Starting phenix.real_space_refine on Sun Mar 17 22:32:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdy_10471/03_2024/6tdy_10471_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdy_10471/03_2024/6tdy_10471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdy_10471/03_2024/6tdy_10471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdy_10471/03_2024/6tdy_10471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdy_10471/03_2024/6tdy_10471_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdy_10471/03_2024/6tdy_10471_trim_updated.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 7 Type Number sf(0) Gaussians P 14 5.49 5 Mg 5 5.21 5 S 238 5.16 5 C 25879 2.51 5 N 6774 2.21 5 O 7694 1.98 5 H 41111 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 179": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 418": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 223": "OD1" <-> "OD2" Residue "M ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ASP 37": "OD1" <-> "OD2" Residue "c TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 81715 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 8292 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 504} Chain breaks: 1 Chain: "B" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 8292 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 504} Chain breaks: 1 Chain: "C" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 8336 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 508} Chain breaks: 1 Chain: "D" Number of atoms: 7407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7407 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain: "E" Number of atoms: 7408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7408 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 466} Chain: "F" Number of atoms: 7407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7407 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain: "G" Number of atoms: 4898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4898 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 5, 'TRANS': 297} Chain: "H" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2448 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "I" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1077 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "J" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "L" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "M" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3778 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 14, 'TRANS': 228} Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 802 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "O" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "P" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "Q" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "R" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "S" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "T" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "U" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "V" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "W" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "X" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "h" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 807 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "c" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 944 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'TRT': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.35, per 1000 atoms: 0.33 Number of scatterers: 81715 At special positions: 0 Unit cell: (159.6, 174.3, 236.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 238 16.00 P 14 15.00 Mg 5 11.99 O 7694 8.00 N 6774 7.00 C 25879 6.00 H 41111 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 56.80 Conformation dependent library (CDL) restraints added in 7.5 seconds 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 207 helices and 27 sheets defined 48.3% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.08 Creating SS restraints... Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 190 through 207 removed outlier: 3.840A pdb=" N ILE A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 removed outlier: 3.643A pdb=" N ALA A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 255 through 258 No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.984A pdb=" N GLU A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.540A pdb=" N VAL A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.583A pdb=" N HIS A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 360 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 396 through 416 removed outlier: 4.241A pdb=" N LYS A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.503A pdb=" N VAL A 453 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 503 through 509 removed outlier: 3.806A pdb=" N TYR A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 540 Proline residue: A 518 - end of helix removed outlier: 4.447A pdb=" N GLN A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN A 540 " --> pdb=" O GLN A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.614A pdb=" N LEU A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG A 560 " --> pdb=" O TYR A 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 190 through 207 removed outlier: 3.583A pdb=" N ALA B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 204 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 238 Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 255 through 274 Proline residue: B 262 - end of helix removed outlier: 3.672A pdb=" N GLU B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.733A pdb=" N VAL B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 321 removed outlier: 3.724A pdb=" N HIS B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 358 Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 396 through 418 removed outlier: 3.902A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 440 removed outlier: 3.573A pdb=" N GLN B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 460 removed outlier: 3.587A pdb=" N VAL B 453 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 502 through 509 removed outlier: 4.637A pdb=" N ARG B 507 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 509 " --> pdb=" O ILE B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 541 Proline residue: B 518 - end of helix removed outlier: 4.302A pdb=" N GLN B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 538 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 561 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 190 through 207 removed outlier: 3.929A pdb=" N ALA C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LYS C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 237 Processing helix chain 'C' and resid 255 through 274 Proline residue: C 262 - end of helix removed outlier: 4.115A pdb=" N GLU C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 removed outlier: 3.677A pdb=" N SER C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR C 293 " --> pdb=" O GLN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 313 through 321 removed outlier: 3.631A pdb=" N HIS C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 352 through 358 Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 390 through 392 No H-bonds generated for 'chain 'C' and resid 390 through 392' Processing helix chain 'C' and resid 396 through 412 removed outlier: 3.912A pdb=" N LYS C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 440 removed outlier: 3.856A pdb=" N ALA C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 460 removed outlier: 3.759A pdb=" N VAL C 453 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 457 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 480 removed outlier: 4.762A pdb=" N LYS C 472 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE C 473 " --> pdb=" O TYR C 470 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR C 474 " --> pdb=" O SER C 471 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN C 480 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 487 Processing helix chain 'C' and resid 503 through 509 Processing helix chain 'C' and resid 514 through 541 Proline residue: C 518 - end of helix removed outlier: 5.348A pdb=" N ILE C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLN C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 538 " --> pdb=" O ASN C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 561 Processing helix chain 'D' and resid 151 through 154 No H-bonds generated for 'chain 'D' and resid 151 through 154' Processing helix chain 'D' and resid 173 through 187 removed outlier: 4.462A pdb=" N LYS D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 213 removed outlier: 3.803A pdb=" N THR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 239 No H-bonds generated for 'chain 'D' and resid 236 through 239' Processing helix chain 'D' and resid 243 through 255 removed outlier: 3.738A pdb=" N TYR D 252 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE D 253 " --> pdb=" O MET D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 282 removed outlier: 3.555A pdb=" N THR D 272 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN D 275 " --> pdb=" O PHE D 271 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA D 280 " --> pdb=" O SER D 276 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 290 No H-bonds generated for 'chain 'D' and resid 288 through 290' Processing helix chain 'D' and resid 295 through 303 removed outlier: 3.695A pdb=" N LEU D 302 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 330 through 338 removed outlier: 4.515A pdb=" N SER D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS D 338 " --> pdb=" O THR D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 375 through 398 removed outlier: 3.678A pdb=" N LYS D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 397 " --> pdb=" O GLU D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 408 through 423 removed outlier: 3.642A pdb=" N ILE D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS D 422 " --> pdb=" O ARG D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 435 removed outlier: 3.532A