A 132 HIS cc_start: 0.8337 (t-90) cc_final: 0.7747 (t-170) REVERT: A 163 THR cc_start: 0.8611 (p) cc_final: 0.8370 (m) REVERT: A 324 TYR cc_start: 0.8890 (t80) cc_final: 0.8635 (t80) REVERT: A 438 PHE cc_start: 0.8236 (m-80) cc_final: 0.7952 (m-10) REVERT: A 442 TYR cc_start: 0.9228 (t80) cc_final: 0.8787 (t80) REVERT: B 10 MET cc_start: 0.7944 (mmm) cc_final: 0.7628 (mmp) REVERT: B 17 GLN cc_start: 0.8747 (tt0) cc_final: 0.8478 (tt0) REVERT: C 90 TYR cc_start: 0.8782 (m-80) cc_final: 0.8411 (m-80) REVERT: C 473 MET cc_start: 0.7268 (tpp) cc_final: 0.7020 (tpp) REVERT: D 52 TYR cc_start: 0.7901 (m-80) cc_final: 0.7328 (m-80) REVERT: E 49 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7333 (tp30) REVERT: E 98 ASP cc_start: 0.7787 (m-30) cc_final: 0.7554 (m-30) REVERT: E 170 GLU cc_start: 0.8001 (tt0) cc_final: 0.7717 (mp0) REVERT: E 258 MET cc_start: 0.8727 (tpt) cc_final: 0.8426 (tpt) REVERT: E 368 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7285 (tm-30) REVERT: E 400 PHE cc_start: 0.7898 (t80) cc_final: 0.7561 (t80) REVERT: F 10 MET cc_start: 0.8439 (mmp) cc_final: 0.7996 (mmp) REVERT: F 14 THR cc_start: 0.9056 (t) cc_final: 0.8762 (p) REVERT: F 68 MET cc_start: 0.8790 (mmm) cc_final: 0.8273 (mmm) REVERT: H 10 GLU cc_start: 0.7977 (tt0) cc_final: 0.7721 (tt0) REVERT: H 12 LYS cc_start: 0.8338 (mttp) cc_final: 0.8093 (mttm) REVERT: L 49 MET cc_start: 0.6518 (mmt) cc_final: 0.5871 (mmt) REVERT: L 71 SER cc_start: 0.8863 (m) cc_final: 0.8566 (p) REVERT: L 107 LEU cc_start: 0.5967 (tp) cc_final: 0.5699 (tp) REVERT: O 132 HIS cc_start: 0.8332 (t-90) cc_final: 0.7745 (t-170) REVERT: O 163 THR cc_start: 0.8611 (p) cc_final: 0.8368 (m) REVERT: O 324 TYR cc_start: 0.8886 (t80) cc_final: 0.8630 (t80) REVERT: O 438 PHE cc_start: 0.8231 (m-80) cc_final: 0.7945 (m-10) REVERT: O 442 TYR cc_start: 0.9228 (t80) cc_final: 0.8788 (t80) REVERT: P 10 MET cc_start: 0.7927 (mmm) cc_final: 0.7619 (mmp) REVERT: P 17 GLN cc_start: 0.8745 (tt0) cc_final: 0.8472 (tt0) REVERT: Q 90 TYR cc_start: 0.8785 (m-80) cc_final: 0.8416 (m-80) REVERT: Q 473 MET cc_start: 0.7257 (tpp) cc_final: 0.7012 (tpp) REVERT: R 52 TYR cc_start: 0.7898 (m-80) cc_final: 0.7322 (m-80) REVERT: S 49 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7325 (tp30) REVERT: S 98 ASP cc_start: 0.7780 (m-30) cc_final: 0.7555 (m-30) REVERT: S 170 GLU cc_start: 0.8007 (tt0) cc_final: 0.7718 (mp0) REVERT: S 258 MET cc_start: 0.8745 (tpt) cc_final: 0.8428 (tpt) REVERT: S 368 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7294 (tm-30) REVERT: S 400 PHE cc_start: 0.7900 (t80) cc_final: 0.7566 (t80) REVERT: T 10 MET cc_start: 0.8444 (mmp) cc_final: 0.7991 (mmp) REVERT: T 14 THR cc_start: 0.9055 (t) cc_final: 0.8767 (p) REVERT: T 68 MET cc_start: 0.8800 (mmm) cc_final: 0.8270 (mmm) REVERT: U 10 GLU cc_start: 0.7979 (tt0) cc_final: 0.7726 (tt0) REVERT: U 12 LYS cc_start: 0.8345 (mttp) cc_final: 0.8098 (mttm) REVERT: V 49 MET cc_start: 0.6510 (mmt) cc_final: 0.5852 (mmt) REVERT: V 71 SER cc_start: 0.8844 (m) cc_final: 0.8561 (p) outliers start: 0 outliers final: 0 residues processed: 744 average time/residue: 0.4264 time to fit residues: 495.1492 Evaluate side-chains 493 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 7.9990 chunk 288 optimal weight: 0.6980 chunk 159 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 297 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 181 optimal weight: 0.0570 chunk 221 optimal weight: 8.9990 chunk 345 optimal weight: 10.0000 overall best weight: 2.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 375 ASN B 51 HIS C 8 ASN C 132 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN O 134 ASN O 375 ASN P 51 HIS Q 8 ASN Q 132 HIS ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 GLN ** S 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 6 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30572 Z= 0.271 Angle : 0.645 13.676 41418 Z= 0.334 Chirality : 0.046 0.278 4848 Planarity : 0.004 0.037 5162 Dihedral : 8.266 66.904 4632 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.94 % Allowed : 11.19 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3838 helix: 1.68 (0.18), residues: 852 sheet: -1.59 (0.15), residues: 1104 loop : -1.23 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 451 HIS 0.007 0.001 HIS E 144 PHE 0.025 0.002 PHE C 420 TYR 0.015 0.002 TYR B 52 ARG 0.004 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 545 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.8414 (t-90) cc_final: 0.7690 (t-170) REVERT: A 324 TYR cc_start: 0.8867 (t80) cc_final: 0.8599 (t80) REVERT: A 438 PHE cc_start: 0.8254 (m-80) cc_final: 0.8004 (m-10) REVERT: A 442 TYR cc_start: 0.9183 (t80) cc_final: 0.8818 (t80) REVERT: B 10 MET cc_start: 0.7980 (mmm) cc_final: 0.7693 (mmp) REVERT: B 17 GLN cc_start: 0.8745 (tt0) cc_final: 0.8469 (tt0) REVERT: C 473 MET cc_start: 0.7269 (tpp) cc_final: 0.7027 (tpp) REVERT: D 52 TYR cc_start: 0.7858 (m-80) cc_final: 0.7353 (m-80) REVERT: E 49 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7457 (tp30) REVERT: E 98 ASP cc_start: 0.7874 (m-30) cc_final: 0.7605 (m-30) REVERT: E 176 TYR cc_start: 0.9011 (m-80) cc_final: 0.8780 (m-80) REVERT: E 247 GLU cc_start: 0.7372 (pm20) cc_final: 0.7171 (pm20) REVERT: E 258 MET cc_start: 0.8540 (tpt) cc_final: 0.8275 (tpt) REVERT: E 297 TYR cc_start: 0.7945 (m-80) cc_final: 0.7639 (m-80) REVERT: E 400 PHE cc_start: 0.7943 (t80) cc_final: 0.7562 (t80) REVERT: F 10 MET cc_start: 