Starting phenix.real_space_refine on Sun Mar 24 20:14:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r2k_14245/03_2024/7r2k_14245.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r2k_14245/03_2024/7r2k_14245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r2k_14245/03_2024/7r2k_14245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r2k_14245/03_2024/7r2k_14245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r2k_14245/03_2024/7r2k_14245.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r2k_14245/03_2024/7r2k_14245.pdb" } resolution = 3.3 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= -0.002 sd= 0.072 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: 6 Type Number sf(0) Gaussians Ni 2 6.56 5 P 69 5.49 5 S 99 5.16 5 C 27843 2.51 5 N 7529 2.21 5 O 8389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 602": "OD1" <-> "OD2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 26": "OD1" <-> "OD2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "J GLU 59": "OE1" <-> "OE2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "K GLU 264": "OE1" <-> "OE2" Residue "K GLU 327": "OE1" <-> "OE2" Residue "M GLU 28": "OE1" <-> "OE2" Residue "M PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 265": "OE1" <-> "OE2" Residue "P ASP 65": "OD1" <-> "OD2" Residue "P GLU 108": "OE1" <-> "OE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "P GLU 169": "OE1" <-> "OE2" Residue "P ASP 201": "OD1" <-> "OD2" Residue "P GLU 216": "OE1" <-> "OE2" Residue "P ASP 285": "OD1" <-> "OD2" Residue "Q PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 131": "OE1" <-> "OE2" Residue "Q ASP 140": "OD1" <-> "OD2" Residue "R TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "R TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 284": "OE1" <-> "OE2" Residue "R PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 46": "OE1" <-> "OE2" Residue "T PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 264": "OE1" <-> "OE2" Residue "T GLU 272": "OE1" <-> "OE2" Residue "T TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 305": "OE1" <-> "OE2" Residue "T TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 316": "OD1" <-> "OD2" Residue "V TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V ASP 117": "OD1" <-> "OD2" Residue "V PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 227": "OD1" <-> "OD2" Residue "V GLU 236": "OE1" <-> "OE2" Residue "V ASP 285": "OD1" <-> "OD2" Residue "W PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 150": "OE1" <-> "OE2" Residue "W GLU 217": "OE1" <-> "OE2" Residue "W PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 53": "OE1" <-> "OE2" Residue "Y TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 236": "OE1" <-> "OE2" Residue "Y PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43931 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4304 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 26, 'TRANS': 545} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 168 Chain: "C" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "I" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "J" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "K" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1822 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 226} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "S" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "T" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "U" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1215 Classifications: {'RNA': 57} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 15, 'rna3p_pyr': 13} Link IDs: {'rna2p': 27, 'rna3p': 29} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "V" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "W" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2350 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "X" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "Y" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.17, per 1000 atoms: 0.50 Number of scatterers: 43931 At special positions: 0 Unit cell: (143.91, 173.225, 265.167, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 2 28.00 S 99 16.00 P 69 15.00 O 8389 8.00 N 7529 7.00 C 27843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS I 63 " - pdb=" SG CYS I 108 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 65 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.38 Conformation dependent library (CDL) restraints added in 7.1 seconds 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10114 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 61 sheets defined 38.5% alpha, 10.4% beta 3 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 12.30 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.980A pdb=" N PHE A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 94 Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.395A pdb=" N GLU A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.745A pdb=" N TYR A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 removed outlier: 4.190A pdb=" N GLN A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.935A pdb=" N GLU A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.860A pdb=" N MET A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 removed outlier: 3.653A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 246' Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.930A pdb=" N LYS A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.589A pdb=" N GLU A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.842A pdb=" N HIS A 370 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.547A pdb=" N ILE A 421 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.911A pdb=" N LEU A 480 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 587 removed outlier: 3.564A pdb=" N TRP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'C' and resid 5 through 15 removed outlier: 3.908A pdb=" N LEU C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 33 Processing helix chain 'C' and resid 36 through 49 removed outlier: 4.176A pdb=" N LEU C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 41 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 59 removed outlier: 4.592A pdb=" N GLU C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 removed outlier: 3.700A pdb=" N ILE C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 96 removed outlier: 4.185A pdb=" N LYS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 93 " --> pdb=" O ASP C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'E' and resid 5 through 16 removed outlier: 3.576A pdb=" N VAL E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 33 removed outlier: 4.506A pdb=" N VAL E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.924A pdb=" N LEU E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 59 removed outlier: 4.220A pdb=" N GLU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 removed outlier: 3.866A pdb=" N ILE E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 89 removed outlier: 3.548A pdb=" N ASP E 89 " --> pdb=" O ASN E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 89' Processing helix chain 'E' and resid 90 through 98 Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 24 through 33 removed outlier: 4.396A pdb=" N VAL F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 50 removed outlier: 3.629A pdb=" N LEU F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 62 Processing helix chain 'F' and resid 70 through 82 removed outlier: 3.750A pdb=" N GLU F 75 " --> pdb=" O PRO F 71 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 101 removed outlier: 3.634A pdb=" N LEU F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU F 93 " --> pdb=" O ASP F 89 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 14 removed outlier: 3.604A pdb=" N ASN G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.814A pdb=" N VAL G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 50 removed outlier: 3.795A pdb=" N LEU G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 61 removed outlier: 4.102A pdb=" N GLU G 59 " --> pdb=" O LYS