pdb=" N GLU D 432 " --> pdb=" O ALA D 429 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL D 433 " --> pdb=" O VAL D 430 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 435 " --> pdb=" O GLU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 474 through 500 removed outlier: 3.597A pdb=" N GLU D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET D 490 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 52 No H-bonds generated for 'chain 'E' and resid 49 through 52' Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 149 through 154 removed outlier: 3.638A pdb=" N ILE E 154 " --> pdb=" O VAL E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 186 Processing helix chain 'E' and resid 201 through 208 removed outlier: 3.761A pdb=" N THR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 213 No H-bonds generated for 'chain 'E' and resid 210 through 213' Processing helix chain 'E' and resid 236 through 241 removed outlier: 4.055A pdb=" N ARG E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 255 removed outlier: 3.599A pdb=" N TYR E 252 " --> pdb=" O THR E 248 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE E 253 " --> pdb=" O MET E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 282 removed outlier: 3.582A pdb=" N ALA E 274 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN E 275 " --> pdb=" O PHE E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 305 removed outlier: 3.793A pdb=" N LEU E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG E 305 " --> pdb=" O MET E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 325 No H-bonds generated for 'chain 'E' and resid 323 through 325' Processing helix chain 'E' and resid 330 through 336 Processing helix chain 'E' and resid 347 through 351 Processing helix chain 'E' and resid 375 through 398 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 408 through 424 removed outlier: 3.662A pdb=" N LEU E 412 " --> pdb=" O GLU E 408 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE E 413 " --> pdb=" O GLU E 409 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG E 418 " --> pdb=" O VAL E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 Processing helix chain 'E' and resid 465 through 467 No H-bonds generated for 'chain 'E' and resid 465 through 467' Processing helix chain 'E' and resid 473 through 500 removed outlier: 3.776A pdb=" N LYS E 477 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 52 No H-bonds generated for 'chain 'F' and resid 49 through 52' Processing helix chain 'F' and resid 99 through 101 No H-bonds generated for 'chain 'F' and resid 99 through 101' Processing helix chain 'F' and resid 149 through 153 removed outlier: 3.562A pdb=" N LEU F 153 " --> pdb=" O LYS F 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 149 through 153' Processing helix chain 'F' and resid 173 through 183 Processing helix chain 'F' and resid 201 through 213 Processing helix chain 'F' and resid 236 through 239 No H-bonds generated for 'chain 'F' and resid 236 through 239' Processing helix chain 'F' and resid 243 through 255 removed outlier: 3.601A pdb=" N MET F 249 " --> pdb=" O THR F 245 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE F 253 " --> pdb=" O MET F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 282 removed outlier: 3.665A pdb=" N LEU F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.675A pdb=" N LEU F 302 " --> pdb=" O ASP F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 330 through 338 removed outlier: 4.598A pdb=" N SER F 337 " --> pdb=" O ALA F 333 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS F 338 " --> pdb=" O THR F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 351 No H-bonds generated for 'chain 'F' and resid 348 through 351' Processing helix chain 'F' and resid 375 through 398 removed outlier: 3.605A pdb=" N GLU F 393 " --> pdb=" O THR F 389 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP F 396 " --> pdb=" O LYS F 392 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE F 397 " --> pdb=" O GLU F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 405 No H-bonds generated for 'chain 'F' and resid 403 through 405' Processing helix chain 'F' and resid 408 through 424 removed outlier: 3.831A pdb=" N LYS F 419 " --> pdb=" O ASP F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 435 No H-bonds generated for 'chain 'F' and resid 432 through 435' Processing helix chain 'F' and resid 444 through 455 removed outlier: 3.748A pdb=" N SER F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP F 450 " --> pdb=" O ASP F 446 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE F 451 " --> pdb=" O CYS F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 467 No H-bonds generated for 'chain 'F' and resid 465 through 467' Processing helix chain 'F' and resid 473 through 500 removed outlier: 3.528A pdb=" N ARG F 491 " --> pdb=" O ALA F 487 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 44 removed outlier: 3.762A pdb=" N GLN G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ARG G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG G 43 " --> pdb=" O VAL G 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 44 " --> pdb=" O VAL G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 56 Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.874A pdb=" N GLU G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 99 removed outlier: 3.698A pdb=" N LEU G 96 " --> pdb=" O MET G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 120 removed outlier: 4.201A pdb=" N ASP G 115 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET G 117 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR G 118 " --> pdb=" O ASP G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.529A pdb=" N HIS G 148 " --> pdb=" O TYR G 144 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 192 removed outlier: 3.818A pdb=" N GLN G 185 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 214 removed outlier: 3.709A pdb=" N GLY G 213 " --> pdb=" O LYS G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 294 removed outlier: 4.086A pdb=" N ILE G 248 " --> pdb=" O TYR G 244 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL G 249 " --> pdb=" O ALA G 245 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 30 removed outlier: 3.527A pdb=" N PHE H 30 " --> pdb=" O GLY H 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 27 through 30' Processing helix chain 'H' and resid 131 through 133 No H-bonds generated for 'chain 'H' and resid 131 through 133' Processing helix chain 'H' and resid 136 through 151 removed outlier: 3.760A pdb=" N LYS H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU H 145 " --> pdb=" O LYS H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 175 removed outlier: 4.048A pdb=" N ILE H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) Proline residue: H 170 - end of helix Processing helix chain 'I' and resid 10 through 24 Processing helix chain 'I' and resid 29 through 34 Processing helix chain 'J' and resid 40 through 47 removed outlier: 3.603A pdb=" N GLU J 44 " --> pdb=" O GLY J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 64 removed outlier: 3.921A pdb=" N VAL J 60 " --> pdb=" O GLY J 56 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 83 Processing helix chain 'J' and resid 97 through 109 Processing helix chain 'J' and resid 118 through 131 removed outlier: 4.350A pdb=" N TYR J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU J 128 " --> pdb=" O VAL J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 144 Processing helix chain 'J' and resid 153 through 168 Processing helix chain 'K' and resid 40 through 47 removed outlier: 3.609A pdb=" N GLU K 45 " --> pdb=" O PRO K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 63 removed outlier: 3.935A pdb=" N GLY K 56 " --> pdb=" O TYR K 52 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 83 removed outlier: 3.585A pdb=" N ALA K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 109 removed outlier: 3.719A pdb=" N MET K 101 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU K 105 " --> pdb=" O MET K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 131 removed outlier: 3.566A pdb=" N VAL K 124 " --> pdb=" O SER K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 146 removed outlier: 3.645A pdb=" N VAL K 139 " --> pdb=" O ARG K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 168 removed outlier: 3.576A pdb=" N ALA K 158 " --> pdb=" O ALA K 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 47 removed outlier: 3.851A pdb=" N GLU L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 65 removed outlier: 3.737A pdb=" N ALA L 65 " --> pdb=" O LYS L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 83 Processing helix chain 'L' and resid 97 through 109 removed outlier: 3.917A pdb=" N MET L 101 " --> pdb=" O LYS L 97 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU L 106 " --> pdb=" O MET L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 131 removed outlier: 3.638A pdb=" N GLU L 127 " --> pdb=" O TYR L 123 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU L 128 " --> pdb=" O VAL L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 147 removed outlier: 3.635A pdb=" N TRP L 138 " --> pdb=" O PHE L 134 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS L 145 " --> pdb=" O ILE L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 168 removed outlier: 3.570A pdb=" N ALA L 158 " --> pdb=" O ALA L 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 32 removed outlier: 3.696A pdb=" N ILE M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.890A pdb=" N LEU M 56 " --> pdb=" O PHE M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 85 removed outlier: 3.754A pdb=" N PHE M 75 " --> pdb=" O VAL M 72 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 102 removed outlier: 4.020A pdb=" N GLY M 102 " --> pdb=" O THR M 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 99 through 102' Processing helix chain 'M' and resid 105 through 117 Processing helix chain 'M' and resid 120 through 122 No H-bonds generated for 'chain 'M' and resid 120 through 122' Processing helix chain 'M' and resid 124 through 137 removed outlier: 3.895A pdb=" N ALA M 129 " --> pdb=" O ASN M 125 