0.8575 (mmp) cc_final: 0.8239 (mmp) REVERT: H 10 GLU cc_start: 0.8202 (tt0) cc_final: 0.7962 (mt-10) REVERT: H 110 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7635 (p0) REVERT: L 37 TYR cc_start: 0.8179 (m-80) cc_final: 0.7918 (m-80) REVERT: L 49 MET cc_start: 0.6422 (mmt) cc_final: 0.5835 (mmt) REVERT: L 71 SER cc_start: 0.8727 (m) cc_final: 0.8439 (p) REVERT: L 107 LEU cc_start: 0.6086 (tp) cc_final: 0.5848 (tp) REVERT: O 132 HIS cc_start: 0.8410 (t-90) cc_final: 0.7693 (t-170) REVERT: O 324 TYR cc_start: 0.8865 (t80) cc_final: 0.8596 (t80) REVERT: O 438 PHE cc_start: 0.8245 (m-80) cc_final: 0.7998 (m-10) REVERT: O 442 TYR cc_start: 0.9183 (t80) cc_final: 0.8824 (t80) REVERT: P 10 MET cc_start: 0.7963 (mmm) cc_final: 0.7685 (mmp) REVERT: P 17 GLN cc_start: 0.8748 (tt0) cc_final: 0.8467 (tt0) REVERT: Q 473 MET cc_start: 0.7260 (tpp) cc_final: 0.7021 (tpp) REVERT: R 52 TYR cc_start: 0.7853 (m-80) cc_final: 0.7345 (m-80) REVERT: S 49 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7450 (tp30) REVERT: S 98 ASP cc_start: 0.7878 (m-30) cc_final: 0.7611 (m-30) REVERT: S 176 TYR cc_start: 0.9015 (m-80) cc_final: 0.8782 (m-80) REVERT: S 247 GLU cc_start: 0.7371 (pm20) cc_final: 0.7171 (pm20) REVERT: S 258 MET cc_start: 0.8561 (tpt) cc_final: 0.8276 (tpt) REVERT: S 297 TYR cc_start: 0.7940 (m-80) cc_final: 0.7639 (m-80) REVERT: S 400 PHE cc_start: 0.7942 (t80) cc_final: 0.7564 (t80) REVERT: T 10 MET cc_start: 0.8574 (mmp) cc_final: 0.8230 (mmp) REVERT: U 10 GLU cc_start: 0.8199 (tt0) cc_final: 0.7959 (mt-10) REVERT: U 110 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7635 (p0) REVERT: V 37 TYR cc_start: 0.8184 (m-80) cc_final: 0.7913 (m-80) REVERT: V 49 MET cc_start: 0.6415 (mmt) cc_final: 0.5825 (mmt) REVERT: V 71 SER cc_start: 0.8722 (m) cc_final: 0.8435 (p) outliers start: 62 outliers final: 40 residues processed: 581 average time/residue: 0.3794 time to fit residues: 359.8474 Evaluate side-chains 534 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 492 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 110 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 287 optimal weight: 7.9990 chunk 234 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 373 optimal weight: 6.9990 chunk 307 optimal weight: 4.9990 chunk 342 optimal weight: 10.0000 chunk 117 optimal weight: 0.0370 chunk 277 optimal weight: 0.4980 overall best weight: 3.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 314 GLN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN O 134 ASN O 314 GLN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30572 Z= 0.296 Angle : 0.626 13.169 41418 Z= 0.322 Chirality : 0.046 0.276 4848 Planarity : 0.003 0.037 5162 Dihedral : 6.675 55.135 4632 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.06 % Allowed : 14.78 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 3838 helix: 1.55 (0.18), residues: 876 sheet: -1.43 (0.15), residues: 1070 loop : -1.27 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 451 HIS 0.007 0.001 HIS S 149 PHE 0.023 0.002 PHE Q 420 TYR 0.015 0.002 TYR O 297 ARG 0.006 0.001 ARG U 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 502 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.8404 (t-90) cc_final: 0.7772 (t-170) REVERT: A 324 TYR cc_start: 0.8787 (t80) cc_final: 0.8520 (t80) REVERT: A 438 PHE cc_start: 0.8248 (m-80) cc_final: 0.8029 (m-10) REVERT: A 442 TYR cc_start: 0.9205 (t80) cc_final: 0.8855 (t80) REVERT: B 10 MET cc_start: 0.8043 (mmm) cc_final: 0.7580 (mmp) REVERT: B 17 GLN cc_start: 0.8781 (tt0) cc_final: 0.8512 (tt0) REVERT: C 41 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8104 (pp) REVERT: C 181 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7754 (pp) REVERT: C 485 LEU cc_start: 0.9047 (mm) cc_final: 0.8823 (mm) REVERT: D 52 TYR cc_start: 0.7997 (m-80) cc_final: 0.7527 (m-80) REVERT: E 49 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7419 (tp30) REVERT: E 98 ASP cc_start: 0.7961 (m-30) cc_final: 0.7709 (m-30) REVERT: E 247 GLU cc_start: 0.7515 (pm20) cc_final: 0.7189 (pm20) REVERT: E 258 MET cc_start: 0.8512 (tpt) cc_final: 0.8210 (tpt) REVERT: E 400 PHE cc_start: 0.8015 (t80) cc_final: 0.7573 (t80) REVERT: F 10 MET cc_start: 0.8581 (mmp) cc_final: 0.8244 (mmp) REVERT: F 68 MET cc_start: 0.8687 (mmm) cc_final: 0.8346 (mmm) REVERT: H 10 GLU cc_start: 0.8151 (tt0) cc_final: 0.7820 (mt-10) REVERT: H 73 ASP cc_start: 0.7807 (t70) cc_final: 0.6952 (t0) REVERT: L 49 MET cc_start: 0.6206 (mmt) cc_final: 0.5834 (mmt) REVERT: L 71 SER cc_start: 0.8573 (m) cc_final: 0.8266 (p) REVERT: L 107 LEU cc_start: 0.6775 (tp) cc_final: 0.6567 (tt) REVERT: O 132 HIS cc_start: 0.8403 (t-90) cc_final: 0.7774 (t-170) REVERT: O 324 TYR cc_start: 0.8782 (t80) cc_final: 0.8515 (t80) REVERT: O 438 PHE cc_start: 0.8240 (m-80) cc_final: 0.8027 (m-10) REVERT: O 442 TYR cc_start: 0.9204 (t80) cc_final: 0.8858 (t80) REVERT: P 10 MET cc_start: 0.8027 (mmm) cc_final: 0.7584 (mmp) REVERT: P 17 GLN cc_start: 0.8781 (tt0) cc_final: 0.8511 (tt0) REVERT: Q 41 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8113 (pp) REVERT: Q 181 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7768 (pp) REVERT: Q 485 LEU cc_start: 0.9049 (mm) cc_final: 0.8829 (mm) REVERT: R 52 TYR cc_start: 0.7996 (m-80) cc_final: 0.7520 (m-80) REVERT: S 49 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7415 (tp30) REVERT: S 98 ASP cc_start: 0.7962 (m-30) cc_final: 0.7716 (m-30) REVERT: S 247 GLU cc_start: 0.7508 (pm20) cc_final: 0.7195 (pm20) REVERT: S 258 MET cc_start: 0.8530 (tpt) cc_final: 0.8195 (tpt) REVERT: S 400 PHE cc_start: 0.8015 (t80) cc_final: 0.7576 (t80) REVERT: T 10 MET cc_start: 0.8579 (mmp) cc_final: 0.8232 (mmp) REVERT: T 68 MET cc_start: 0.8699 (mmm) cc_final: 0.8352 (mmm) REVERT: U 10 GLU cc_start: 0.8156 (tt0) cc_final: 0.7819 (mt-10) REVERT: U 73 ASP cc_start: 0.7806 (t70) cc_final: 0.6955 (t0) REVERT: V 49 MET cc_start: 0.6202 (mmt) cc_final: 0.5833 (mmt) REVERT: V 71 SER cc_start: 0.8570 (m) cc_final: 0.8263 (p) outliers start: 98 outliers final: 66 residues processed: 570 average time/residue: 0.3845 time to fit residues: 360.1766 Evaluate side-chains 549 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 479 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 251 LEU Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 213 ASP Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 102 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 346 optimal weight: 5.9990 chunk 367 optimal weight: 20.0000 chunk 181 optimal weight: 0.0170 chunk 328 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS O 134 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30572 Z= 0.269 Angle : 0.602 13.145 41418 Z= 0.309 Chirality : 0.045 0.267 4848 Planarity : 0.003 0.046 5162 Dihedral : 6.298 54.664 4632 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.09 % Allowed : 17.03 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3838 helix: 1.67 (0.18), residues: 876 sheet: -1.37 (0.15), residues: 1070 loop : -1.27 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 451 HIS 0.006 0.001 HIS E 144 PHE 0.021 0.002 PHE C 420 TYR 0.014 0.001 TYR A 297 ARG 0.006 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 499 time to evaluate : 3.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.8299 (t-90) cc_final: 0.7603 (t-90) REVERT: A 324 TYR cc_start: 0.8854 (t80) cc_final: 0.8609 (t80) REVERT: A 438 PHE cc_start: 0.8264 (m-80) cc_final: 0.8031 (m-10) REVERT: A 442 TYR cc_start: 0.9202 (t80) cc_final: 0.8827 (t80) REVERT: B 10 MET cc_start: 0.8012 (mmm) cc_final: 0.7551 (mmp) REVERT: B 17 GLN cc_start: 0.8687 (tt0) cc_final: 0.8414 (tt0) REVERT: C 41 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8142 (pp) REVERT: C 181 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7702 (pp) REVERT: C 485 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8814 (mm) REVERT: D 52 TYR cc_start: 0.7884 (m-80) cc_final: 0.7374 (m-80) REVERT: E 49 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7364 (tp30) REVERT: E 98 ASP cc_start: 0.7970 (m-30) cc_final: 0.7726 (m-30) REVERT: E 247 GLU cc_start: 0.7633 (pm20) cc_final: 0.7224 (pm20) REVERT: E 297 TYR cc_start: 0.7861 (m-80) cc_final: 0.7479 (m-80) REVERT: E 400 PHE cc_start: 0.8016 (t80) cc_final: 0.7461 (t80) REVERT: F 20 MET cc_start: 0.9050 (mtm) cc_final: 0.8691 (mtm) REVERT: F 68 MET cc_start: 0.8699 (mmm) cc_final: 0.8342 (mmm) REVERT: H 10 GLU cc_start: 0.8105 (tt0) cc_final: 0.7785 (mt-10) REVERT: H 81 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6594 (ttm) REVERT: H 100 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7351 (mmm-85) REVERT: L 49 MET cc_start: 0.6400 (mmt) cc_final: 0.5795 (mmt) REVERT: L 71 SER cc_start: 0.8517 (m) cc_final: 0.8253 (p) REVERT: L 107 LEU cc_start: 0.6802 (tp) cc_final: 0.6583 (tp) REVERT: O 132 HIS cc_start: 0.8296 (t-90) cc_final: 0.7600 (t-90) REVERT: O 324 TYR cc_start: 0.8851 (t80) cc_final: 0.8603 (t80) REVERT: O 438 PHE cc_start: 0.8255 (m-80) cc_final: 0.8022 (m-10) REVERT: O 442 TYR cc_start: 0.9203 (t80) cc_final: 0.8825 (t80) REVERT: P 10 MET cc_start: 0.7992 (mmm) cc_final: 0.7507 (mmp) REVERT: P 17 GLN cc_start: 0.8689 (tt0) cc_final: 0.8418 (tt0) REVERT: Q 41 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8143 (pp) REVERT: Q 181 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7706 (pp) REVERT: Q 485 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8820 (mm) REVERT: R 52 TYR cc_start: 0.7880 (m-80) cc_final: 0.7367 (m-80) REVERT: S 49 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7360 (tp30) REVERT: S 98 ASP cc_start: 0.7973 (m-30) cc_final: 0.7731 (m-30) REVERT: S 247 GLU cc_start: 0.7622 (pm20) cc_final: 0.7234 (pm20) REVERT: S 297 TYR cc_start: 0.7861 (m-80) cc_final: 0.7484 (m-80) REVERT: S 400 PHE cc_start: 0.8014 (t80) cc_final: 0.7463 (t80) REVERT: T 20 MET cc_start: 0.9034 (mtm) cc_final: 0.8687 (mtm) REVERT: T 68 MET cc_start: 0.8714 (mmm) cc_final: 0.8347 (mmm) REVERT: U 10 GLU cc_start: 0.8108 (tt0) cc_final: 0.7792 (mt-10) REVERT: U 81 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6591 (ttm) REVERT: U 100 ARG cc_start: 0.7787 (mmm-85) cc_final: 0.7355 (mmm-85) REVERT: V 49 MET cc_start: 0.6398 (mmt) cc_final: 0.5796 (mmt) REVERT: V 71 SER cc_start: 0.8517 (m) cc_final: 0.8252 (p) outliers start: 131 outliers final: 95 residues processed: 595 average time/residue: 0.3730 time to fit residues: 369.4677 Evaluate side-chains 577 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 474 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 363 VAL Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 81 MET Chi-restraints excluded: chain U residue 102 PHE Chi-restraints excluded: chain U residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 313 optimal weight: 0.8980 chunk 253 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 30.0000 chunk 329 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30572 Z= 0.274 