G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 84 Processing helix chain 'G' and resid 86 through 100 removed outlier: 4.145A pdb=" N TRP G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 16 removed outlier: 3.686A pdb=" N LEU H 15 " --> pdb=" O TYR H 11 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 34 removed outlier: 4.001A pdb=" N VAL H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 Processing helix chain 'H' and resid 50 through 62 removed outlier: 4.659A pdb=" N GLU H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 4.014A pdb=" N GLU H 82 " --> pdb=" O GLU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 100 removed outlier: 3.660A pdb=" N LEU H 90 " --> pdb=" O ASN H 86 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP H 100 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'I' and resid 5 through 15 removed outlier: 3.549A pdb=" N LEU I 15 " --> pdb=" O TYR I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 33 removed outlier: 3.797A pdb=" N VAL I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 49 Processing helix chain 'I' and resid 50 through 61 removed outlier: 3.757A pdb=" N GLU I 59 " --> pdb=" O LYS I 55 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS I 61 " --> pdb=" O LYS I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 84 Processing helix chain 'I' and resid 86 through 98 removed outlier: 3.565A pdb=" N LEU I 90 " --> pdb=" O ASN I 86 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 15 removed outlier: 3.675A pdb=" N LEU J 15 " --> pdb=" O TYR J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 33 removed outlier: 4.437A pdb=" N VAL J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 49 Processing helix chain 'J' and resid 50 through 59 removed outlier: 4.648A pdb=" N GLU J 59 " --> pdb=" O LYS J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 83 removed outlier: 3.828A pdb=" N LEU J 77 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU J 78 " --> pdb=" O ILE J 74 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU J 79 " --> pdb=" O GLU J 75 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN J 83 " --> pdb=" O GLU J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 100 removed outlier: 3.878A pdb=" N LEU J 90 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS J 92 " --> pdb=" O LYS J 88 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU J 93 " --> pdb=" O ASP J 89 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA J 94 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 70 removed outlier: 3.746A pdb=" N LEU K 55 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR K 70 " --> pdb=" O TYR K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 75 removed outlier: 4.278A pdb=" N VAL K 74 " --> pdb=" O PRO K 71 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN K 75 " --> pdb=" O TYR K 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 71 through 75' Processing helix chain 'K' and resid 77 through 82 removed outlier: 3.690A pdb=" N LEU K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 82' Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 116 through 122 Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 227 through 242 removed outlier: 3.786A pdb=" N LEU K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 301 removed outlier: 3.510A pdb=" N ALA K 289 " --> pdb=" O ASP K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 333 Processing helix chain 'L' and resid 51 through 69 removed outlier: 3.723A pdb=" N LEU L 55 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR L 69 " --> pdb=" O ASP L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 75 removed outlier: 4.422A pdb=" N VAL L 74 " --> pdb=" O PRO L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 82 removed outlier: 3.675A pdb=" N ARG L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 115 Processing helix chain 'L' and resid 116 through 121 Processing helix chain 'L' and resid 144 through 152 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 242 through 243 No H-bonds generated for 'chain 'L' and resid 242 through 243' Processing helix chain 'L' and resid 244 through 248 removed outlier: 3.600A pdb=" N SER L 247 " --> pdb=" O PRO L 244 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY L 248 " --> pdb=" O MET L 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 244 through 248' Processing helix chain 'L' and resid 285 through 301 removed outlier: 3.592A pdb=" N ALA L 289 " --> pdb=" O ASP L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 334 Processing helix chain 'M' and resid 51 through 69 removed outlier: 3.564A pdb=" N LEU M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 75 removed outlier: 4.488A pdb=" N VAL M 74 " --> pdb=" O PRO M 71 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN M 75 " --> pdb=" O TYR M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 removed outlier: 3.600A pdb=" N LEU M 81 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 77 through 82' Processing helix chain 'M' and resid 107 through 115 Processing helix chain 'M' and resid 115 through 122 Processing helix chain 'M' and resid 144 through 152 Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 242 through 247 Processing helix chain 'M' and resid 286 through 300 Processing helix chain 'M' and resid 324 through 335 removed outlier: 3.915A pdb=" N MET M 335 " --> pdb=" O ASN M 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 68 removed outlier: 3.506A pdb=" N LYS N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 75 removed outlier: 4.431A pdb=" N VAL N 74 " --> pdb=" O PRO N 71 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN N 75 " --> pdb=" O TYR N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 removed outlier: 3.501A pdb=" N LEU N 81 " --> pdb=" O THR N 77 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG N 82 " --> pdb=" O GLU N 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 77 through 82' Processing helix chain 'N' and resid 107 through 115 Processing helix chain 'N' and resid 115 through 122 Processing helix chain 'N' and resid 144 through 151 Processing helix chain 'N' and resid 227 through 241 Processing helix chain 'N' and resid 283 through 285 No H-bonds generated for 'chain 'N' and resid 283 through 285' Processing helix chain 'N' and resid 286 through 301 Processing helix chain 'N' and resid 324 through 335 removed outlier: 3.900A pdb=" N MET N 335 " --> pdb=" O ASN N 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 69 removed outlier: 3.752A pdb=" N LEU O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR O 69 " --> pdb=" O ASP O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 75 removed outlier: 4.182A pdb=" N VAL O 74 " --> pdb=" O PRO O 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN O 75 " --> pdb=" O TYR O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 removed outlier: 3.689A pdb=" N LEU O 81 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 77 through 82' Processing helix chain 'O' and resid 107 through 115 removed outlier: 3.690A pdb=" N ILE O 111 " --> pdb=" O ASP O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 122 Processing helix chain 'O' and resid 144 through 149 Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 227 through 241 Processing helix chain 'O' and resid 242 through 247 removed outlier: 3.743A pdb=" N SER O 247 " --> pdb=" O ILE O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 285 through 301 removed outlier: 3.545A pdb=" N ALA O 289 " --> pdb=" O ASP O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 335 removed outlier: 3.951A pdb=" N MET O 335 " --> pdb=" O ASN O 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 69 removed outlier: 3.745A pdb=" N LEU P 55 " --> pdb=" O THR P 51 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 82 removed outlier: 3.674A pdb=" N LEU P 81 " --> pdb=" O THR P 77 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG P 82 " --> pdb=" O GLU P 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 77 through 82' Processing helix chain 'P' and resid 107 through 115 removed outlier: 3.780A pdb=" N ILE P 111 " --> pdb=" O ASP