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU M 132 " --> pdb=" O LEU M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 169 removed outlier: 4.115A pdb=" N LYS M 161 " --> pdb=" O ALA M 157 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN M 162 " --> pdb=" O GLU M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 221 removed outlier: 3.728A pdb=" N ALA M 209 " --> pdb=" O ALA M 205 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU M 214 " --> pdb=" O GLU M 210 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA M 215 " --> pdb=" O THR M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 245 Processing helix chain 'M' and resid 250 through 262 Processing helix chain 'N' and resid 45 through 67 removed outlier: 3.581A pdb=" N ALA N 57 " --> pdb=" O ASP N 53 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 46 removed outlier: 4.050A pdb=" N ILE O 37 " --> pdb=" O ALA O 34 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLY O 38 " --> pdb=" O ASN O 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY O 40 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA O 42 " --> pdb=" O ALA O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 66 removed outlier: 3.674A pdb=" N PHE O 57 " --> pdb=" O VAL O 53 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER O 59 " --> pdb=" O MET O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 98 removed outlier: 4.207A pdb=" N ALA O 72 " --> pdb=" O ASN O 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU O 74 " --> pdb=" O SER O 71 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU O 75 " --> pdb=" O ALA O 72 " (cutoff:3.500A) Proline residue: O 76 - end of helix removed outlier: 3.559A pdb=" N SER O 85 " --> pdb=" O PHE O 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 45 removed outlier: 3.769A pdb=" N ILE P 37 " --> pdb=" O ALA P 34 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY P 38 " --> pdb=" O ASN P 35 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA P 39 " --> pdb=" O LEU P 36 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA P 42 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER P 44 " --> pdb=" O MET P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 66 removed outlier: 4.024A pdb=" N GLY P 52 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET P 55 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS P 56 " --> pdb=" O GLY P 52 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE P 57 " --> pdb=" O VAL P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 98 removed outlier: 4.201A pdb=" N ALA P 72 " --> pdb=" O ASN P 69 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU P 74 " --> pdb=" O SER P 71 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU P 75 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 4.004A pdb=" N LEU P 80 " --> pdb=" O TYR P 77 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA P 83 " --> pdb=" O LEU P 80 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU P 84 " --> pdb=" O GLY P 81 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU P 86 " --> pdb=" O ALA P 83 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU P 88 " --> pdb=" O SER P 85 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE P 95 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA P 96 " --> pdb=" O LEU P 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 46 removed outlier: 4.128A pdb=" N ILE Q 37 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY Q 38 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA Q 42 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 66 removed outlier: 3.877A pdb=" N GLY Q 52 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET Q 55 " --> pdb=" O ILE Q 51 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS Q 56 " --> pdb=" O GLY Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 70 No H-bonds generated for 'chain 'Q' and resid 68 through 70' Processing helix chain 'Q' and resid 75 through 98 removed outlier: 4.018A pdb=" N PHE Q 82 " --> pdb=" O CYS Q 78 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU Q 84 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER Q 85 " --> pdb=" O GLY Q 81 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA Q 89 " --> pdb=" O SER Q 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 45 removed outlier: 4.078A pdb=" N ILE R 37 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY R 38 " --> pdb=" O ASN R 35 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA R 42 " --> pdb=" O ALA R 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA R 43 " --> pdb=" O GLY R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 66 removed outlier: 4.105A pdb=" N GLY R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS R 56 " --> pdb=" O GLY R 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE R 57 " --> pdb=" O VAL R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 98 removed outlier: 4.041A pdb=" N ALA R 72 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU R 74 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU R 75 " --> pdb=" O ALA R 72 " (cutoff:3.500A) Proline residue: R 76 - end of helix removed outlier: 3.866A pdb=" N ILE R 79 " --> pdb=" O PRO R 76 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU R 80 " --> pdb=" O TYR R 77 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY R 81 " --> pdb=" O CYS R 78 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA R 83 " --> pdb=" O LEU R 80 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU R 84 " --> pdb=" O GLY R 81 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER R 85 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA R 87 " --> pdb=" O LEU R 84 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU R 88 " --> pdb=" O SER R 85 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE R 95 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA R 96 " --> pdb=" O LEU R 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 45 removed outlier: 4.374A pdb=" N GLY S 38 " --> pdb=" O ASN S 35 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA S 39 " --> pdb=" O LEU S 36 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA S 42 " --> pdb=" O ALA S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 66 removed outlier: 4.390A pdb=" N GLY S 52 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS S 56 " --> pdb=" O GLY S 52 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE S 57 " --> pdb=" O VAL S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 98 removed outlier: 4.169A pdb=" N ALA S 72 " --> pdb=" O ASN S 69 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU S 74 " --> pdb=" O SER S 71 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU S 75 " --> pdb=" O ALA S 72 " (cutoff:3.500A) Proline residue: S 76 - end of helix removed outlier: 3.871A pdb=" N ILE S 79 " --> pdb=" O PRO S 76 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU S 80 " --> pdb=" O TYR S 77 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA S 83 " --> pdb=" O LEU S 80 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU S 84 " --> pdb=" O GLY S 81 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA S 87 " --> pdb=" O LEU S 84 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU S 88 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU S 94 " --> pdb=" O PHE S 91 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE S 95 " --> pdb=" O THR S 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 35 Processing helix chain 'T' and resid 39 through 46 Processing helix chain 'T' and resid 48 through 66 removed outlier: 4.627A pdb=" N ALA T 54 " --> pdb=" O ILE T 51 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER T 58 " --> pdb=" O MET T 55 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET T 61 " --> pdb=" O SER T 58 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA T 63 " --> pdb=" O TYR T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 71 No H-bonds generated for 'chain 'T' and resid 69 through 71' Processing helix chain 'T' and resid 75 through 98 Processing helix chain 'U' and resid 32 through 43 removed outlier: 3.869A pdb=" N ILE U 37 " --> pdb=" O ALA U 34 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLY U 38 " --> pdb=" O ASN U 35 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA U 39 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA U 42 " --> pdb=" O ALA U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 47 No H-bonds generated for 'chain 'U' and resid 45 through 47' Processing helix chain 'U' and resid 49 through 66 Processing helix chain 'U' and resid 68 through 98 removed outlier: 4.050A pdb=" N ALA U 72 " --> pdb=" O ASN U 69 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU U 75 " --> pdb=" O ALA U 72 " (cutoff:3.500A) Proline residue: U 76 - end of helix removed outlier: 3.779A pdb=" N PHE U 82 " --> pdb=" O ILE U 79 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU U 84 " --> pdb=" O GLY U 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 46 removed outlier: 3.887A pdb=" N ILE V 37 " --> pdb=" O ALA V 34 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY V 38 " --> pdb=" O ASN V 35 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA V 42 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER V 44 " --> pdb=" O MET V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 66 removed outlier: 3.714A pdb=" N ILE V 51 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL V 53 " --> pdb=" O ALA V 50 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER V 58 " --> pdb=" O MET V 55 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU V 62 " --> pdb=" O SER V 59 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 98 removed outlier: 4.430A pdb=" N ALA V 72 " --> pdb=" O ASN V 69 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU V 74 " --> pdb=" O SER V 71 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU V 75 " --> pdb=" O ALA V 72 " (cutoff:3.500A) Proline residue: V 76 - end of helix removed outlier: 4.284A pdb=" N ILE V 79 " --> pdb=" O PRO V 76 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU V 80 " --> pdb=" O TYR V 77 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE V 82 " --> pdb=" O ILE V 79 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU V 84 " --> pdb=" O GLY V 81 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU V 88 " --> pdb=" O SER V 85 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE V 91 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR V 92 " --> pdb=" O ALA V 89 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE V 95 " --> pdb=" O THR V 92 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA V 96 " --> pdb=" O LEU V 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 45 removed outlier: 3.996A pdb=" N ILE W 37 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY W 38 " --> pdb=" O ASN W 35 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA W 42 " --> pdb=" O ALA W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 66 removed outlier: 3.505A pdb=" N SER W 59 " --> pdb=" O MET W 55 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 98 removed outlier: 4.184A pdb=" N ALA W 72 " --> pdb=" O ASN W 69 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU W 74 " --> pdb=" O SER W 71 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU W 75 " --> pdb=" O ALA W 72 " (cutoff:3.500A) Proline residue: W 76 - end of helix removed outlier: 3.534A pdb=" N ILE W 79 " --> pdb=" O PRO W 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 46 removed outlier: 3.856A pdb=" N ILE X 37 " --> pdb=" O ALA X 34 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLY X 38 " --> pdb=" O ASN X 35 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA X 42 " --> pdb=" O ALA X 39 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER X 44 " --> pdb=" O MET X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 66 removed outlier: 4.070A pdb=" N ALA X 54 " --> pdb=" O ILE X 51 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER X 59 " --> pdb=" O CYS X 56 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET X 61 " --> pdb=" O SER X 58 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA X 63 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 71 through 74 No H-bonds generated for 'chain 'X' and resid 71 through 74' Processing helix chain 'X' and resid 76 through 98 removed outlier: 4.364A pdb=" N GLY X 81 " --> pdb=" O TYR X 77 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE X 82 " --> pdb=" O CYS X 78 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU X 88 " --> pdb=" O LEU X 84 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE X 95 " --> pdb=" O PHE X 91 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA X 96 " --> pdb=" O THR X 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 282 through 292 Processing helix chain 'h' and resid 294 through 297 No H-bonds generated for 'chain 'h' and resid 294 through 297' Processing helix chain 'h' and resid 300 through 306 Processing helix chain 'h' and resid 310 through 328 removed outlier: 3.710A pdb=" N TYR h 320 " --> pdb=" O LYS h 316 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU h 321 " --> pdb=" O ARG h 317 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR h 322 " --> pdb=" O ASP h 318 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 24 Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 37 through 43 Processing helix chain 'c' and resid 79 through 87 Processing helix chain 'c' and resid 90 through 96 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.644A pdb=" N GLY A 30 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA A 99 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS A 28 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR A 41 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 105 through 107 Processing sheet with id= C, first strand: chain 'A' and resid 364 through 366 removed outlier: 5.997A pdb=" N LEU A 181 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 184 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 217 through 221 removed outlier: 6.587A pdb=" N THR A 245 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N SER A 220 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 247 " --> pdb=" O SER A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.683A pdb=" N GLY A 81 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.666A pdb=" N THR B 41 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 73 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE B 83 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL B 71 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 57 through 59 Processing sheet with id= H, first strand: chain 'B' and resid 105 through 107 Processing sheet with id= I, first strand: chain 'B' and resid 245 through 249 removed outlier: 6.544A pdb=" N LEU B 280 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL B 219 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 282 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE B 221 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASP B 284 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR B 337 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N TYR B 283 " --> pdb=" O THR B 337 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU B 339 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.672A pdb=" N GLY C 30 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA C 99 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LYS C 28 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR C 41 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE C 39 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 80 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 83 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL C 71 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 116 through 118 removed outlier: 6.238A pdb=" N ILE C 246 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 364 through 367 removed outlier: 7.008A pdb=" N LEU C 181 " --> pdb=" O ILE C 365 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU C 367 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 183 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 184 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 19 through 21 Processing sheet with id= N, first strand: chain 'D' and resid 22 through 26 removed outlier: 6.605A pdb=" N ASP D 31 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE D 25 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL D 29 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN D 62 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE D 72 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE D 60 " --> pdb=" O ILE D 72 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 341 through 344 removed outlier: 7.545A pdb=" N ILE D 163 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER D 316 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU D 165 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN D 318 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLY D 167 " --> pdb=" O GLN D 318 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL D 320 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 263 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR D 191 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N PHE D 264 " --> pdb=" O TYR D 191 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL D 193 " --> pdb=" O PHE D 264 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ASP D 266 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA D 195 " --> pdb=" O ASP D 266 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 85 through 87 removed outlier: 6.655A pdb=" N ASP E 31 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE E 25 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL E 29 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 44 through 47 removed outlier: 3.643A pdb=" N LEU E 56 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG E 70 " --> pdb=" O VAL E 61 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 316 through 319 removed outlier: 6.555A pdb=" N ALA E 341 " --> pdb=" O GLY E 164 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE E 166 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR E 343 " --> pdb=" O PHE E 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 192 through 199 Processing sheet with id= T, first strand: chain 'F' and resid 19 through 21 Processing sheet with id= U, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.116A pdb=" N ILE F 72 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE F 60 " --> pdb=" O ILE F 72 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 94 through 96 Processing sheet with id= W, first strand: chain 'F' and resid 341 through 344 removed outlier: 7.740A pdb=" N ILE F 163 " --> pdb=" O ILE F 314 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER F 316 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU F 165 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN F 318 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 74 through 77 removed outlier: 6.428A pdb=" N SER G 169 " --> pdb=" O HIS G 165 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 62 through 64 removed outlier: 3.867A pdb=" N ALA H 113 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN H 87 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 75 through 78 removed outlier: 4.285A pdb=" N ARG H 70 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE H 93 " --> pdb=" O ARG H 70 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 176 through 182 1574 hydrogen bonds defined for protein. 3972 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: 29.41 Time building geometry restraints manager: 59.