Angle : 0.599 13.209 41418 Z= 0.307 Chirality : 0.045 0.272 4848 Planarity : 0.003 0.039 5162 Dihedral : 6.120 54.432 4632 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.03 % Allowed : 17.28 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3838 helix: 1.71 (0.18), residues: 876 sheet: -1.46 (0.15), residues: 1114 loop : -1.26 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 451 HIS 0.008 0.001 HIS S 144 PHE 0.020 0.002 PHE C 420 TYR 0.019 0.001 TYR H 27 ARG 0.004 0.000 ARG U 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 493 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.8214 (t-90) cc_final: 0.7663 (t-170) REVERT: A 324 TYR cc_start: 0.8865 (t80) cc_final: 0.8630 (t80) REVERT: A 438 PHE cc_start: 0.8264 (m-80) cc_final: 0.8023 (m-10) REVERT: A 442 TYR cc_start: 0.9187 (t80) cc_final: 0.8795 (t80) REVERT: B 10 MET cc_start: 0.8024 (mmm) cc_final: 0.7553 (mmp) REVERT: B 17 GLN cc_start: 0.8748 (tt0) cc_final: 0.8492 (tt0) REVERT: C 41 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8203 (pp) REVERT: C 181 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7736 (pp) REVERT: C 485 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8810 (mm) REVERT: D 52 TYR cc_start: 0.7895 (m-80) cc_final: 0.7446 (m-80) REVERT: E 49 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7194 (tp30) REVERT: E 176 TYR cc_start: 0.8800 (m-80) cc_final: 0.8562 (m-80) REVERT: E 297 TYR cc_start: 0.7809 (m-80) cc_final: 0.7375 (m-80) REVERT: E 400 PHE cc_start: 0.7927 (t80) cc_final: 0.7459 (t80) REVERT: F 20 MET cc_start: 0.9038 (mtm) cc_final: 0.8691 (mtm) REVERT: F 68 MET cc_start: 0.8721 (mmm) cc_final: 0.8366 (mmm) REVERT: H 10 GLU cc_start: 0.8066 (tt0) cc_final: 0.7750 (mt-10) REVERT: H 100 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7400 (mmm-85) REVERT: H 106 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: L 4 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7814 (pp) REVERT: L 48 LEU cc_start: 0.7896 (tt) cc_final: 0.7495 (tt) REVERT: L 49 MET cc_start: 0.6229 (mmt) cc_final: 0.5916 (mmt) REVERT: L 71 SER cc_start: 0.8516 (m) cc_final: 0.8255 (p) REVERT: L 107 LEU cc_start: 0.6819 (tp) cc_final: 0.6577 (tp) REVERT: O 132 HIS cc_start: 0.8201 (t-90) cc_final: 0.7659 (t-170) REVERT: O 324 TYR cc_start: 0.8862 (t80) cc_final: 0.8625 (t80) REVERT: O 438 PHE cc_start: 0.8256 (m-80) cc_final: 0.8018 (m-10) REVERT: O 442 TYR cc_start: 0.9186 (t80) cc_final: 0.8794 (t80) REVERT: P 10 MET cc_start: 0.7982 (mmm) cc_final: 0.7566 (mmp) REVERT: P 17 GLN cc_start: 0.8749 (tt0) cc_final: 0.8493 (tt0) REVERT: Q 41 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8209 (pp) REVERT: Q 181 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7742 (pp) REVERT: Q 485 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8818 (mm) REVERT: R 52 TYR cc_start: 0.7891 (m-80) cc_final: 0.7438 (m-80) REVERT: S 49 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7197 (tp30) REVERT: S 176 TYR cc_start: 0.8804 (m-80) cc_final: 0.8562 (m-80) REVERT: S 297 TYR cc_start: 0.7802 (m-80) cc_final: 0.7377 (m-80) REVERT: S 400 PHE cc_start: 0.7921 (t80) cc_final: 0.7455 (t80) REVERT: T 20 MET cc_start: 0.9020 (mtm) cc_final: 0.8693 (mtm) REVERT: T 68 MET cc_start: 0.8739 (mmm) cc_final: 0.8373 (mmm) REVERT: U 10 GLU cc_start: 0.8072 (tt0) cc_final: 0.7754 (mt-10) REVERT: U 100 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7399 (mmm-85) REVERT: U 106 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: V 4 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7817 (pp) REVERT: V 48 LEU cc_start: 0.7901 (tt) cc_final: 0.7498 (tt) REVERT: V 49 MET cc_start: 0.6226 (mmt) cc_final: 0.5914 (mmt) REVERT: V 71 SER cc_start: 0.8517 (m) cc_final: 0.8251 (p) outliers start: 161 outliers final: 110 residues processed: 603 average time/residue: 0.3658 time to fit residues: 367.6156 Evaluate side-chains 599 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 479 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 363 VAL Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 346 ASN Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 213 ASP Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 102 PHE Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 367 optimal weight: 20.0000 chunk 305 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30572 Z= 0.185 Angle : 0.566 13.328 41418 Z= 0.289 Chirality : 0.044 0.259 4848 Planarity : 0.003 0.037 5162 Dihedral : 5.870 54.144 4632 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.19 % Allowed : 19.12 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 3838 helix: 1.84 (0.18), residues: 870 sheet: -1.43 (0.15), residues: 1148 loop : -1.18 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.006 0.001 HIS E 144 PHE 0.016 0.001 PHE C 420 TYR 0.023 0.001 TYR H 27 ARG 0.005 0.000 ARG U 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 517 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.8197 (t-90) cc_final: 0.7643 (t-170) REVERT: A 324 TYR cc_start: 0.8909 (t80) cc_final: 0.8672 (t80) REVERT: A 438 PHE cc_start: 0.8221 (m-80) cc_final: 0.7992 (m-10) REVERT: A 442 TYR cc_start: 0.9163 (t80) cc_final: 0.8748 (t80) REVERT: B 10 MET cc_start: 0.7911 (mmm) cc_final: 0.7444 (mmp) REVERT: B 17 GLN cc_start: 0.8738 (tt0) cc_final: 0.8491 (tt0) REVERT: C 13 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7703 (tm-30) REVERT: C 41 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8136 (pp) REVERT: C 485 