P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 122 Processing helix chain 'P' and resid 144 through 150 Processing helix chain 'P' and resid 203 through 205 No H-bonds generated for 'chain 'P' and resid 203 through 205' Processing helix chain 'P' and resid 227 through 241 Processing helix chain 'P' and resid 285 through 301 Processing helix chain 'P' and resid 324 through 335 removed outlier: 3.898A pdb=" N LEU P 328 " --> pdb=" O SER P 324 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET P 335 " --> pdb=" O ASN P 331 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 41 removed outlier: 4.167A pdb=" N ALA Q 17 " --> pdb=" O GLU Q 13 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE Q 24 " --> pdb=" O ALA Q 20 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN Q 27 " --> pdb=" O GLU Q 23 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS Q 28 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) Proline residue: Q 31 - end of helix removed outlier: 4.325A pdb=" N THR Q 39 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL Q 40 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY Q 41 " --> pdb=" O MET Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 60 Processing helix chain 'Q' and resid 68 through 75 Processing helix chain 'Q' and resid 83 through 101 removed outlier: 4.374A pdb=" N VAL Q 87 " --> pdb=" O ARG Q 83 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS Q 101 " --> pdb=" O LYS Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 removed outlier: 3.610A pdb=" N PHE Q 107 " --> pdb=" O GLU Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 145 Processing helix chain 'Q' and resid 151 through 164 Processing helix chain 'Q' and resid 175 through 191 Processing helix chain 'Q' and resid 196 through 207 Processing helix chain 'Q' and resid 211 through 216 Processing helix chain 'Q' and resid 222 through 227 Processing helix chain 'Q' and resid 228 through 230 No H-bonds generated for 'chain 'Q' and resid 228 through 230' Processing helix chain 'R' and resid 19 through 23 removed outlier: 3.687A pdb=" N GLY R 23 " --> pdb=" O GLY R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 68 removed outlier: 3.776A pdb=" N LEU R 55 " --> pdb=" O THR R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 82 removed outlier: 3.583A pdb=" N LEU R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG R 82 " --> pdb=" O GLU R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 77 through 82' Processing helix chain 'R' and resid 107 through 115 removed outlier: 3.643A pdb=" N ILE R 111 " --> pdb=" O ASP R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 122 Processing helix chain 'R' and resid 144 through 150 Processing helix chain 'R' and resid 203 through 205 No H-bonds generated for 'chain 'R' and resid 203 through 205' Processing helix chain 'R' and resid 227 through 241 Processing helix chain 'R' and resid 285 through 301 removed outlier: 3.750A pdb=" N ALA R 289 " --> pdb=" O ASP R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 335 removed outlier: 3.961A pdb=" N MET R 335 " --> pdb=" O ASN R 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.548A pdb=" N LEU S 38 " --> pdb=" O LEU S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 70 Processing helix chain 'S' and resid 129 through 141 removed outlier: 4.569A pdb=" N LEU S 135 " --> pdb=" O GLU S 131 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET S 141 " --> pdb=" O LEU S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 182 removed outlier: 3.875A pdb=" N SER S 181 " --> pdb=" O THR S 177 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 23 removed outlier: 4.213A pdb=" N GLY T 22 " --> pdb=" O GLN T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 69 removed outlier: 3.799A pdb=" N LEU T 55 " --> pdb=" O THR T 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR T 69 " --> pdb=" O ASP T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 82 removed outlier: 3.619A pdb=" N LEU T 81 " --> pdb=" O THR T 77 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG T 82 " --> pdb=" O GLU T 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 77 through 82' Processing helix chain 'T' and resid 107 through 115 removed outlier: 3.756A pdb=" N ILE T 111 " --> pdb=" O ASP T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 122 Processing helix chain 'T' and resid 144 through 152 removed outlier: 3.797A pdb=" N GLU T 152 " --> pdb=" O ILE T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 227 through 241 Processing helix chain 'T' and resid 285 through 301 removed outlier: 3.953A pdb=" N ALA T 289 " --> pdb=" O ASP T 285 " (cutoff:3.500A) Processing helix chain 'T' and resid 325 through 335 removed outlier: 4.306A pdb=" N MET T 335 " --> pdb=" O ASN T 331 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 69 removed outlier: 4.245A pdb=" N THR V 69 " --> pdb=" O ASP V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 82 removed outlier: 4.027A pdb=" N LEU V 81 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG V 82 " --> pdb=" O GLU V 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 77 through 82' Processing helix chain 'V' and resid 107 through 114 Processing helix chain 'V' and resid 116 through 122 Processing helix chain 'V' and resid 144 through 152 removed outlier: 3.501A pdb=" N ILE V 148 " --> pdb=" O THR V 144 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU V 150 " --> pdb=" O ASP V 146 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU V 152 " --> pdb=" O ILE V 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 241 Processing helix chain 'V' and resid 285 through 301 removed outlier: 3.868A pdb=" N ALA V 289 " --> pdb=" O ASP V 285 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA V 297 " --> pdb=" O ILE V 293 " (cutoff:3.500A) Processing helix chain 'V' and resid 325 through 334 Processing helix chain 'W' and resid 20 through 24 removed outlier: 3.513A pdb=" N GLY W 23 " --> pdb=" O GLY W 20 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR W 24 " --> pdb=" O GLY W 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 20 through 24' Processing helix chain 'W' and resid 51 through 68 removed outlier: 3.583A pdb=" N LEU W 55 " --> pdb=" O THR W 51 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS W 68 " --> pdb=" O VAL W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 70 through 75 removed outlier: 3.927A pdb=" N VAL W 74 " --> pdb=" O PRO W 71 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN W 75 " --> pdb=" O TYR W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 82 removed outlier: 3.722A pdb=" N LEU W 81 " --> pdb=" O THR W 77 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG W 82 " --> pdb=" O GLU W 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 77 through 82' Processing helix chain 'W' and resid 107 through 115 removed outlier: 3.671A pdb=" N ILE W 111 " --> pdb=" O ASP W 107 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS W 113 " --> pdb=" O ALA W 109 " (cutoff:3.500A) Processing helix chain 'W' and resid 116 through 122 Processing helix chain 'W' and resid 144 through 152 removed outlier: 4.029A pdb=" N GLU W 152 " --> pdb=" O ILE W 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 205 Processing helix chain 'W' and resid 227 through 241 Processing helix chain 'W' and resid 242 through 247 removed outlier: 3.939A pdb=" N LEU W 246 " --> pdb=" O LEU W 242 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER W 247 " --> pdb=" O ILE W 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 242 through 247' Processing helix chain 'W' and resid 285 through 301 removed outlier: 3.978A pdb=" N ALA W 289 " --> pdb=" O ASP W 285 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY W 301 " --> pdb=" O ALA W 297 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 333 Processing helix chain 'Y' and resid 13 through 28 removed outlier: 4.450A pdb=" N VAL Y 23 " --> pdb=" O ALA Y 19 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL Y 24 " --> pdb=" O TYR Y 20 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG Y 28 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 