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.75 - 0.96: 18266 0.96 - 1.18: 22778 1.18 - 1.39: 16181 1.39 - 1.60: 24755 1.60 - 1.81: 422 Bond restraints: 82402 Sorted by residual: bond pdb=" C4 ATP F 601 " pdb=" C5 ATP F 601 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.01e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.86e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.79e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.39e+01 bond pdb=" C5 ATP F 601 " pdb=" C6 ATP F 601 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.77e+01 ... (remaining 82397 not shown) Histogram of bond angle deviations from ideal: 93.44 - 102.74: 238 102.74 - 112.04: 96704 112.04 - 121.33: 36671 121.33 - 130.63: 15707 130.63 - 139.93: 100 Bond angle restraints: 149420 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 117.81 22.06 1.00e+00 1.00e+00 4.87e+02 angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 119.09 20.78 1.00e+00 1.00e+00 4.32e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.31 20.56 1.00e+00 1.00e+00 4.23e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.02 19.85 1.00e+00 1.00e+00 3.94e+02 angle pdb=" PA ATP F 601 " pdb=" O3A ATP F 601 " pdb=" PB ATP F 601 " ideal model delta sigma weight residual 136.83 121.03 15.80 1.00e+00 1.00e+00 2.50e+02 ... (remaining 149415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 37378 23.98 - 47.97: 1037 47.97 - 71.95: 272 71.95 - 95.94: 8 95.94 - 119.92: 2 Dihedral angle restraints: 38697 sinusoidal: 21369 harmonic: 17328 Sorted by residual: dihedral pdb=" CA ASP C 284 " pdb=" C ASP C 284 " pdb=" N ASP C 285 " pdb=" CA ASP C 285 " ideal model delta harmonic sigma weight residual -180.00 -139.85 -40.15 0 5.00e+00 4.00e-02 6.45e+01 dihedral pdb=" CA ALA F 288 " pdb=" C ALA F 288 " pdb=" N VAL F 289 " pdb=" CA VAL F 289 " ideal model delta harmonic sigma weight residual -180.00 -144.86 -35.14 0 5.00e+00 4.00e-02 4.94e+01 dihedral pdb=" CA ASP E 266 " pdb=" C ASP E 266 " pdb=" N ASN E 267 " pdb=" CA ASN E 267 " ideal model delta harmonic sigma weight residual 180.00 -147.33 -32.67 0 5.00e+00 4.00e-02 4.27e+01 ... (remaining 38694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.255: 6503 0.255 - 0.510: 1 0.510 - 0.765: 0 0.765 - 1.020: 0 1.020 - 1.275: 1 Chirality restraints: 6505 Sorted by residual: chirality pdb=" CG LEU M 246 " pdb=" CB LEU M 246 " pdb=" CD1 LEU M 246 " pdb=" CD2 LEU M 246 " both_signs ideal model delta sigma weight residual False -2.59 -1.32 -1.27 2.00e-01 2.50e+01 4.06e+01 chirality pdb=" C2' ATP F 601 " pdb=" C1' ATP F 601 " pdb=" C3' ATP F 601 " pdb=" O2' ATP F 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.40 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.46 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 6502 not shown) Planarity restraints: 12192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 395 " -0.057 2.00e-02 2.50e+03 6.42e-02 6.18e+01 pdb=" CG ASN A 395 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 395 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 395 " 0.064 2.00e-02 2.50e+03 pdb="HD21 ASN A 395 " -0.116 2.00e-02 2.50e+03 pdb="HD22 ASN A 395 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 160 " 0.060 2.00e-02 2.50e+03 6.04e-02 5.48e+01 pdb=" CG ASN A 160 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN A 160 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN A 160 " 0.045 2.00e-02 2.50e+03 pdb="HD21 ASN A 160 " -0.079 2.00e-02 2.50e+03 pdb="HD22 ASN A 160 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 239 " -0.040 2.00e-02 2.50e+03 3.78e-02 2.14e+01 pdb=" CG ASN G 239 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN G 239 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN G 239 " -0.023 2.00e-02 2.50e+03 pdb="HD21 ASN G 239 " 0.040 2.00e-02 2.50e+03 pdb="HD22 ASN G 239 " -0.037 2.00e-02 2.50e+03 ... (remaining 12189 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 3394 2.18 - 2.79: 173842 2.79 - 3.39: 226665 3.39 - 4.00: 302509 4.00 - 4.60: 483707 Nonbonded interactions: 1190117 Sorted by model distance: nonbonded pdb=" O GLN E 273 " pdb=" HG SER E 276 " model vdw 1.576 1.850 nonbonded pdb=" O LYS B 166 " pdb=" HG1 THR B 170 " model vdw 1.600 1.850 nonbonded pdb=" O ALA F 288 " pdb=" H GLY F 290 " model vdw 1.601 1.850 nonbonded pdb=" O MET G 117 " pdb=" H PHE G 121 " model vdw 1.611 1.850 nonbonded pdb=" O LEU S 94 " pdb=" H LEU S 98 " model vdw 1.621 1.850 ... (remaining 1190112 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 27 through 562 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and resid 15 through 501) selection = (chain 'E' and (resid 15 through 173 or (resid 174 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 175 through 501)) selection = (chain 'F' and resid 15 through 501) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.940 Extract box with map and model: 18.910 Check model and map are aligned: 0.930 Set scattering table: 0.580 Process input model: 219.330 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.560 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 250.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.125 41291 Z= 0.615 Angle : 0.868 22.064 55958 Z= 0.508 Chirality : 0.052 1.275 6505 Planarity : 0.005 0.071 7145 Dihedral : 10.106 119.919 15309 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.00 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.32 (0.10), residues: 5229 helix: -2.08 (0.08), residues: 2578 sheet: -2.79 (0.18), residues: 580 loop : -1.92 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 224 HIS 0.015 0.002 HIS h 308 PHE 0.034 0.003 PHE X 82 TYR 0.020 0.002 TYR A 53 ARG 0.010 0.001 ARG M 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 1407 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1407 time to evaluate : 4.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 VAL cc_start: 0.7556 (m) cc_final: 0.7271 (t) REVERT: B 253 ASP cc_start: 0.7546 (m-30) cc_final: 0.7334 (m-30) REVERT: B 391 SER cc_start: 0.7756 (t) cc_final: 0.7556 (p) REVERT: E 109 MET cc_start: 0.6913 (mpp) cc_final: 0.6641 (mpp) REVERT: E 401 LEU cc_start: 0.7579 (mm) cc_final: 0.7267 (mm) REVERT: F 74 MET cc_start: 0.8202 (mmt) cc_final: 0.7574 (mmt) REVERT: F 188 HIS cc_start: 0.4528 (t-90) cc_final: 0.4308 (t70) REVERT: G 12 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6766 (mt-10) REVERT: G 79 THR cc_start: 0.6748 (p) cc_final: 0.6452 (p) REVERT: G 190 ASP cc_start: 0.7516 (m-30) cc_final: 0.6812 (m-30) REVERT: H 85 THR cc_start: 0.8587 (t) cc_final: 0.7990 (p) REVERT: H 122 ASP cc_start: 0.7482 (m-30) cc_final: 0.6370 (t0) REVERT: H 135 ASP cc_start: 0.5277 (p0) cc_final: 0.4801 (p0) REVERT: I 45 LEU cc_start: 0.7533 (mt) cc_final: 0.7090 (mm) REVERT: J 70 ASP cc_start: 0.6199 (t70) cc_final: 0.5996 (m-30) REVERT: K 72 GLN cc_start: 0.6523 (mm110) cc_final: 0.6137 (mm110) REVERT: K 73 THR cc_start: 0.8415 (m) cc_final: 0.7750 (m) REVERT: K 84 CYS cc_start: 0.6736 (m) cc_final: 0.6019 (m) REVERT: K 120 SER cc_start: 0.8829 (t) cc_final: 0.8592 (m) REVERT: M 70 VAL cc_start: 0.8693 (t) cc_final: 0.8411 (t) REVERT: M 74 ASP cc_start: 0.7678 (m-30) cc_final: 0.7413 (m-30) REVERT: M 175 TYR cc_start: 0.6079 (m-80) cc_final: 0.5831 (m-10) REVERT: S 77 TYR cc_start: 0.8453 (m-80) cc_final: 0.8172 (m-80) REVERT: U 37 ILE cc_start: 0.8133 (mt) cc_final: 0.7731 (tt) REVERT: V 57 PHE cc_start: 0.7177 (m-80) cc_final: 0.6962 (m-80) REVERT: W 71 SER cc_start: 0.7990 (t) cc_final: 0.7726 (t) REVERT: W 73 LYS cc_start: 0.8477 (ptpp) cc_final: 0.8248 (tttp) REVERT: X 55 MET cc_start: 0.8068 (ttm) cc_final: 0.7584 (ttm) outliers start: 0 outliers final: 0 residues processed: 1407 average time/residue: 1.1772 time to fit residues: 2606.2490 Evaluate side-chains 877 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 877 time to evaluate : 4.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 439 optimal weight: 8.9990 chunk 394 optimal weight: 0.9990 chunk 218 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 265 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 407 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 247 optimal weight: 0.9980 chunk 303 optimal weight: 1.9990 chunk 472 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 330 GLN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 550 GLN B 201 GLN ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 GLN ** C 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 ASN G 165 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 ASN K 130 GLN L 130 GLN N 55 GLN ** V 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 67 GLN c 21 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 41291 Z= 0.257 Angle : 0.632 13.440 55958 Z= 0.329 Chirality : 0.042 0.180 6505 Planarity : 0.005 0.076 7145 Dihedral : 6.754 104.710 5852 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.98 % Favored : 96.88 % Rotamer: Outliers : 1.09 % Allowed : 8.77 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.11), residues: 5229 helix: -0.97 (0.09), residues: 2630 sheet: -2.20 (0.20), residues: 530 loop : -1.45 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 89 HIS 0.011 0.002 HIS B 111 PHE 0.025 0.002 PHE W 91 TYR 0.021 0.002 TYR C 474 ARG 0.009 0.001 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 993 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 946 time to evaluate : 5.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 TYR cc_start: 0.8001 (m-80) cc_final: 0.7079 (m-80) REVERT: A 490 VAL cc_start: 0.7578 (m) cc_final: 0.7296 (t) REVERT: B 112 MET cc_start: 0.8727 (tpp) cc_final: 0.8473 (tpp) REVERT: C 326 MET cc_start: 0.7981 (mmm) cc_final: 0.7720 (tpt) REVERT: C 407 MET cc_start: 0.4863 (mmm) cc_final: 0.4661 (mmm) REVERT: D 109 MET cc_start: 0.4664 (tpp) cc_final: 0.4413 (tpp) REVERT: D 130 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7668 (mtpp) REVERT: D 382 MET cc_start: 0.6604 (mmp) cc_final: 0.6232 (mmp) REVERT: E 109 MET cc_start: 0.7440 (mpp) cc_final: 0.7102 (mpp) REVERT: E 368 MET cc_start: 0.7192 (mmm) cc_final: 0.6926 (mmm) REVERT: F 184 VAL cc_start: 0.8192 (t) cc_final: 0.7868 (t) REVERT: F 437 MET cc_start: 0.6976 (mtm) cc_final: 0.6774 (mtt) REVERT: G 19 LYS cc_start: 0.7858 (tmmt) cc_final: 0.7580 (tptt) REVERT: H 116 ASN cc_start: 0.8267 (m-40) cc_final: 0.7556 (t0) REVERT: H 122 ASP cc_start: 0.7607 (m-30) cc_final: 0.6639 (t0) REVERT: K 84 CYS cc_start: 0.7119 (m) cc_final: 0.6365 (m) REVERT: K 130 GLN cc_start: 0.7335 (mp-120) cc_final: 0.7092 (mp10) REVERT: L 88 ARG cc_start: 0.6938 (ptp-110) cc_final: 0.6546 (ptp-170) REVERT: M 154 ASN cc_start: 0.8263 (p0) cc_final: 0.8021 (p0) REVERT: N 42 ARG cc_start: 0.7773 (mmt-90) cc_final: 0.7373 (mpt180) REVERT: Q 61 MET cc_start: 0.7162 (mmm) cc_final: 0.6909 (mtp) REVERT: R 55 MET cc_start: 0.7449 (mtp) cc_final: 0.7215 (mtm) REVERT: S 67 GLN cc_start: 0.8233 (mt0) cc_final: 0.7968 (mm-40) REVERT: S 77 TYR cc_start: 0.8457 (m-80) cc_final: 0.8185 (m-80) REVERT: U 37 ILE cc_start: 0.8308 (mt) cc_final: 0.7967 (tt) REVERT: U 55 MET cc_start: 0.7831 (mtp) cc_final: 0.7020 (tpt) REVERT: V 27 TYR cc_start: 0.6105 (m-10) cc_final: 0.5746 (m-80) REVERT: c 96 TYR cc_start: 0.7367 (m-10) cc_final: 0.7049 (m-10) outliers start: 47 outliers final: 29 residues processed: 968 average time/residue: 1.1599 time to fit residues: 1807.8609 Evaluate side-chains 822 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 793 time to evaluate : 4.