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8876 (mm) REVERT: D 52 TYR cc_start: 0.7914 (m-80) cc_final: 0.7562 (m-80) REVERT: E 49 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6794 (tp30) REVERT: E 297 TYR cc_start: 0.7856 (m-80) cc_final: 0.7451 (m-80) REVERT: E 400 PHE cc_start: 0.7857 (t80) cc_final: 0.7469 (t80) REVERT: F 20 MET cc_start: 0.9039 (mtm) cc_final: 0.8719 (mtm) REVERT: F 68 MET cc_start: 0.8703 (mmm) cc_final: 0.8317 (mmm) REVERT: H 10 GLU cc_start: 0.8041 (tt0) cc_final: 0.7710 (mt-10) REVERT: H 100 ARG cc_start: 0.7766 (mmm-85) cc_final: 0.7374 (mmm-85) REVERT: H 106 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: L 4 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7631 (pp) REVERT: L 48 LEU cc_start: 0.7973 (tt) cc_final: 0.7763 (tp) REVERT: L 49 MET cc_start: 0.6102 (mmt) cc_final: 0.5733 (mmt) REVERT: L 71 SER cc_start: 0.8517 (m) cc_final: 0.8266 (p) REVERT: L 107 LEU cc_start: 0.6787 (tp) cc_final: 0.6558 (tt) REVERT: O 324 TYR cc_start: 0.8907 (t80) cc_final: 0.8668 (t80) REVERT: O 438 PHE cc_start: 0.8220 (m-80) cc_final: 0.7989 (m-10) REVERT: O 442 TYR cc_start: 0.9160 (t80) cc_final: 0.8746 (t80) REVERT: P 10 MET cc_start: 0.7877 (mmm) cc_final: 0.7532 (mmp) REVERT: P 17 GLN cc_start: 0.8740 (tt0) cc_final: 0.8491 (tt0) REVERT: Q 13 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7704 (tm-30) REVERT: Q 41 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8136 (pp) REVERT: Q 485 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8879 (mm) REVERT: R 52 TYR cc_start: 0.7906 (m-80) cc_final: 0.7555 (m-80) REVERT: S 49 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6793 (tp30) REVERT: S 297 TYR cc_start: 0.7848 (m-80) cc_final: 0.7453 (m-80) REVERT: S 400 PHE cc_start: 0.7856 (t80) cc_final: 0.7469 (t80) REVERT: T 20 MET cc_start: 0.9014 (mtm) cc_final: 0.8714 (mtm) REVERT: T 68 MET cc_start: 0.8719 (mmm) cc_final: 0.8327 (mmm) REVERT: U 10 GLU cc_start: 0.8047 (tt0) cc_final: 0.7721 (mt-10) REVERT: U 100 ARG cc_start: 0.7763 (mmm-85) cc_final: 0.7376 (mmm-85) REVERT: U 106 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: V 4 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7644 (pp) REVERT: V 48 LEU cc_start: 0.7977 (tt) cc_final: 0.7768 (tp) REVERT: V 49 MET cc_start: 0.6097 (mmt) cc_final: 0.5728 (mmt) REVERT: V 71 SER cc_start: 0.8514 (m) cc_final: 0.8264 (p) outliers start: 134 outliers final: 96 residues processed: 609 average time/residue: 0.3555 time to fit residues: 361.9315 Evaluate side-chains 586 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 482 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 363 VAL Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 205 MET Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 346 ASN Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 213 ASP Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 365 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 268 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 chunk 366 optimal weight: 8.9990 chunk 229 optimal weight: 10.0000 chunk 223 optimal weight: 0.7980 chunk 169 optimal weight: 8.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 GLN ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30572 Z= 0.326 Angle : 0.617 12.853 41418 Z= 0.317 Chirality : 0.046 0.239 4848 Planarity : 0.004 0.072 5162 Dihedral : 6.011 54.544 4632 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.69 % Allowed : 19.44 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 3838 helix: 1.71 (0.18), residues: 876 sheet: -1.52 (0.15), residues: 1122 loop : -1.26 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 50 HIS 0.008 0.001 HIS S 144 PHE 0.021 0.002 PHE Q 420 TYR 0.024 0.002 TYR U 27 ARG 0.004 0.001 ARG U 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 495 time to evaluate : 3.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.8269 (t-90) cc_final: 0.7757 (t-170) REVERT: A 324 TYR cc_start: 0.8863 (t80) cc_final: 0.8638 (t80) REVERT: A 438 PHE cc_start: 0.8271 (m-80) cc_final: 0.8034 (m-10) REVERT: A 442 TYR cc_start: 0.9181 (t80) cc_final: 0.8782 (t80) REVERT: B 10 MET cc_start: 0.8081 (mmm) cc_final: 0.7517 (mmp) REVERT: C 13 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7780 (tm-30) REVERT: C 41 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8296 (pp) REVERT: C 181 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7856 (pp) REVERT: C 485 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8807 (mm) REVERT: D 52 TYR cc_start: 0.7955 (m-80) cc_final: 0.7610 (m-80) REVERT: E 49 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7076 (tp30) REVERT: E 176 TYR cc_start: 0.8703 (m-80) cc_final: 0.8457 (m-80) REVERT: E 297 TYR cc_start: 0.7952 (m-80) cc_final: 0.7648 (m-80) REVERT: E 400 PHE cc_start: 0.7921 (t80) cc_final: 0.7443 (t80) REVERT: F 68 MET cc_start: 0.8774 (mmm) cc_final: 0.8413 (mmm) REVERT: H 10 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: H 106 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: L 4 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7797 (pp) REVERT: L 48 LEU cc_start: 0.8045 (tt) cc_final: 0.7714 (tt) REVERT: L 49 MET cc_start: 0.6160 (mmt) cc_final: 0.5809 (mmt) REVERT: L 71 SER cc_start: 0.8556 (m) cc_final: 0.8265 (p) REVERT: L 107 LEU cc_start: 0.7010 (tp) cc_final: 0.6791 (tp) REVERT: O 132 HIS cc_start: 0.8256 (t-90) cc_final: 0.7744 (t-170) REVERT: O 324 TYR cc_start: 0.8859 (t80) cc_final: 0.8635 (t80) REVERT: O 438 PHE cc_start: 0.8266 (m-80) cc_final: 0.8031 (m-10) REVERT: O 442 TYR cc_start: 0.9182 (t80) cc_final: 0.8782 (t80) REVERT: P 10 MET cc_start: 0.8040 (mmm) cc_final: 0.7634 (mmp) REVERT: Q 13 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7777 (tm-30) REVERT: Q 41 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8291 (pp) REVERT: Q 181 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7865 (pp) REVERT: Q 485 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8816 (mm) REVERT: R 52 TYR cc_start: 0.7948 (m-80) cc_final: 0.7605 (m-80) REVERT: S 49 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7070 (tp30) REVERT: S 176 TYR cc_start: 0.8705 (m-80) cc_final: 0.8462 (m-80) REVERT: S 297 TYR cc_start: 0.7945 (m-80) cc_final: 0.7649 (m-80) REVERT: S 400 PHE cc_start: 0.7915 (t80) cc_final: 0.7439 (t80) REVERT: T 68 MET cc_start: 0.8789 (mmm) cc_final: 0.8420 (mmm) REVERT: U 10 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: U 106 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: V 4 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7814 (pp) REVERT: V 48 LEU cc_start: 0.8050 (tt) cc_final: 0.7827 (tp) REVERT: V 49 MET cc_start: 0.6154 (mmt) cc_final: 0.5776 (mmt) REVERT: V 71 SER cc_start: 0.8559 (m) cc_final: 0.8262 (p) outliers start: 150 outliers final: 116 residues processed: 599 average time/residue: 0.3611 time to fit residues: 358.8877 Evaluate side-chains 598 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 470 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 363 VAL Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 168 THR Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 346 ASN Chi-restraints excluded: chain Q residue 394 SER Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 365 ILE Chi-restraints excluded: chain S residue 380 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 232 optimal weight: 0.6980 chunk 249 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 287 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 240 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 375 ASN ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 30572 Z= 0.398 Angle : 0.664 12.898 41418 Z= 0.341 Chirality : 0.047 0.251 4848 Planarity : 0.004 0.069 5162 Dihedral : 6.214 54.743 4632 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.06 % Allowed : 19.75 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3838 helix: 1.48 (0.18), residues: 876 sheet: -1.59 (0.14), residues: 1208 loop : -1.32 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP U 50 HIS 0.008 0.001 HIS E 144 PHE 0.025 0.002 PHE C 420 TYR 0.025 0.002 TYR U 27 ARG 0.007 0.001 ARG U 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 495 time to evaluate : 3.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.8326 (t-90) cc_final: 0.7828 (t-170) REVERT: A 324 TYR cc_start: 0.8871 (t80) cc_final: 0.8629 (t80) REVERT: A 438 PHE cc_start: 0.8315 (m-80) cc_final: 0.8078 (m-10) REVERT: A 442 TYR cc_start: 0.9190 (t80) cc_final: 0.8769 (t80) REVERT: B 10 MET cc_start: 0.8178 (mmm) cc_final: 0.7625 (mmp) REVERT: C 13 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7730 (tm-30) REVERT: C 41 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8360 (pp) REVERT: C 181 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8044 (pp) REVERT: C 485 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8867 (mm) REVERT: E 176 TYR cc_start: 0.8720 (m-80) cc_final: 0.8474 (m-80) REVERT: E 400 PHE cc_start: 0.7926 (t80) cc_final: 0.7437 (t80) REVERT: F 20 MET cc_start: 0.9076 (mtm) cc_final: 0.8774 (mtm) REVERT: F 68 MET cc_start: 0.8807 (mmm) cc_final: 0.8458 (mmm) REVERT: H 10 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: H 106 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: L 4 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7879 (pp) REVERT: L 37 TYR cc_start: 0.8241 (m-80) cc_final: 0.7995 (m-80) REVERT: L 49 MET cc_start: 0.6036 (mmt) cc_final: 0.5703 (mmt) REVERT: L 55 ARG cc_start: 0.8398 (mtm110) cc_final: 0.7949 (mtm110) REVERT: L 71 SER cc_start: 0.8595 (m) cc_final: 0.8272 (p) REVERT: L 107 LEU cc_start: 0.7083 (tp) cc_final: 0.6827 (tp) REVERT: O 132 HIS cc_start: 0.8315 (t-90) cc_final: 0.7820 (t-170) REVERT: O 324 TYR cc_start: 0.8868 (t80) cc_final: 0.8624 (t80) REVERT: O 438 PHE cc_start: 0.8313 (m-80) cc_final: 0.8075 (m-10) REVERT: O 442 TYR cc_start: 0.9194 (t80) cc_final: 0.8770 (t80) REVERT: P 10 MET cc_start: 0.8138 (mmm) cc_final: 0.7684 (mmp) REVERT: Q 13 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7803 (tm-30) REVERT: Q 41 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8369 (pp) REVERT: Q 181 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8047 (pp) REVERT: Q 485 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8880 (mm) REVERT: S 176 TYR cc_start: 0.8720 (m-80) cc_final: 0.8477 (m-80) REVERT: S 400 PHE cc_start: 0.7922 (t80) cc_final: 0.7436 (t80) REVERT: T 20 MET cc_start: 0.9052 (mtm) cc_final: 0.8765 (mtm) REVERT: T 68 MET cc_start: 0.8822 (mmm) cc_final: 0.8465 (mmm) REVERT: U 10 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: U 106 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: V 4 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7915 (pp) REVERT: V 37 TYR cc_start: 0.8242 (m-80) cc_final: 0.7989 (m-80) REVERT: V 48 LEU cc_start: 0.8023 (tt) cc_final: 0.7820 (tp) REVERT: V 49 MET cc_start: 0.6041 (mmt) cc_final: 0.5707 (mmt) REVERT: V 55 ARG cc_start: 