71 removed outlier: 3.624A pdb=" N PHE Y 54 " --> pdb=" O SER Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 116 removed outlier: 3.538A pdb=" N TRP Y 100 " --> pdb=" O ASN Y 96 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP Y 101 " --> pdb=" O ASN Y 97 " (cutoff:3.500A) Proline residue: Y 104 - end of helix removed outlier: 4.300A pdb=" N LYS Y 116 " --> pdb=" O LYS Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 154 through 167 Processing helix chain 'Y' and resid 193 through 204 removed outlier: 3.685A pdb=" N LEU Y 203 " --> pdb=" O SER Y 199 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS Y 204 " --> pdb=" O LEU Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 219 removed outlier: 3.729A pdb=" N LEU Y 218 " --> pdb=" O LEU Y 215 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE Y 219 " --> pdb=" O ASP Y 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 215 through 219' Processing helix chain 'Y' and resid 220 through 231 removed outlier: 3.676A pdb=" N HIS Y 231 " --> pdb=" O TYR Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 240 removed outlier: 3.795A pdb=" N THR Y 239 " --> pdb=" O GLU Y 236 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 278 removed outlier: 3.598A pdb=" N MET Y 271 " --> pdb=" O ILE Y 267 " (cutoff:3.500A) Processing helix chain 'Y' and resid 285 through 295 Processing helix chain 'Y' and resid 296 through 310 Processing helix chain 'Y' and resid 311 through 326 removed outlier: 4.174A pdb=" N PHE Y 315 " --> pdb=" O ARG Y 311 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR Y 316 " --> pdb=" O LEU Y 312 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA Y 325 " --> pdb=" O LEU Y 321 " (cutoff:3.500A) Processing helix chain 'Y' and resid 330 through 342 removed outlier: 3.560A pdb=" N VAL Y 334 " --> pdb=" O SER Y 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.853A pdb=" N ILE A 197 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 39 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A 199 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A 196 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 164 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 69 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR A 131 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TYR A 71 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 236 removed outlier: 6.528A pdb=" N LYS A 233 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ILE A 361 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ARG A 235 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 332 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 258 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 2 through 14 current: chain 'K' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 184 through 201 current: chain 'K' and resid 305 through 309 Processing sheet with id=AA5, first strand: chain 'K' and resid 31 through 37 Processing sheet with id=AA6, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AA7, first strand: chain 'K' and resid 123 through 125 removed outlier: 6.914A pdb=" N PHE K 123 " --> pdb=" O ARG K 131 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG K 131 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 125 " --> pdb=" O GLY K 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 2 through 14 current: chain 'L' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 184 through 201 current: chain 'L' and resid 305 through 309 removed outlier: 7.008A pdb=" N VAL L 306 " --> pdb=" O THR L 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'L' and resid 31 through 36 Processing sheet with id=AB1, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AB2, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AB3, first strand: chain 'M' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 14 current: chain 'M' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 184 through 201 current: chain 'M' and resid 304 through 309 removed outlier: 9.172A pdb=" N THR M 320 " --> pdb=" O ILE M 304 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL M 306 " --> pdb=" O THR M 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 31 through 36 Processing sheet with id=AB5, first strand: chain 'M' and resid 94 through 96 Processing sheet with id=AB6, first strand: chain 'M' and resid 123 through 124 Processing sheet with id=AB7, first strand: chain 'N' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 2 through 14 current: chain 'N' and resid 183 through 196 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 183 through 196 current: chain 'N' and resid 305 through 309 removed outlier: 6.825A pdb=" N VAL N 306 " --> pdb=" O THR N 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'N' and resid 31 through 36 Processing sheet with id=AB9, first strand: chain 'N' and resid 94 through 96 Processing sheet with id=AC1, first strand: chain 'N' and resid 123 through 124 removed outlier: 3.745A pdb=" N ARG N 132 " --> pdb=" O PHE N 123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 2 through 14 current: chain 'O' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 190 through 196 current: chain 'O' and resid 306 through 309 Processing sheet with id=AC3, first strand: chain 'O' and resid 31 through 36 Processing sheet with id=AC4, first strand: chain 'O' and resid 94 through 96 Processing sheet with id=AC5, first strand: chain 'O' and resid 123 through 124 removed outlier: 3.669A pdb=" N PHE O 123 " --> pdb=" O ARG O 132 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG O 132 " --> pdb=" O PHE O 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'O' and resid 160 through 161 Processing sheet with id=AC7, first strand: chain 'O' and resid 213 through 215 Processing sheet with id=AC8, first strand: chain 'P' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 2 through 14 current: chain 'P' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 190 through 196 current: chain 'P' and resid 306 through 309 Processing sheet with id=AC9, first strand: chain 'P' and resid 26 through 27 Processing sheet with id=AD1, first strand: chain 'P' and resid 31 through 36 Processing sheet with id=AD2, first strand: chain 'P' and resid 94 through 96 Processing sheet with id=AD3, first strand: chain 'P' and resid 123 through 124 removed outlier: 3.675A pdb=" N PHE P 123 " --> pdb=" O ARG P 132 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 213 through 215 Processing sheet with id=AD5, first strand: chain 'R' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 2 through 14 current: chain 'R' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 190 through 196 current: chain 'R' and resid 306 through 309 Processing sheet with id=AD6, first strand: chain 'R' and resid 31 through 36 Processing sheet with id=AD7, first strand: chain 'R' and resid 94 through 96 Processing sheet with id=AD8, first strand: chain 'R' and resid 123 through 124 Processing sheet with id=AD9, first strand: chain 'R' and resid 213 through 215 Processing sheet with id=AE1, first strand: chain 'S' and resid 77 through 79 removed outlier: 3.639A pdb=" N LEU S 120 " --> pdb=" O ALA S 79 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE S 3 " --> pdb=" O PHE S 160 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE S 160 " --> pdb=" O ILE S 3 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU S 5 " --> pdb=" O ALA S 158 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA S 158 " --> pdb=" O LEU S 5 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N CYS S 7 " --> pdb=" O VAL S 156 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 12 through 13 Processing sheet with id=AE3, first strand: chain 'S' and resid 168 through 169 removed outlier: 3.652A pdb=" N ALA S 168 " --> pdb=" O VAL S 240 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 174 through 175 removed outlier: 4.135A pdb=" N ALA S 174 " --> pdb=" O TYR S 218 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 242 through 246 removed outlier: 3.996A pdb=" N LYS S 242 " --> pdb=" O ILE S 253 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 