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 461 ASN Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 84 CYS Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain S residue 99 GLU Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain W residue 37 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 262 optimal weight: 0.5980 chunk 146 optimal weight: 0.4980 chunk 393 optimal weight: 0.9990 chunk 321 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 473 optimal weight: 9.9990 chunk 511 optimal weight: 10.0000 chunk 421 optimal weight: 7.9990 chunk 469 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 379 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 GLN ** C 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN E 267 ASN ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 ASN V 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 41291 Z= 0.305 Angle : 0.624 14.321 55958 Z= 0.324 Chirality : 0.042 0.233 6505 Planarity : 0.005 0.105 7145 Dihedral : 6.721 89.567 5852 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.16 % Favored : 96.75 % Rotamer: Outliers : 1.51 % Allowed : 9.65 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.35 (0.11), residues: 5229 helix: -0.38 (0.10), residues: 2651 sheet: -1.84 (0.20), residues: 587 loop : -1.09 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 138 HIS 0.008 0.002 HIS C 513 PHE 0.046 0.002 PHE X 82 TYR 0.020 0.002 TYR P 27 ARG 0.011 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 894 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 829 time to evaluate : 5.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6987 (mp0) REVERT: A 239 ASP cc_start: 0.7366 (t0) cc_final: 0.7021 (t0) REVERT: A 539 MET cc_start: 0.8574 (mtt) cc_final: 0.8232 (mtt) REVERT: B 368 ASP cc_start: 0.7788 (t0) cc_final: 0.7565 (t0) REVERT: B 398 MET cc_start: 0.8250 (tpt) cc_final: 0.7950 (tpt) REVERT: D 109 MET cc_start: 0.5498 (tpp) cc_final: 0.5246 (tpp) REVERT: D 130 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7955 (mtpp) REVERT: D 469 MET cc_start: 0.8430 (mmm) cc_final: 0.8226 (mmm) REVERT: E 74 MET cc_start: 0.8692 (mmm) cc_final: 0.8083 (mmt) REVERT: E 206 ASP cc_start: 0.7511 (m-30) cc_final: 0.7207 (m-30) REVERT: E 211 MET cc_start: 0.7668 (mtt) cc_final: 0.7102 (mtt) REVERT: F 220 GLN cc_start: 0.6871 (mp10) cc_final: 0.6363 (mp10) REVERT: G 19 LYS cc_start: 0.8116 (tmmt) cc_final: 0.7719 (ptpt) REVERT: H 93 ILE cc_start: 0.8012 (pt) cc_final: 0.7578 (mt) REVERT: H 116 ASN cc_start: 0.8382 (m-40) cc_final: 0.7668 (t0) REVERT: J 73 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8402 (m) REVERT: K 102 MET cc_start: 0.7714 (mmm) cc_final: 0.7455 (mmm) REVERT: L 88 ARG cc_start: 0.7874 (ptp-110) cc_final: 0.7524 (ptp-170) REVERT: N 50 TYR cc_start: 0.7700 (t80) cc_final: 0.7476 (t80) REVERT: Q 61 MET cc_start: 0.7264 (mmm) cc_final: 0.6973 (mtp) REVERT: R 55 MET cc_start: 0.7273 (mtp) cc_final: 0.7037 (mtm) REVERT: R 61 MET cc_start: 0.5304 (mtp) cc_final: 0.5046 (mtp) REVERT: S 67 GLN cc_start: 0.8310 (mt0) cc_final: 0.7972 (mm110) REVERT: S 77 TYR cc_start: 0.8430 (m-80) cc_final: 0.8107 (m-80) REVERT: U 55 MET cc_start: 0.7765 (mtp) cc_final: 0.7350 (tpt) REVERT: V 27 TYR cc_start: 0.6461 (m-10) cc_final: 0.6076 (m-80) REVERT: W 82 PHE cc_start: 0.7866 (t80) cc_final: 0.7642 (t80) REVERT: X 41 MET cc_start: 0.6719 (mmt) cc_final: 0.6347 (mmt) REVERT: c 96 TYR cc_start: 0.7340 (m-10) cc_final: 0.7131 (m-10) outliers start: 65 outliers final: 45 residues processed: 869 average time/residue: 1.1217 time to fit residues: 1559.6474 Evaluate side-chains 752 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 706 time to evaluate : 5.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 84 CYS Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain S residue 44 SER Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain U residue 67 GLN Chi-restraints excluded: chain U residue 70 MET Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain c residue 101 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 467 optimal weight: 9.9990 chunk 355 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 317 optimal weight: 1.9990 chunk 474 optimal weight: 8.9990 chunk 502 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 449 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN B 492 ASN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 GLN E 63 HIS E 137 GLN F 24 GLN F 121 ASN F 188 HIS G 185 GLN ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 GLN X 67 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 41291 Z= 0.391 Angle : 0.637 13.236 55958 Z= 0.334 Chirality : 0.044 0.233 6505 Planarity : 0.005 0.101 7145 Dihedral : 6.850 85.120 5852 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 2.11 % Allowed : 10.62 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.10 (0.11), residues: 5229 helix: -0.16 (0.10), residues: 2584 sheet: -1.70 (0.20), residues: 577 loop : -0.99 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 42 HIS 0.010 0.002 HIS F 377 PHE 0.040 0.002 PHE X 82 TYR 0.020 0.002 TYR C 504 ARG 0.009 0.001 ARG M 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 852 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 761 time to evaluate : 5.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.7619 (t0) cc_final: 0.7309 (t0) REVERT: A 104 LEU cc_start: 0.8674 (tp) cc_final: 0.8463 (tp) REVERT: A 239 ASP cc_start: 0.7714 (t0) cc_final: 0.7371 (t0) REVERT: B 112 MET cc_start: 0.8772 (tpp) cc_final: 0.8495 (tpp) REVERT: B 398 MET cc_start: 0.8478 (tpt) cc_final: 0.8164 (tpt) REVERT: C 223 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8116 (mm110) REVERT: C 281 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8982 (mm) REVERT: C 409 MET cc_start: 0.7974 (mmt) cc_final: 0.7561 (mmt) REVERT: D 130 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8172 (mtpp) REVERT: E 411 LYS cc_start: 0.7603 (ptpt) cc_final: 0.6797 (mttt) REVERT: F 211 MET cc_start: 0.8028 (mmp) cc_final: 0.7719 (mmp) REVERT: F 220 GLN cc_start: 0.7384 (mp10) cc_final: 0.7112 (mp10) REVERT: G 19 LYS cc_start: 0.8198 (tmmt) cc_final: 0.7751 (ptpt) REVERT: G 149 MET cc_start: 0.8734 (mtp) cc_final: 0.8531 (mtp) REVERT: G 291 MET cc_start: 0.8174 (mtt) cc_final: 0.7878 (mtt) REVERT: H 88 GLN cc_start: 0.8206 (mt0) cc_final: 0.7855 (mt0) REVERT: H 116 ASN cc_start: 0.8331 (m-40) cc_final: 0.7806 (t0) REVERT: J 73 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8607 (m) REVERT: K 102 MET cc_start: 0.8470 (mmm) cc_final: 0.8267 (mmm) REVERT: L 88 ARG cc_start: 0.8433 (ptp-110) cc_final: 0.7923 (ptp-170) REVERT: M 154 ASN cc_start: 0.8114 (p0) cc_final: 0.7843 (p0) REVERT: N 31 ASP cc_start: 0.7343 (m-30) cc_final: 0.7025 (m-30) REVERT: Q 61 MET cc_start: 0.7587 (mmm) cc_final: 0.7121 (mtp) REVERT: R 55 MET cc_start: 0.7642 (mtp) cc_final: 0.7412 (mtm) REVERT: S 73 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8610 (mtmm) REVERT: S 77 TYR cc_start: 0.8414 (m-80) cc_final: 0.8079 (m-80) REVERT: U 55 MET cc_start: 0.7954 (mtp) cc_final: 0.7265 (tpt) REVERT: U 61 MET cc_start: 0.6932 (mtt) cc_final: 0.6319 (mtt) REVERT: V 27 TYR cc_start: 0.6295 (m-10) cc_final: 0.5992 (m-80) REVERT: X 41 MET cc_start: 0.6768 (mmt) cc_final: 0.6440 (mmt) REVERT: X 55 MET cc_start: 0.7777 (ttm) cc_final: 0.7300 (ttm) REVERT: c 89 THR cc_start: 0.8434 (m) cc_final: 0.7992 (p) REVERT: c 92 GLU cc_start: 0.8306 (pt0) cc_final: 0.7604 (pt0) REVERT: c 96 TYR cc_start: 0.7417 (m-10) cc_final: 0.7103 (m-10) outliers start: 91 outliers final: 59 residues processed: 821 average time/residue: 1.1328 time to fit residues: 1495.9809 Evaluate side-chains 723 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 661 time to evaluate : 5.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 452 ILE Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 461 ASN Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 157 ASP Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 84 CYS Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 179 LYS Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain V residue 41 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 418 optimal weight: 5.9990 chunk 285 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 374 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 428 optimal weight: 2.9990 chunk 347 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 256 optimal weight: 0.9980 chunk 451 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 356 ASN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN D 23 GLN F 24 GLN F 121 ASN ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.7288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41291 Z= 0.272 Angle : 0.542 11.923 55958 Z= 0.280 Chirality : 0.040 0.152 6505 Planarity : 0.004 0.101 7145 Dihedral : 6.653 89.828 5852 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.27 % Rotamer: Outliers : 1.46 % Allowed : 12.13 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.75 (0.11), residues: 5229 helix: 0.14 (0.10), residues: 2596 sheet: -1.53 (0.20), residues: 572 loop : -0.84 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 183 HIS 0.017 0.001 HIS I 22 PHE 0.025 0.001 PHE X 82 TYR 0.016 0.001 TYR C 504 ARG 0.005 0.000 ARG K 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 756 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 693 time to evaluate : 4.