0.8394 (mtm110) cc_final: 0.7947 (mtm110) REVERT: V 71 SER cc_start: 0.8605 (m) cc_final: 0.8277 (p) outliers start: 162 outliers final: 134 residues processed: 607 average time/residue: 0.3715 time to fit residues: 373.3170 Evaluate side-chains 626 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 480 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 125 ILE Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 363 VAL Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 168 THR Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 346 ASN Chi-restraints excluded: chain Q residue 394 SER Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 365 ILE Chi-restraints excluded: chain S residue 380 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 76 MET Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 0.6980 chunk 350 optimal weight: 0.9980 chunk 320 optimal weight: 7.9990 chunk 341 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 268 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 308 optimal weight: 8.9990 chunk 322 optimal weight: 1.9990 chunk 340 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30572 Z= 0.288 Angle : 0.616 13.044 41418 Z= 0.315 Chirality : 0.046 0.348 4848 Planarity : 0.004 0.063 5162 Dihedral : 6.090 54.409 4632 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 4.72 % Allowed : 20.56 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3838 helix: 1.57 (0.18), residues: 870 sheet: -1.66 (0.14), residues: 1166 loop : -1.33 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP U 50 HIS 0.006 0.001 HIS S 144 PHE 0.020 0.002 PHE Q 420 TYR 0.025 0.002 TYR H 27 ARG 0.007 0.001 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 500 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.8319 (t-90) cc_final: 0.7841 (t-170) REVERT: A 324 TYR cc_start: 0.8834 (t80) cc_final: 0.8627 (t80) REVERT: A 438 PHE cc_start: 0.8296 (m-80) cc_final: 0.8061 (m-10) REVERT: A 442 TYR cc_start: 0.9183 (t80) cc_final: 0.8777 (t80) REVERT: B 10 MET cc_start: 0.8116 (mmm) cc_final: 0.7540 (mmp) REVERT: B 17 GLN cc_start: 0.8781 (tt0) cc_final: 0.8553 (tt0) REVERT: C 13 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7670 (tm-30) REVERT: C 41 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8283 (pp) REVERT: C 485 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8866 (mm) REVERT: D 52 TYR cc_start: 0.7975 (m-80) cc_final: 0.7646 (m-80) REVERT: E 49 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7255 (tp30) REVERT: E 297 TYR cc_start: 0.7902 (m-80) cc_final: 0.7633 (m-80) REVERT: E 400 PHE cc_start: 0.7913 (t80) cc_final: 0.7433 (t80) REVERT: F 68 MET cc_start: 0.8784 (mmm) cc_final: 0.8424 (mmm) REVERT: H 10 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: H 106 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: L 4 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7722 (pp) REVERT: L 37 TYR cc_start: 0.8189 (m-80) cc_final: 0.7971 (m-80) REVERT: L 49 MET cc_start: 0.6013 (mmt) cc_final: 0.5615 (mmt) REVERT: L 55 ARG cc_start: 0.8429 (mtm110) cc_final: 0.7956 (mtm110) REVERT: L 71 SER cc_start: 0.8558 (m) cc_final: 0.8254 (p) REVERT: L 107 LEU cc_start: 0.6670 (tp) cc_final: 0.6432 (tp) REVERT: O 132 HIS cc_start: 0.8308 (t-90) cc_final: 0.7820 (t-170) REVERT: O 324 TYR cc_start: 0.8835 (t80) cc_final: 0.8626 (t80) REVERT: O 438 PHE cc_start: 0.8291 (m-80) cc_final: 0.8058 (m-10) REVERT: O 442 TYR cc_start: 0.9187 (t80) cc_final: 0.8781 (t80) REVERT: P 10 MET cc_start: 0.8065 (mmm) cc_final: 0.7667 (mmp) REVERT: Q 13 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7669 (tm-30) REVERT: Q 41 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8288 (pp) REVERT: Q 485 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8875 (mm) REVERT: R 52 TYR cc_start: 0.7967 (m-80) cc_final: 0.7639 (m-80) REVERT: S 49 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7238 (tp30) REVERT: S 297 TYR cc_start: 0.7897 (m-80) cc_final: 0.7630 (m-80) REVERT: S 400 PHE cc_start: 0.7911 (t80) cc_final: 0.7432 (t80) REVERT: T 68 MET cc_start: 0.8802 (mmm) cc_final: 0.8433 (mmm) REVERT: U 10 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: U 106 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: V 4 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7869 (pp) REVERT: V 37 TYR cc_start: 0.8206 (m-80) cc_final: 0.7967 (m-80) REVERT: V 49 MET cc_start: 0.6164 (mmt) cc_final: 0.5808 (mmt) REVERT: V 55 ARG cc_start: 0.8381 (mtm110) cc_final: 0.7935 (mtm110) REVERT: V 71 SER cc_start: 0.8575 (m) cc_final: 0.8257 (p) outliers start: 151 outliers final: 124 residues processed: 605 average time/residue: 0.3678 time to fit residues: 369.2123 Evaluate side-chains 622 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 488 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 125 ILE Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 363 VAL Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 168 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 346 ASN Chi-restraints excluded: chain Q residue 394 SER Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 213 ASP Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 365 ILE Chi-restraints excluded: chain S residue 380 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 20.0000 chunk 360 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 378 optimal weight: 9.9990 chunk 348 optimal weight: 0.9990 chunk 301 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 232 