2 through 14 current: chain 'T' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 190 through 196 current: chain 'T' and resid 306 through 309 removed outlier: 6.998A pdb=" N VAL T 306 " --> pdb=" O THR T 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'T' and resid 31 through 36 Processing sheet with id=AE8, first strand: chain 'T' and resid 94 through 96 Processing sheet with id=AE9, first strand: chain 'T' and resid 123 through 124 removed outlier: 3.632A pdb=" N PHE T 123 " --> pdb=" O ARG T 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 160 through 161 Processing sheet with id=AF2, first strand: chain 'T' and resid 213 through 215 Processing sheet with id=AF3, first strand: chain 'V' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 2 through 14 current: chain 'V' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 190 through 196 current: chain 'V' and resid 306 through 309 Processing sheet with id=AF4, first strand: chain 'V' and resid 26 through 27 removed outlier: 3.909A pdb=" N ARG V 187 " --> pdb=" O ILE V 160 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE V 160 " --> pdb=" O ARG V 187 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 31 through 36 Processing sheet with id=AF6, first strand: chain 'V' and resid 95 through 96 Processing sheet with id=AF7, first strand: chain 'V' and resid 123 through 124 removed outlier: 3.640A pdb=" N PHE V 123 " --> pdb=" O ARG V 132 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG V 132 " --> pdb=" O PHE V 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'V' and resid 213 through 215 Processing sheet with id=AF9, first strand: chain 'W' and resid 3 through 12 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 3 through 12 current: chain 'W' and resid 306 through 309 Processing sheet with id=AG1, first strand: chain 'W' and resid 31 through 36 Processing sheet with id=AG2, first strand: chain 'W' and resid 95 through 96 Processing sheet with id=AG3, first strand: chain 'W' and resid 123 through 124 Processing sheet with id=AG4, first strand: chain 'W' and resid 213 through 215 Processing sheet with id=AG5, first strand: chain 'Y' and resid 35 through 37 Processing sheet with id=AG6, first strand: chain 'Y' and resid 123 through 124 Processing sheet with id=AG7, first strand: chain 'Y' and resid 170 through 173 removed outlier: 3.833A pdb=" N ALA Y 258 " --> pdb=" O GLU Y 251 " (cutoff:3.500A) 1330 hydrogen bonds defined for protein. 3807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 14.35 Time building geometry restraints manager: 18.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13568 1.34 - 1.46: 8279 1.46 - 1.58: 22763 1.58 - 1.70: 136 1.70 - 1.82: 178 Bond restraints: 44924 Sorted by residual: bond pdb=" N VAL Y 98 " pdb=" CA VAL Y 98 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.30e-02 5.92e+03 7.76e+00 bond pdb=" N THR Y 125 " pdb=" CA THR Y 125 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.30e-02 5.92e+03 5.18e+00 bond pdb=" N GLY A 611 " pdb=" CA GLY A 611 " ideal model delta sigma weight residual 1.449 1.481 -0.031 1.45e-02 4.76e+03 4.71e+00 bond pdb=" N TYR Y 99 " pdb=" CA TYR Y 99 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.28e-02 6.10e+03 4.71e+00 bond pdb=" O3' DG D 48 " pdb=" P DG D 49 " ideal model delta sigma weight residual 1.607 1.633 -0.026 1.50e-02 4.44e+03 3.10e+00 ... (remaining 44919 not shown) Histogram of bond angle deviations from ideal: 95.27 - 103.03: 394 103.03 - 110.79: 14726 110.79 - 118.55: 21090 118.55 - 126.31: 24264 126.31 - 134.07: 736 Bond angle restraints: 61210 Sorted by residual: angle pdb=" N PRO A 529 " pdb=" CA PRO A 529 " pdb=" CB PRO A 529 " ideal model delta sigma weight residual 103.25 111.19 -7.94 1.05e+00 9.07e-01 5.72e+01 angle pdb=" N PRO A 595 " pdb=" CA PRO A 595 " pdb=" CB PRO A 595 " ideal model delta sigma weight residual 103.25 110.59 -7.34 1.05e+00 9.07e-01 4.89e+01 angle pdb=" N PRO A 521 " pdb=" CA PRO A 521 " pdb=" CB PRO A 521 " ideal model delta sigma weight residual 103.25 110.00 -6.75 1.05e+00 9.07e-01 4.14e+01 angle pdb=" N PRO Q 224 " pdb=" CA PRO Q 224 " pdb=" CB PRO Q 224 " ideal model delta sigma weight residual 103.33 110.24 -6.91 1.10e+00 8.26e-01 3.94e+01 angle pdb=" C ARG A 351 " pdb=" CA ARG A 351 " pdb=" CB ARG A 351 " ideal model delta sigma weight residual 116.63 110.50 6.13 1.16e+00 7.43e-01 2.79e+01 ... (remaining 61205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.52: 26213 31.52 - 63.04: 865 63.04 - 94.55: 95 94.55 - 126.07: 1 126.07 - 157.59: 5 Dihedral angle restraints: 27179 sinusoidal: 11426 harmonic: 15753 Sorted by residual: dihedral pdb=" CB CYS I 63 " pdb=" SG CYS I 63 " pdb=" SG CYS I 108 " pdb=" CB CYS I 108 " ideal model delta sinusoidal sigma weight residual -86.00 -167.89 81.89 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" O4' C U 40 " pdb=" C1' C U 40 " pdb=" N1 C U 40 " pdb=" C2 C U 40 " ideal model delta sinusoidal sigma weight residual 200.00 42.41 157.59 1 1.50e+01 4.44e-03 8.21e+01 dihedral pdb=" O4' U U 42 " pdb=" C1' U U 42 " pdb=" N1 U U 42 " pdb=" C2 U U 42 " ideal model delta sinusoidal sigma weight residual 200.00 45.30 154.70 1 1.50e+01 4.44e-03 8.12e+01 ... (remaining 27176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 5864 0.059 - 0.119: 1071 0.119 - 0.178: 87 0.178 - 0.237: 8 0.237 - 0.297: 4 Chirality restraints: 7034 Sorted by residual: chirality pdb=" CB VAL Q 202 " pdb=" CA VAL Q 202 " pdb=" CG1 VAL Q 202 " pdb=" CG2 VAL Q 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA GLU G 82 " pdb=" N GLU G 82 " pdb=" C GLU G 82 " pdb=" CB GLU G 82 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA TRP T 58 " pdb=" N TRP T 58 " pdb=" C TRP T 58 " pdb=" CB TRP T 58 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 7031 not shown) Planarity restraints: 7612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 610 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C LEU A 610 " 0.079 2.00e-02 2.50e+03 pdb=" O LEU A 610 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY A 611 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 64 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO A 65 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 155 " -0.020 2.00e-02 2.50e+03 1.78e-02 5.56e+00 pdb=" CG PHE Q 155 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 155 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 155 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 155 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 155 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE Q 155 " -0.008 2.00e-02 2.50e+03 ... (remaining 7609 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 712 2.64 - 3.21: 42547 3.21 - 3.77: 70390 3.77 - 4.34: 95660 4.34 - 4.90: 151904 Nonbonded interactions: 361213 Sorted by model distance: nonbonded pdb=" O ALA J 34 " pdb=" NH2 ARG J 91 " model vdw 2.077 2.520 nonbonded pdb=" NZ LYS T 262 " pdb=" OE1 GLU T 264 " model vdw 2.112 2.520 nonbonded pdb=" NH2 ARG S 228 " pdb=" OE1 GLU Y 265 " model vdw 2.120 2.520 nonbonded pdb=" ND2 ASN V 17 " pdb=" OG1 THR V 30 " model vdw 2.123 2.520 nonbonded pdb=" NE2 HIS Q 117 " pdb="NI NI Q 302 " model vdw 2.152 2.260 ... (remaining 361208 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 'C' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 3 through 109) selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 157 or resid 190 th \ rough 335)) selection = (chain 'L' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 157 or resid 190 through 335)) selection = (chain 'M' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'N' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'O' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'P' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'R' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'T' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'V' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'W' and resid 1 through 335) } 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 9.510 Check model and map are aligned: 0.640 Set scattering table: 0.390 Process input model: 112.590 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.180 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 : 0.003 0.047 44924 Z= 0.175 Angle : 0.672 12.549 61210 Z= 0.358 Chirality : 0.045 0.297 7034 Planarity : 0.004 0.082 7612 Dihedral : 15.109 157.589 17041 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.43 % Favored : 92.29 % Rotamer: Outliers : 0.04 % Allowed : 0.43 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.11), residues: 5407 helix: 0.22 (0.13), residues: 1801 sheet: -0.24 (0.18), residues: 779 loop : -1.51 (0.11), residues: 2827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP V 58 HIS 0.010 0.001 HIS Y 56 PHE 0.041 0.001 PHE Q 155 TYR 0.027 0.001 TYR S 20 ARG 0.010 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 601 time to evaluate : 5.