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: A 239 ASP cc_start: 0.7639 (t0) cc_final: 0.7317 (t0) REVERT: A 366 TYR cc_start: 0.7885 (t80) cc_final: 0.7200 (t80) REVERT: B 112 MET cc_start: 0.8681 (tpp) cc_final: 0.8472 (tpp) REVERT: C 223 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8122 (mm110) REVERT: C 281 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9018 (mm) REVERT: C 452 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8831 (tp) REVERT: D 107 ASN cc_start: 0.7933 (m-40) cc_final: 0.7493 (m-40) REVERT: D 130 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8205 (mtpp) REVERT: F 211 MET cc_start: 0.8081 (mmp) cc_final: 0.7681 (mmp) REVERT: G 19 LYS cc_start: 0.8177 (tmmt) cc_final: 0.7886 (tptt) REVERT: G 29 MET cc_start: 0.8031 (mmt) cc_final: 0.7664 (mmp) REVERT: G 291 MET cc_start: 0.8400 (mtt) cc_final: 0.7997 (mtt) REVERT: H 88 GLN cc_start: 0.8010 (mt0) cc_final: 0.7646 (mt0) REVERT: H 116 ASN cc_start: 0.7910 (m-40) cc_final: 0.7658 (t0) REVERT: I 18 THR cc_start: 0.8700 (m) cc_final: 0.8389 (m) REVERT: L 88 ARG cc_start: 0.8288 (ptp-110) cc_final: 0.7922 (ptp-170) REVERT: M 37 ARG cc_start: 0.8081 (mpt-90) cc_final: 0.7819 (mpt-90) REVERT: N 31 ASP cc_start: 0.7376 (m-30) cc_final: 0.7045 (m-30) REVERT: P 25 ILE cc_start: 0.7649 (pt) cc_final: 0.7440 (tp) REVERT: Q 61 MET cc_start: 0.7571 (mmm) cc_final: 0.7150 (mtp) REVERT: R 55 MET cc_start: 0.7406 (mtp) cc_final: 0.7191 (mtp) REVERT: S 77 TYR cc_start: 0.8380 (m-80) cc_final: 0.8049 (m-80) REVERT: U 55 MET cc_start: 0.7958 (mtp) cc_final: 0.7225 (tpt) REVERT: U 61 MET cc_start: 0.6918 (mtt) cc_final: 0.6176 (mtt) REVERT: V 27 TYR cc_start: 0.6266 (m-10) cc_final: 0.5925 (m-80) REVERT: c 92 GLU cc_start: 0.8280 (pt0) cc_final: 0.7880 (pt0) REVERT: c 96 TYR cc_start: 0.7436 (m-10) cc_final: 0.7130 (m-10) outliers start: 63 outliers final: 43 residues processed: 733 average time/residue: 1.1292 time to fit residues: 1336.5044 Evaluate side-chains 701 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 654 time to evaluate : 4.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 452 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain S residue 82 PHE Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 82 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 169 optimal weight: 0.7980 chunk 452 optimal weight: 6.9990 chunk 99 optimal weight: 0.1980 chunk 295 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 503 optimal weight: 0.9990 chunk 417 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 264 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN G 185 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.7530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41291 Z= 0.187 Angle : 0.502 9.277 55958 Z= 0.257 Chirality : 0.039 0.165 6505 Planarity : 0.004 0.088 7145 Dihedral : 6.204 85.399 5852 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer: Outliers : 1.28 % Allowed : 12.69 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.12), residues: 5229 helix: 0.51 (0.10), residues: 2573 sheet: -1.37 (0.21), residues: 551 loop : -0.66 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 125 HIS 0.007 0.001 HIS I 22 PHE 0.020 0.001 PHE X 82 TYR 0.014 0.001 TYR M 31 ARG 0.007 0.000 ARG M 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 725 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 670 time to evaluate : 5.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.7519 (t0) cc_final: 0.7214 (t0) REVERT: A 239 ASP cc_start: 0.7699 (t0) cc_final: 0.7356 (t0) REVERT: A 366 TYR cc_start: 0.7861 (t80) cc_final: 0.7245 (t80) REVERT: C 223 GLN cc_start: 0.8443 (tp40) cc_final: 0.8090 (mm110) REVERT: C 281 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8989 (mm) REVERT: D 107 ASN cc_start: 0.7986 (m-40) cc_final: 0.7713 (m-40) REVERT: D 130 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8155 (mtpp) REVERT: E 362 GLU cc_start: 0.6752 (tp30) cc_final: 0.6519 (tp30) REVERT: E 392 LYS cc_start: 0.8339 (tttt) cc_final: 0.8071 (ttpp) REVERT: F 211 MET cc_start: 0.8058 (mmp) cc_final: 0.7650 (mmp) REVERT: G 19 LYS cc_start: 0.8174 (tmmt) cc_final: 0.7872 (tptm) REVERT: G 29 MET cc_start: 0.8027 (mmt) cc_final: 0.7704 (mmp) REVERT: H 88 GLN cc_start: 0.7924 (mt0) cc_final: 0.7606 (mt0) REVERT: I 26 LYS cc_start: 0.8303 (mttm) cc_final: 0.7959 (mttm) REVERT: L 88 ARG cc_start: 0.8245 (ptp-110) cc_final: 0.7886 (ptp-170) REVERT: O 55 MET cc_start: 0.7217 (mtm) cc_final: 0.6829 (mtp) REVERT: O 57 PHE cc_start: 0.8322 (m-10) cc_final: 0.8068 (m-10) REVERT: Q 61 MET cc_start: 0.7654 (mmm) cc_final: 0.7265 (mtp) REVERT: S 77 TYR cc_start: 0.8316 (m-80) cc_final: 0.8026 (m-80) REVERT: U 55 MET cc_start: 0.8034 (mtp) cc_final: 0.7279 (tpt) REVERT: U 61 MET cc_start: 0.6868 (mtt) cc_final: 0.6155 (mtt) REVERT: X 55 MET cc_start: 0.7760 (ttm) cc_final: 0.7270 (ttm) REVERT: c 92 GLU cc_start: 0.8272 (pt0) cc_final: 0.7771 (pt0) REVERT: c 96 TYR cc_start: 0.7434 (m-10) cc_final: 0.7157 (m-10) outliers start: 55 outliers final: 43 residues processed: 699 average time/residue: 1.0865 time to fit residues: 1210.4014 Evaluate side-chains 684 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 640 time to evaluate : 4.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 452 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 437 MET Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 82 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 485 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 286 optimal weight: 0.9990 chunk 367 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 423 optimal weight: 8.9990 chunk 280 optimal weight: 0.9990 chunk 501 optimal weight: 20.0000 chunk 313 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 ASN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.7759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41291 Z= 0.221 Angle : 0.504 8.967 55958 Z= 0.258 Chirality : 0.039 0.142 6505 Planarity : 0.004 0.079 7145 Dihedral : 6.205 88.687 5852 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 1.60 % Allowed : 12.36 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.22 (0.12), residues: 5229 helix: 0.60 (0.10), residues: 2598 sheet: -1.32 (0.21), residues: 548 loop : -0.62 (0.14), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 3 HIS 0.006 0.001 HIS B 111 PHE 0.013 0.001 PHE B 495 TYR 0.021 0.001 TYR M 31 ARG 0.008 0.000 ARG M 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 713 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 644 time to evaluate : 5.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.7557 (t0) cc_final: 0.7223 (t0) REVERT: A 239 ASP cc_start: 0.7743 (t0) cc_final: 0.7405 (t0) REVERT: A 366 TYR cc_start: 0.7898 (t80) cc_final: 0.7244 (t80) REVERT: C 223 GLN cc_start: 0.8460 (tp40) cc_final: 0.8122 (mm110) REVERT: C 519 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: D 107 ASN cc_start: 0.8012 (m-40) cc_final: 0.7722 (m-40) REVERT: D 130 LYS cc_start: 0.8387 (mmmt) cc_final: 0.8180 (mtpp) REVERT: E 362 GLU cc_start: 0.6857 (tp30) cc_final: 0.6623 (tp30) REVERT: E 392 LYS cc_start: 0.8347 (tttt) cc_final: 0.8104 (ttpp) REVERT: F 211 MET cc_start: 0.8052 (mmp) cc_final: 0.7581 (mmp) REVERT: G 19 LYS cc_start: 0.8198 (tmmt) cc_final: 0.7962 (tptm) REVERT: G 29 MET cc_start: 0.8024 (mmt) cc_final: 0.7718 (mmp) REVERT: G 291 MET cc_start: 0.8591 (mtt) cc_final: 0.7856 (mtt) REVERT: H 88 GLN cc_start: 0.7897 (mt0) cc_final: 0.7530 (mt0) REVERT: L 88 ARG cc_start: 0.8255 (ptp-110) cc_final: 0.7940 (ptp-170) REVERT: O 55 MET cc_start: 0.7177 (mtm) cc_final: 0.6761 (mtp) REVERT: O 57 PHE cc_start: 0.8443 (m-10) cc_final: 0.8174 (m-10) REVERT: Q 61 MET cc_start: 0.7646 (mmm) cc_final: 0.7264 (mtp) REVERT: S 73 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8533 (mtmm) REVERT: S 77 TYR cc_start: 0.8320 (m-80) cc_final: 0.8035 (m-80) REVERT: U 55 MET cc_start: 0.7994 (mtp) cc_final: 0.7305 (tpt) REVERT: U 61 MET cc_start: 0.6935 (mtt) cc_final: 0.6220 (mtt) REVERT: V 27 TYR cc_start: 0.6491 (m-10) cc_final: 0.6154 (m-10) REVERT: X 55 MET cc_start: 0.7735 (ttm) cc_final: 0.7234 (ttm) REVERT: c 92 GLU cc_start: 0.8161 (pt0) cc_final: 0.7739 (pt0) REVERT: c 96 TYR cc_start: 0.7426 (m-10) cc_final: 0.7163 (m-10) outliers start: 69 outliers final: 55 residues processed: 679 average time/residue: 1.1397 time to fit residues: 1239.1127 Evaluate side-chains 683 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 627 time to evaluate : 4.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 452 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain c residue 23 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 310 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 318 optimal weight: 5.9990 chunk 341 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 393 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN H 116 ASN ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.8112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 41291 Z= 0.376 Angle : 0.560 10.695 55958 Z= 0.289 Chirality : 0.041 0.146 6505 Planarity : 0.004 0.083 7145 Dihedral : 6.647 87.630 5852 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.02 % Favored : 96.88 % Rotamer: Outliers : 1.81 % Allowed : 12.29 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 5229 helix: 0.55 (0.10), residues: 2592 sheet: -1.33 (0.20), residues: 579 loop : -0.68 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 138 HIS 0.009 0.002 HIS F 377 PHE 0.018 0.001 PHE C 495 TYR 0.029 0.002 TYR R 60 ARG 0.012 0.001 ARG K 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 701 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 623 time to evaluate : 5.