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30572 Z= 0.200 Angle : 0.577 13.106 41418 Z= 0.293 Chirality : 0.044 0.249 4848 Planarity : 0.003 0.065 5162 Dihedral : 5.839 54.044 4632 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.06 % Allowed : 21.44 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 3838 helix: 1.82 (0.18), residues: 876 sheet: -1.54 (0.15), residues: 1076 loop : -1.22 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 50 HIS 0.003 0.001 HIS A 144 PHE 0.015 0.001 PHE Q 420 TYR 0.023 0.002 TYR U 27 ARG 0.007 0.000 ARG U 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 516 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.8311 (t-90) cc_final: 0.7804 (t-170) REVERT: A 324 TYR cc_start: 0.8835 (t80) cc_final: 0.8625 (t80) REVERT: A 364 ASN cc_start: 0.8951 (m-40) cc_final: 0.8670 (m110) REVERT: A 438 PHE cc_start: 0.8255 (m-80) cc_final: 0.8020 (m-10) REVERT: A 442 TYR cc_start: 0.9165 (t80) cc_final: 0.8766 (t80) REVERT: B 10 MET cc_start: 0.7999 (mmm) cc_final: 0.7511 (mmp) REVERT: B 17 GLN cc_start: 0.8776 (tt0) cc_final: 0.8565 (tt0) REVERT: C 13 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 41 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8270 (pp) REVERT: C 485 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8876 (mm) REVERT: D 52 TYR cc_start: 0.7930 (m-80) cc_final: 0.7629 (m-80) REVERT: E 91 VAL cc_start: 0.8969 (p) cc_final: 0.8686 (p) REVERT: E 297 TYR cc_start: 0.7987 (m-80) cc_final: 0.7781 (m-80) REVERT: E 400 PHE cc_start: 0.7892 (t80) cc_final: 0.7452 (t80) REVERT: F 68 MET cc_start: 0.8747 (mmm) cc_final: 0.8371 (mmm) REVERT: H 10 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: H 47 TRP cc_start: 0.9132 (t60) cc_final: 0.8727 (t60) REVERT: H 63 ARG cc_start: 0.8749 (ttt90) cc_final: 0.8403 (tmm-80) REVERT: H 106 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: L 4 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7623 (pp) REVERT: L 37 TYR cc_start: 0.8114 (m-80) cc_final: 0.7840 (m-80) REVERT: L 49 MET cc_start: 0.6365 (mmt) cc_final: 0.5793 (mmt) REVERT: L 71 SER cc_start: 0.8608 (m) cc_final: 0.8324 (p) REVERT: L 107 LEU cc_start: 0.6565 (tp) cc_final: 0.6333 (tp) REVERT: O 324 TYR cc_start: 0.8834 (t80) cc_final: 0.8623 (t80) REVERT: O 364 ASN cc_start: 0.8947 (m-40) cc_final: 0.8669 (m110) REVERT: O 438 PHE cc_start: 0.8254 (m-80) cc_final: 0.8021 (m-10) REVERT: O 442 TYR cc_start: 0.9170 (t80) cc_final: 0.8766 (t80) REVERT: P 10 MET cc_start: 0.7896 (mmm) cc_final: 0.7581 (mmp) REVERT: P 17 GLN cc_start: 0.8776 (tt0) cc_final: 0.8562 (tt0) REVERT: Q 13 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7567 (tm-30) REVERT: Q 41 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8270 (pp) REVERT: Q 485 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8884 (mm) REVERT: R 52 TYR cc_start: 0.7926 (m-80) cc_final: 0.7627 (m-80) REVERT: S 91 VAL cc_start: 0.8962 (p) cc_final: 0.8678 (p) REVERT: S 297 TYR cc_start: 0.7986 (m-80) cc_final: 0.7785 (m-80) REVERT: S 400 PHE cc_start: 0.7888 (t80) cc_final: 0.7449 (t80) REVERT: T 68 MET cc_start: 0.8763 (mmm) cc_final: 0.8379 (mmm) REVERT: U 10 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: U 47 TRP cc_start: 0.9135 (t60) cc_final: 0.8733 (t60) REVERT: U 63 ARG cc_start: 0.8747 (ttt90) cc_final: 0.8403 (tmm-80) REVERT: U 106 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: V 4 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7652 (pp) REVERT: V 37 TYR cc_start: 0.8110 (m-80) cc_final: 0.7835 (m-80) REVERT: V 49 MET cc_start: 0.6356 (mmt) cc_final: 0.5861 (mmt) REVERT: V 55 ARG cc_start: 0.8498 (mtm110) cc_final: 0.8037 (mtm110) REVERT: V 71 SER cc_start: 0.8615 (m) cc_final: 0.8337 (p) outliers start: 130 outliers final: 108 residues processed: 605 average time/residue: 0.3642 time to fit residues: 363.8156 Evaluate side-chains 608 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 490 time to evaluate : 3.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 363 VAL Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 168 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 346 ASN Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 380 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 8.9990 chunk 321 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 277 optimal weight: 0.0050 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 301 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 310 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.113664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100535 restraints weight = 42204.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.103076 restraints weight = 28798.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.104245 restraints weight = 17191.518| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30572 Z= 0.155 Angle : 0.558 13.050 41418 Z= 0.283 Chirality : 0.043 0.212 4848 Planarity : 0.003 0.060 5162 Dihedral : 5.609 53.806 4632 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.81 % Allowed : 21.72 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 3838 helix: 2.22 (0.18), residues: 810 sheet: -1.37 (0.16), residues: 1052 loop : -1.18 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 50 HIS 0.004 0.001 HIS A 144 PHE 0.015 0.001 PHE F 42 TYR 0.019 0.001 TYR U 27 ARG 0.007 0.000 ARG U 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6681.89 seconds wall clock time: 120 minutes 31.93 seconds (7231.93 seconds total)