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.4376 (mtt) cc_final: 0.4138 (mtt) REVERT: A 197 ILE cc_start: 0.7799 (pt) cc_final: 0.7516 (pt) REVERT: A 198 MET cc_start: 0.6992 (mmt) cc_final: 0.6424 (ppp) REVERT: A 209 MET cc_start: 0.7624 (ptp) cc_final: 0.7363 (ptp) REVERT: C 78 GLU cc_start: 0.7132 (tp30) cc_final: 0.6829 (tp30) REVERT: F 29 ASP cc_start: 0.8514 (m-30) cc_final: 0.8142 (m-30) REVERT: H 88 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8728 (tptt) REVERT: J 23 TYR cc_start: 0.8305 (m-80) cc_final: 0.8100 (m-10) REVERT: J 57 LYS cc_start: 0.8631 (tptp) cc_final: 0.8350 (tptp) REVERT: J 106 ASN cc_start: 0.7556 (t0) cc_final: 0.7214 (t0) REVERT: N 245 MET cc_start: 0.7982 (mmt) cc_final: 0.7639 (mmm) REVERT: Q 57 ILE cc_start: 0.9122 (mm) cc_final: 0.8808 (mm) REVERT: Q 90 TYR cc_start: 0.8679 (t80) cc_final: 0.7993 (t80) REVERT: Q 115 MET cc_start: 0.9108 (mpp) cc_final: 0.8678 (mpp) REVERT: Q 116 HIS cc_start: 0.8219 (t-90) cc_final: 0.7762 (t-90) REVERT: Q 117 HIS cc_start: 0.5960 (m-70) cc_final: 0.5260 (m-70) REVERT: Q 122 MET cc_start: 0.6787 (ppp) cc_final: 0.6309 (ppp) REVERT: Q 145 PHE cc_start: 0.8928 (t80) cc_final: 0.8411 (t80) REVERT: Q 170 VAL cc_start: 0.7581 (p) cc_final: 0.7357 (t) REVERT: R 1 MET cc_start: 0.6260 (mpp) cc_final: 0.5995 (mpp) REVERT: R 189 TYR cc_start: 0.7545 (m-10) cc_final: 0.7084 (m-10) REVERT: R 309 TYR cc_start: 0.7981 (t80) cc_final: 0.7669 (t80) REVERT: S 109 MET cc_start: 0.7555 (mmm) cc_final: 0.6780 (mmm) REVERT: T 17 ASN cc_start: 0.6841 (t160) cc_final: 0.6481 (t0) REVERT: T 51 THR cc_start: 0.8813 (t) cc_final: 0.8601 (p) REVERT: T 117 ASP cc_start: 0.8115 (p0) cc_final: 0.7842 (p0) REVERT: T 316 ASP cc_start: 0.8615 (p0) cc_final: 0.8413 (p0) REVERT: V 6 SER cc_start: 0.8443 (m) cc_final: 0.8239 (m) REVERT: V 123 PHE cc_start: 0.7696 (p90) cc_final: 0.7303 (p90) REVERT: V 124 LEU cc_start: 0.7517 (tp) cc_final: 0.7084 (tt) REVERT: V 239 LEU cc_start: 0.9131 (pp) cc_final: 0.8922 (pp) REVERT: V 307 PHE cc_start: 0.8233 (m-80) cc_final: 0.7822 (m-80) REVERT: W 140 PHE cc_start: 0.7125 (m-10) cc_final: 0.5905 (m-80) REVERT: W 229 ASN cc_start: 0.8373 (m-40) cc_final: 0.7856 (p0) REVERT: W 230 GLU cc_start: 0.8706 (mp0) cc_final: 0.8407 (pm20) REVERT: Y 65 MET cc_start: 0.9064 (ttt) cc_final: 0.8510 (mtp) outliers start: 2 outliers final: 0 residues processed: 603 average time/residue: 0.5288 time to fit residues: 530.5008 Evaluate side-chains 451 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 455 optimal weight: 9.9990 chunk 408 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 275 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 422 optimal weight: 40.0000 chunk 163 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 489 optimal weight: 40.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN ** O 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** P 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 ASN ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 9 GLN ** Y 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 44924 Z= 0.334 Angle : 0.691 13.951 61210 Z= 0.354 Chirality : 0.046 0.217 7034 Planarity : 0.005 0.060 7612 Dihedral : 11.989 157.117 6969 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.45 % Favored : 91.29 % Rotamer: Outliers : 1.28 % Allowed : 11.13 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.11), residues: 5407 helix: 0.21 (0.13), residues: 1879 sheet: -0.58 (0.17), residues: 854 loop : -1.64 (0.12), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 24 HIS 0.019 0.002 HIS Q 72 PHE 0.045 0.002 PHE V 185 TYR 0.036 0.002 TYR R 189 ARG 0.021 0.001 ARG Q 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 473 time to evaluate : 5.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.4478 (mtt) cc_final: 0.4096 (ttm) REVERT: A 69 LEU cc_start: 0.8723 (tt) cc_final: 0.8046 (mt) REVERT: A 133 TRP cc_start: 0.7968 (t60) cc_final: 0.7682 (t60) REVERT: A 197 ILE cc_start: 0.7602 (pt) cc_final: 0.7219 (pt) REVERT: A 198 MET cc_start: 0.6887 (mmt) cc_final: 0.6455 (ppp) REVERT: C 39 GLU cc_start: 0.7396 (pt0) cc_final: 0.7137 (pm20) REVERT: C 67 ARG cc_start: 0.6567 (tpt90) cc_final: 0.6216 (tmt170) REVERT: C 78 GLU cc_start: 0.7110 (tp30) cc_final: 0.6739 (tp30) REVERT: F 29 ASP cc_start: 0.8630 (m-30) cc_final: 0.8161 (m-30) REVERT: F 53 LYS cc_start: 0.9397 (tttp) cc_final: 0.9144 (tmtt) REVERT: F 92 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8526 (mmtm) REVERT: H 89 ASP cc_start: 0.9215 (m-30) cc_final: 0.8994 (m-30) REVERT: I 23 TYR cc_start: 0.7953 (m-80) cc_final: 0.7511 (m-80) REVERT: J 42 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8464 (mt-10) REVERT: J 45 TYR cc_start: 0.6276 (m-80) cc_final: 0.5514 (m-80) REVERT: J 57 LYS cc_start: 0.8692 (tptp) cc_final: 0.8395 (tptp) REVERT: J 106 ASN cc_start: 0.7445 (t0) cc_final: 0.7212 (t0) REVERT: O 1 MET cc_start: 0.7960 (mmm) cc_final: 0.7254 (tpp) REVERT: Q 90 TYR cc_start: 0.8645 (t80) cc_final: 0.8263 (t80) REVERT: Q 116 HIS cc_start: 0.8251 (t-90) cc_final: 0.7953 (t-90) REVERT: Q 122 MET cc_start: 0.6619 (ppp) cc_final: 0.6152 (ppp) REVERT: Q 145 PHE cc_start: 0.8860 (t80) cc_final: 0.8212 (t80) REVERT: R 1 MET cc_start: 0.6488 (mpp) cc_final: 0.6019 (mpp) REVERT: R 309 TYR cc_start: 0.8103 (t80) cc_final: 0.7717 (t80) REVERT: S 109 MET cc_start: 0.7589 (mmm) cc_final: 0.6842 (mmm) REVERT: T 14 HIS cc_start: 0.9054 (p90) cc_final: 0.7702 (p90) REVERT: T 17 ASN cc_start: 0.6562 (t0) cc_final: 0.6011 (t0) REVERT: T 19 GLN cc_start: 0.7533 (tp-100) cc_final: 0.7230 (tp-100) REVERT: T 117 ASP cc_start: 0.8075 (p0) cc_final: 0.7777 (p0) REVERT: T 316 ASP cc_start: 0.8645 (p0) cc_final: 0.8418 (p0) REVERT: V 6 SER cc_start: 0.8163 (m) cc_final: 0.7771 (m) REVERT: V 231 ARG cc_start: 0.7399 (mmm-85) cc_final: 0.6557 (mtt180) REVERT: V 286 TYR cc_start: 0.7602 (p90) cc_final: 0.7327 (p90) REVERT: V 307 PHE cc_start: 0.8290 (m-80) cc_final: 0.7675 (m-80) REVERT: W 229 ASN cc_start: 0.8390 (m-40) cc_final: 0.7891 (p0) REVERT: W 230 GLU cc_start: 0.8827 (mp0) cc_final: 0.8527 (pm20) REVERT: W 246 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8242 (mm) REVERT: W 295 LYS cc_start: 0.8940 (ptmm) cc_final: 0.8301 (mttt) REVERT: Y 65 MET cc_start: 0.9149 (ttt) cc_final: 0.8941 (mtp) REVERT: Y 222 ARG cc_start: 0.8046 (tpp-160) cc_final: 0.7526 (tpp80) outliers start: 57 outliers final: 32 residues processed: 506 average time/residue: 0.5495 time to fit residues: 462.6031 Evaluate side-chains 459 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 426 time to evaluate : 4.