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.7591 (t0) cc_final: 0.7223 (t0) REVERT: A 66 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8418 (tp) REVERT: A 239 ASP cc_start: 0.7888 (t0) cc_final: 0.7601 (t0) REVERT: A 366 TYR cc_start: 0.7964 (t80) cc_final: 0.7255 (t80) REVERT: C 519 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: D 83 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7891 (mtm110) REVERT: D 107 ASN cc_start: 0.8106 (m-40) cc_final: 0.7773 (m-40) REVERT: E 101 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9103 (p) REVERT: E 362 GLU cc_start: 0.6901 (tp30) cc_final: 0.6651 (tp30) REVERT: E 392 LYS cc_start: 0.8320 (tttt) cc_final: 0.8064 (ttpp) REVERT: F 211 MET cc_start: 0.8100 (mmp) cc_final: 0.7646 (mmp) REVERT: G 19 LYS cc_start: 0.8297 (tmmt) cc_final: 0.8032 (tptt) REVERT: G 29 MET cc_start: 0.8017 (mmt) cc_final: 0.7691 (mmp) REVERT: G 291 MET cc_start: 0.8709 (mtt) cc_final: 0.8052 (mtt) REVERT: H 88 GLN cc_start: 0.7910 (mt0) cc_final: 0.7558 (mt0) REVERT: H 160 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7926 (mp10) REVERT: L 88 ARG cc_start: 0.8348 (ptp-110) cc_final: 0.7970 (ptp-170) REVERT: L 127 GLU cc_start: 0.7919 (tp30) cc_final: 0.7660 (tp30) REVERT: L 133 ASP cc_start: 0.7705 (t0) cc_final: 0.7483 (m-30) REVERT: N 31 ASP cc_start: 0.7499 (m-30) cc_final: 0.7091 (m-30) REVERT: O 55 MET cc_start: 0.7264 (mtm) cc_final: 0.6850 (mtp) REVERT: O 57 PHE cc_start: 0.8401 (m-10) cc_final: 0.8102 (m-10) REVERT: Q 61 MET cc_start: 0.7721 (mmm) cc_final: 0.7378 (mtp) REVERT: U 55 MET cc_start: 0.8050 (mtp) cc_final: 0.7330 (tpt) REVERT: U 61 MET cc_start: 0.7111 (mtt) cc_final: 0.6369 (mtt) REVERT: X 55 MET cc_start: 0.7798 (ttm) cc_final: 0.7327 (ttm) outliers start: 78 outliers final: 66 residues processed: 667 average time/residue: 1.1324 time to fit residues: 1207.1304 Evaluate side-chains 674 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 605 time to evaluate : 5.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 452 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 437 MET Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain c residue 23 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 30.0000 chunk 480 optimal weight: 20.0000 chunk 438 optimal weight: 6.9990 chunk 467 optimal weight: 6.9990 chunk 281 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 366 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 422 optimal weight: 0.0980 chunk 441 optimal weight: 10.0000 chunk 465 optimal weight: 4.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 ASN S 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.8486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 41291 Z= 0.550 Angle : 0.632 12.789 55958 Z= 0.331 Chirality : 0.046 0.245 6505 Planarity : 0.005 0.071 7145 Dihedral : 7.002 88.023 5852 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.52 % Favored : 96.39 % Rotamer: Outliers : 1.97 % Allowed : 12.71 % Favored : 85.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.59 (0.11), residues: 5229 helix: 0.28 (0.10), residues: 2623 sheet: -1.45 (0.20), residues: 575 loop : -0.79 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 138 HIS 0.012 0.002 HIS F 377 PHE 0.022 0.002 PHE B 495 TYR 0.034 0.002 TYR H 84 ARG 0.013 0.001 ARG L 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 695 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 610 time to evaluate : 5.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.7627 (t0) cc_final: 0.7272 (t0) REVERT: A 66 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 214 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.9057 (p) REVERT: A 239 ASP cc_start: 0.8019 (t0) cc_final: 0.7783 (t70) REVERT: A 366 TYR cc_start: 0.8041 (t80) cc_final: 0.7240 (t80) REVERT: B 260 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8762 (mp) REVERT: C 289 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: C 519 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: D 408 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: E 101 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9176 (p) REVERT: E 362 GLU cc_start: 0.6900 (tp30) cc_final: 0.6640 (tp30) REVERT: E 392 LYS cc_start: 0.8355 (tttt) cc_final: 0.8067 (ttpp) REVERT: F 224 LYS cc_start: 0.8469 (pttt) cc_final: 0.7926 (pttp) REVERT: F 327 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8026 (tp) REVERT: G 19 LYS cc_start: 0.8347 (tmmt) cc_final: 0.8081 (tptt) REVERT: G 29 MET cc_start: 0.8039 (mmt) cc_final: 0.7687 (mmp) REVERT: G 291 MET cc_start: 0.8764 (mtt) cc_final: 0.8224 (mtt) REVERT: H 88 GLN cc_start: 0.7910 (mt0) cc_final: 0.7521 (mt0) REVERT: J 157 ASP cc_start: 0.8004 (m-30) cc_final: 0.7682 (m-30) REVERT: L 88 ARG cc_start: 0.8348 (ptp-110) cc_final: 0.8035 (ptp-170) REVERT: L 127 GLU cc_start: 0.7939 (tp30) cc_final: 0.7698 (tp30) REVERT: L 133 ASP cc_start: 0.7824 (t0) cc_final: 0.7577 (m-30) REVERT: M 94 ILE cc_start: 0.5167 (mp) cc_final: 0.4864 (mp) REVERT: N 31 ASP cc_start: 0.7540 (m-30) cc_final: 0.7133 (m-30) REVERT: O 55 MET cc_start: 0.7298 (mtm) cc_final: 0.6949 (mtp) REVERT: O 57 PHE cc_start: 0.8425 (m-10) cc_final: 0.8153 (m-10) REVERT: U 55 MET cc_start: 0.8039 (mtp) cc_final: 0.7341 (tpt) REVERT: U 61 MET cc_start: 0.7313 (mtt) cc_final: 0.6544 (mtt) REVERT: V 27 TYR cc_start: 0.6598 (m-10) cc_final: 0.6112 (m-80) REVERT: X 55 MET cc_start: 0.7838 (ttm) cc_final: 0.7364 (ttm) REVERT: c 96 TYR cc_start: 0.7480 (m-10) cc_final: 0.7179 (m-10) outliers start: 85 outliers final: 71 residues processed: 659 average time/residue: 1.1010 time to fit residues: 1159.2106 Evaluate side-chains 666 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 587 time to evaluate : 5.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 452 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 437 MET Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain V residue 41 MET Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain c residue 23 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 306 optimal weight: 0.9980 chunk 493 optimal weight: 20.0000 chunk 301 optimal weight: 0.6980 chunk 234 optimal weight: 0.5980 chunk 343 optimal weight: 9.9990 chunk 518 optimal weight: 9.9990 chunk 476 optimal weight: 7.9990 chunk 412 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 252 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS G 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.8558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41291 Z= 0.245 Angle : 0.535 10.584 55958 Z= 0.275 Chirality : 0.040 0.148 6505 Planarity : 0.004 0.063 7145 Dihedral : 6.655 87.590 5852 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 1.53 % Allowed : 13.57 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 5229 helix: 0.51 (0.10), residues: 2622 sheet: -1.36 (0.20), residues: 574 loop : -0.61 (0.14), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 125 HIS 0.007 0.001 HIS F 377 PHE 0.017 0.001 PHE B 495 TYR 0.021 0.001 TYR R 60 ARG 0.009 0.000 ARG M 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10458 Ramachandran restraints generated. 5229 Oldfield, 0 Emsley, 5229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 675 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 609 time to evaluate : 5.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.7535 (t0) cc_final: 0.7189 (t0) REVERT: A 66 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 180 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: A 239 ASP cc_start: 0.7985 (t0) cc_final: 0.7713 (t0) REVERT: A 366 TYR cc_start: 0.7993 (t80) cc_final: 0.7280 (t80) REVERT: C 519 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: D 107 ASN cc_start: 0.8146 (m-40) cc_final: 0.7746 (m-40) REVERT: E 362 GLU cc_start: 0.6763 (tp30) cc_final: 0.6509 (tp30) REVERT: E 392 LYS cc_start: 0.8341 (tttt) cc_final: 0.8072 (ttpp) REVERT: F 47 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8542 (p) REVERT: F 224 LYS cc_start: 0.8436 (pttt) cc_final: 0.7892 (pttp) REVERT: F 327 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8054 (tp) REVERT: G 19 LYS cc_start: 0.8271 (tmmt) cc_final: 0.8017 (tptm) REVERT: G 29 MET cc_start: 0.8007 (mmt) cc_final: 0.7681 (mmp) REVERT: G 291 MET cc_start: 0.8763 (mtt) cc_final: 0.8277 (mtt) REVERT: H 88 GLN cc_start: 0.7840 (mt0) cc_final: 0.7474 (mt0) REVERT: H 98 TYR cc_start: 0.7957 (m-80) cc_final: 0.7530 (m-80) REVERT: J 157 ASP cc_start: 0.7981 (m-30) cc_final: 0.7669 (m-30) REVERT: K 88 ARG cc_start: 0.8412 (mtt90) cc_final: 0.8202 (mtt90) REVERT: L 88 ARG cc_start: 0.8235 (ptp-110) cc_final: 0.7980 (ptp-170) REVERT: L 127 GLU cc_start: 0.7889 (tp30) cc_final: 0.7640 (tp30) REVERT: L 133 ASP cc_start: 0.7739 (t0) cc_final: 0.7532 (m-30) REVERT: M 94 ILE cc_start: 0.5180 (mp) cc_final: 0.4891 (mp) REVERT: N 31 ASP cc_start: 0.7464 (m-30) cc_final: 0.7091 (m-30) REVERT: O 55 MET cc_start: 0.7284 (mtm) cc_final: 0.6931 (mtp) REVERT: O 57 PHE cc_start: 0.8394 (m-10) cc_final: 0.8126 (m-10) REVERT: U 55 MET cc_start: 0.8114 (mtp) cc_final: 0.7358 (tpt) REVERT: U 61 MET cc_start: 0.7239 (mtt) cc_final: 0.6444 (mtt) REVERT: V 27 TYR cc_start: 0.6620 (m-10) cc_final: 0.6136 (m-80) REVERT: W 41 MET cc_start: 0.8072 (mtt) cc_final: 0.7474 (mtm) REVERT: X 55 MET cc_start: 0.7834 (ttm) cc_final: 0.7354 (ttm) REVERT: c 32 GLN cc_start: 0.6831 (mm-40) cc_final: 0.5926 (tm-30) REVERT: c 96 TYR cc_start: 0.7484 (m-10) cc_final: 0.7177 (m-10) outliers start: 66 outliers final: 56 residues processed: 644 average time/residue: 1.1492 time to fit residues: 1190.2664 Evaluate side-chains 652 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 591 time to evaluate : 5.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 437 MET Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain c residue 23 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 327 optimal weight: 1.9990 chunk 439 optimal weight: 9.9990 chunk 126 optimal weight: 0.1980 chunk 380 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 114 optimal weight: 1.9990 chunk 413 optimal weight: 3.9990 chunk 172 optimal weight: 0.2980 chunk 424 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN M 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.088673 restraints weight = 168819.649| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.86 r_work: 0.2940 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.8629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41291 Z= 0.186 Angle : 0.501 8.800 55958 Z= 0.256 Chirality : 0.039 0.143 6505 Planarity : 0.003 0.060 7145 Dihedral : 6.250 88.527 5852 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.32 % Rotamer: Outliers : 1.30 % Allowed : 13.87 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.04 (0.12), residues: 5229 helix: 0.78 (0.10), residues: 2626 sheet: -1.25 (0.21), residues: 573 loop : -0.44 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 125 HIS 0.006 0.001 HIS F 63 PHE 0.013 0.001 PHE B 495 TYR 0.019 0.001 TYR R 60 ARG 0.010 0.000 ARG M 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23213.08 seconds wall clock time: 401 minutes 7.46 seconds (24067.46 seconds total)