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 313 LEU Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 334 LYS Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 201 ASP Chi-restraints excluded: chain V residue 303 ASN Chi-restraints excluded: chain W residue 246 LEU Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain Y residue 54 PHE Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 297 THR Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 0.3980 chunk 407 optimal weight: 9.9990 chunk 333 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 490 optimal weight: 10.0000 chunk 529 optimal weight: 5.9990 chunk 436 optimal weight: 3.9990 chunk 486 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 393 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN K 290 ASN O 12 ASN P 17 ASN P 253 ASN ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 ASN V 331 ASN ** W 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 309 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 44924 Z= 0.195 Angle : 0.608 11.887 61210 Z= 0.304 Chirality : 0.044 0.290 7034 Planarity : 0.004 0.059 7612 Dihedral : 11.933 157.009 6969 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.55 % Favored : 92.23 % Rotamer: Outliers : 1.86 % Allowed : 14.33 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.11), residues: 5407 helix: 0.35 (0.13), residues: 1877 sheet: -0.36 (0.18), residues: 774 loop : -1.59 (0.11), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 24 HIS 0.008 0.001 HIS Q 84 PHE 0.025 0.001 PHE Q 155 TYR 0.032 0.001 TYR Y 20 ARG 0.006 0.000 ARG P 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 470 time to evaluate : 5.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.4368 (mtt) cc_final: 0.4033 (ttm) REVERT: A 127 TRP cc_start: 0.6496 (m-10) cc_final: 0.6030 (m100) REVERT: A 197 ILE cc_start: 0.7602 (pt) cc_final: 0.7384 (pt) REVERT: A 198 MET cc_start: 0.7036 (mmt) cc_final: 0.6644 (tmm) REVERT: C 26 ASP cc_start: 0.8449 (t0) cc_final: 0.8161 (t70) REVERT: C 35 ARG cc_start: 0.7791 (tpt90) cc_final: 0.7204 (mmm160) REVERT: C 75 GLU cc_start: 0.7139 (mp0) cc_final: 0.6736 (mp0) REVERT: C 78 GLU cc_start: 0.7091 (tp30) cc_final: 0.6710 (tp30) REVERT: F 29 ASP cc_start: 0.8580 (m-30) cc_final: 0.8182 (m-30) REVERT: F 53 LYS cc_start: 0.9394 (tttp) cc_final: 0.9148 (tmtt) REVERT: H 89 ASP cc_start: 0.9205 (m-30) cc_final: 0.8978 (m-30) REVERT: I 23 TYR cc_start: 0.7968 (m-80) cc_final: 0.7563 (m-80) REVERT: I 48 LEU cc_start: 0.9355 (tp) cc_final: 0.9131 (tp) REVERT: J 42 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8453 (mt-10) REVERT: J 45 TYR cc_start: 0.6382 (m-80) cc_final: 0.5544 (m-80) REVERT: J 57 LYS cc_start: 0.8676 (tptp) cc_final: 0.8380 (tptp) REVERT: J 106 ASN cc_start: 0.7446 (t0) cc_final: 0.7228 (t0) REVERT: N 245 MET cc_start: 0.8486 (mmp) cc_final: 0.7804 (mmm) REVERT: O 1 MET cc_start: 0.8075 (mmm) cc_final: 0.7554 (tpp) REVERT: P 54 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7966 (mmm) REVERT: Q 84 HIS cc_start: 0.4308 (p-80) cc_final: 0.3623 (p-80) REVERT: Q 90 TYR cc_start: 0.8604 (t80) cc_final: 0.8330 (t80) REVERT: Q 117 HIS cc_start: 0.6353 (m-70) cc_final: 0.6130 (m-70) REVERT: Q 122 MET cc_start: 0.6599 (ppp) cc_final: 0.6141 (ppp) REVERT: Q 145 PHE cc_start: 0.8771 (t80) cc_final: 0.8167 (t80) REVERT: R 1 MET cc_start: 0.6334 (mpp) cc_final: 0.5820 (mpp) REVERT: S 109 MET cc_start: 0.7481 (mmm) cc_final: 0.6827 (mmm) REVERT: T 17 ASN cc_start: 0.6514 (t0) cc_final: 0.5979 (t0) REVERT: T 54 MET cc_start: 0.7748 (mmp) cc_final: 0.7061 (mmp) REVERT: T 58 TRP cc_start: 0.6475 (m-90) cc_final: 0.5947 (m100) REVERT: T 117 ASP cc_start: 0.8068 (p0) cc_final: 0.7797 (p0) REVERT: T 316 ASP cc_start: 0.8605 (p0) cc_final: 0.8366 (p0) REVERT: V 5 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9010 (tp) REVERT: V 68 LYS cc_start: 0.8109 (pttt) cc_final: 0.7752 (pttt) REVERT: V 231 ARG cc_start: 0.7292 (mmm-85) cc_final: 0.6629 (mmt180) REVERT: V 236 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8731 (mm-30) REVERT: V 286 TYR cc_start: 0.7513 (p90) cc_final: 0.7256 (p90) REVERT: V 307 PHE cc_start: 0.8243 (m-80) cc_final: 0.7786 (m-80) REVERT: W 229 ASN cc_start: 0.8450 (m-40) cc_final: 0.8002 (p0) REVERT: W 295 LYS cc_start: 0.8835 (ptmm) cc_final: 0.8159 (mttt) REVERT: Y 65 MET cc_start: 0.9046 (ttt) cc_final: 0.8652 (mtp) REVERT: Y 68 LEU cc_start: 0.8397 (tt) cc_final: 0.7822 (mt) REVERT: Y 111 MET cc_start: 0.7801 (mmp) cc_final: 0.6982 (mmp) REVERT: Y 131 MET cc_start: 0.6411 (ttt) cc_final: 0.6179 (ttt) REVERT: Y 222 ARG cc_start: 0.7989 (tpp-160) cc_final: 0.7329 (tpp80) REVERT: Y 307 ILE cc_start: 0.7396 (mm) cc_final: 0.6853 (tt) outliers start: 83 outliers final: 48 residues processed: 517 average time/residue: 0.5641 time to fit residues: 484.7368 Evaluate side-chains 484 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 433 time to evaluate : 4.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 334 LYS Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 201 ASP Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 253 ASN Chi-restraints excluded: chain V residue 303 ASN Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 333 VAL Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain Y residue 54 PHE Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 484 optimal weight: 20.0000 chunk 368 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 chunk 329 optimal weight: 6.9990 chunk 492 optimal weight: 30.0000 chunk 521 optimal weight: 8.9990 chunk 257 optimal weight: 5.9990 chunk 466 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN L 162 HIS N 162 HIS ** O 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 GLN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 255 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 44924 Z= 0.568 Angle : 0.808 10.828 61210 Z= 0.422 Chirality : 0.050 0.287 7034 Planarity : 0.006 0.079 7612 Dihedral : 12.283 159.246 6969 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.67 % Favored : 90.09 % Rotamer: Outliers : 3.85 % Allowed : 16.63 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.58 (0.11), residues: 5407 helix: -0.06 (0.12), residues: 1851 sheet: -1.10 (0.17), residues: 828 loop : -1.73 (0.12), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 24 HIS 0.016 0.002 HIS Q 117 PHE 0.033 0.003 PHE K 258 TYR 0.029 0.002 TYR Y 20 ARG 0.009 0.001 ARG S 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 422 time to evaluate : 5.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.4388 (mtt) cc_final: 0.4007 (ttm) REVERT: A 133 TRP cc_start: 0.8142 (t60) cc_final: 0.6675 (t-100) REVERT: A 198 MET cc_start: 0.7251 (mmt) cc_final: 0.6610 (tmm) REVERT: F 29 ASP cc_start: 0.8547 (m-30) cc_final: 0.8277 (m-30) REVERT: G 92 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8441 (pptt) REVERT: H 83 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: I 23 TYR cc_start: 0.8294 (m-80) cc_final: 0.7988 (m-80) REVERT: J 57 LYS cc_start: 0.8813 (tptp) cc_final: 0.8520 (tptp) REVERT: J 106 ASN cc_start: 0.7609 (t0) cc_final: 0.7358 (t0) REVERT: L 19 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6512 (mp10) REVERT: L 158 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.9035 (p) REVERT: L 165 VAL cc_start: 0.7939 (OUTLIER) cc_final: 0.7617 (p) REVERT: L 335 MET cc_start: 0.8699 (ppp) cc_final: 0.8393 (ptm) REVERT: M 183 MET cc_start: 0.7110 (tpp) cc_final: 0.6825 (mmp) REVERT: M 335 MET cc_start: 0.8441 (ppp) cc_final: 0.7929 (ptt) REVERT: N 156 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8149 (pp) REVERT: N 245 MET cc_start: 0.8520 (mmp) cc_final: 0.8075 (mmm) REVERT: O 1 MET cc_start: 0.8176 (mmm) cc_final: 0.7610 (tpp) REVERT: O 183 MET cc_start: 0.7467 (pmm) cc_final: 0.6742 (pmm) REVERT: Q 9 GLN cc_start: 0.4780 (mp10) cc_final: 0.4454 (mt0) REVERT: Q 90 TYR cc_start: 0.8565 (t80) cc_final: 0.8151 (t80) REVERT: Q 122 MET cc_start: 0.6642 (ppp) cc_final: 0.6306 (ppp) REVERT: Q 145 PHE cc_start: 0.8720 (t80) cc_final: 0.8133 (t80) REVERT: S 84 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9093 (mt) REVERT: S 109 MET cc_start: 0.7580 (mmm) cc_final: 0.7161 (mmm) REVERT: T 19 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7419 (tp-100) REVERT: T 58 TRP cc_start: 0.6975 (m-90) cc_final: 0.6774 (m100) REVERT: T 249 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: V 5 ILE cc_start: 0.9715 (OUTLIER) cc_final: 0.9196 (tp) REVERT: V 117 ASP cc_start: 0.8150 (p0) cc_final: 0.7938 (m-30) REVERT: V 231 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7294 (mmt90) REVERT: V 236 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8762 (mm-30) REVERT: V 253 ASN cc_start: 0.6864 (t0) cc_final: 0.6416 (t0) REVERT: V 286 TYR cc_start: 0.8089 (p90) cc_final: 0.7572 (p90) REVERT: V 307 PHE cc_start: 0.8304 (m-80) cc_final: 0.7823 (m-80) REVERT: W 229 ASN cc_start: 0.8551 (m-40) cc_final: 0.8165 (p0) REVERT: W 236 GLU cc_start: 0.8595 (mp0) cc_final: 0.7997 (mm-30) REVERT: W 246 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8303 (mm) REVERT: W 290 ASN cc_start: 0.7552 (m-40) cc_final: 0.7313 (m-40) REVERT: Y 111 MET cc_start: 0.7374 (mmp) cc_final: 0.7001 (mmp) REVERT: Y 131 MET cc_start: 0.7102 (ttt) cc_final: 0.6872 (ttt) REVERT: Y 219 ILE cc_start: 0.5355 (OUTLIER) cc_final: 0.5072 (mm) REVERT: Y 222 ARG cc_start: 0.8095 (tpp-160) cc_final: 0.7368 (tpp80) REVERT: Y 307 ILE cc_start: 0.7609 (mm) cc_final: 0.7113 (tt) outliers start: 172 outliers final: 109 residues processed: 554 average time/residue: 0.5383 time to fit residues: 501.3276 Evaluate side-chains 518 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 397 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 61 LYS Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 303 ASN Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain L residue 19 GLN Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain N residue 235 ILE Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 185 PHE Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 201 ASP Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 37 MET Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 148 ASP Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 140 PHE Chi-restraints excluded: chain T residue 249 TYR Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 334 LYS Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 201 ASP Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 303 ASN Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 246 LEU Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 186 ILE Chi-restraints excluded: chain Y residue 219 ILE Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 297 THR Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 433 optimal weight: 9.9990 chunk 295 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 387 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 444 optimal weight: 20.0000 chunk 360 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 266 optimal weight: 2.9990 chunk 467 optimal weight: 0.0070 chunk 131 optimal weight: 3.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN P 182 GLN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 GLN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 44924 Z= 0.217 Angle : 0.644 13.260 61210 Z= 0.324 Chirality : 0.045 0.331 7034 Planarity : 0.004 0.067 7612 Dihedral : 12.240 160.302 6969 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.84 % Favored : 91.94 % Rotamer: Outliers : 2.84 % Allowed : 18.89 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.11), residues: 5407 helix: 0.33 (0.13), residues: 1840 sheet: -0.40 (0.19), residues: 684 loop : -1.72 (0.11), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 24 HIS 0.014 0.001 HIS Q 117 PHE 0.030 0.002 PHE P 185 TYR 0.034 0.001 TYR Y 20 ARG 0.010 0.001 ARG M 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 448 time to evaluate : 5.450 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: A 31 MET cc_start: 0.4369 (mtt) cc_final: 0.3971 (ttm) REVERT: A 133 TRP cc_start: 0.8093 (t60) cc_final: 0.7738 (t60) REVERT: A 198 MET cc_start: 0.7286 (mmt) cc_final: 0.6771 (tmm) REVERT: A 209 MET cc_start: 0.7518 (ptt) cc_final: 0.7116 (ppp) REVERT: C 10 ARG cc_start: 0.6649 (mmp-170) cc_final: 0.6338 (mmm160) REVERT: C 39 GLU cc_start: 0.6302 (pm20) cc_final: 0.5985 (pm20) REVERT: C 67 ARG cc_start: 0.6846 (tpt90) cc_final: 0.6546 (tpt90) REVERT: E 15 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5749 (tt) REVERT: F 29 ASP cc_start: 0.8437 (m-30) cc_final: 0.8139 (m-30) REVERT: G 80 LYS cc_start: 0.9167 (pptt) cc_final: 0.8956 (pptt) REVERT: H 83 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: I 23 TYR cc_start: 0.8082 (m-80) cc_final: 0.7782 (m-80) REVERT: I 46 LYS cc_start: 0.9493 (mmmt) cc_final: 0.8996 (mmtm) REVERT: J 42 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8389 (mt-10) REVERT: J 45 TYR cc_start: 0.6328 (m-80) cc_final: 0.5514 (m-80) REVERT: J 106 ASN cc_start: 0.7563 (t0) cc_final: 0.7314 (t0) REVERT: J 107 ASN cc_start: 0.7918 (p0) cc_final: 0.7670 (p0) REVERT: K 295 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8670 (tppt) REVERT: L 19 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6043 (mt0) REVERT: L 335 MET cc_start: 0.8558 (ppp) cc_final: 0.8186 (ptm) REVERT: M 335 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7820 (ptt) REVERT: N 54 MET cc_start: 0.8942 (tpp) cc_final: 0.8437 (tpp) REVERT: N 156 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7994 (pp) REVERT: N 245 MET cc_start: 0.8519 (mmp) cc_final: 0.8270 (mmm) REVERT: O 1 MET cc_start: 0.8170 (mmm) cc_final: 0.7845 (tpp) REVERT: O 183 MET cc_start: 0.7185 (pmm) cc_final: 0.6654 (pmm) REVERT: Q 90 TYR cc_start: 0.8581 (t80) cc_final: 0.8350 (t80) REVERT: Q 122 MET cc_start: 0.6826 (ppp) cc_final: 0.6409 (ppp) REVERT: Q 145 PHE cc_start: 0.8619 (t80) cc_final: 0.8107 (t80) REVERT: R 332 LEU cc_start: 0.9465 (mt) cc_final: 0.9246 (mp) REVERT: S 105 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7581 (ptmm) REVERT: S 109 MET cc_start: 0.7534 (mmm) cc_final: 0.7031 (mmm) REVERT: T 54 MET cc_start: 0.7813 (mmp) cc_final: 0.7066 (mmp) REVERT: T 58 TRP cc_start: 0.6931 (m-90) cc_final: 0.5925 (m100) REVERT: V 66 TYR cc_start: 0.8052 (m-10) cc_final: 0.7701 (m-10) REVERT: V 68 LYS cc_start: 0.8117 (pttt) cc_final: 0.7790 (pttt) REVERT: V 236 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8750 (mm-30) REVERT: V 253 ASN cc_start: 0.6407 (t0) cc_final: 0.5857 (t0) REVERT: V 286 TYR cc_start: 0.8055 (p90) cc_final: 0.7563 (p90) REVERT: V 307 PHE cc_start: 0.8282 (m-80) cc_final: 0.7870 (m-80) REVERT: W 229 ASN cc_start: 0.8595 (m-40) cc_final: 0.8152 (p0) REVERT: W 236 GLU cc_start: 0.8564 (mp0) cc_final: 0.8051 (mm-30) REVERT: W 290 ASN cc_start: 0.7470 (m-40) cc_final: 0.7204 (m110) REVERT: W 295 LYS cc_start: 0.8957 (ptmm) cc_final: 0.8431 (ptpt) REVERT: Y 7 THR cc_start: 0.7143 (OUTLIER) cc_final: 0.6379 (p) REVERT: Y 65 MET cc_start: 0.9080 (ttt) cc_final: 0.8632 (mmm) REVERT: Y 222 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.7588 (tpp80) REVERT: Y 307 ILE cc_start: 0.7597 (mm) cc_final: 0.7126 (tt) outliers start: 127 outliers final: 80 residues processed: 542 average time/residue: 0.5455 time to fit residues: 490.9313 Evaluate side-chains 511 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 422 time to evaluate : 4.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 295 LYS Chi-restraints excluded: chain L residue 19 GLN Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 106 ASN Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 335 MET Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 185 PHE Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 201 ASP Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 115 MET Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 87 ASN Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 140 PHE Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 334 LYS Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 201 ASP Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 303 ASN Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 333 VAL Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 287 ILE Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 317 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 175 optimal weight: 0.5980 chunk 469 optimal weight: 0.8980 chunk 102 optimal weight: 0.0470 chunk 305 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 521 optimal weight: 9.9990 chunk 432 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN K 17 ASN N 17 ASN N 84 ASN O 218 ASN P 25 ASN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 94 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 44924 Z= 0.165 Angle : 0.618 13.305 61210 Z= 0.308 Chirality : 0.044 0.308 7034 Planarity : 0.004 0.058 7612 Dihedral : 12.132 160.245 6969 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.29 % Favored : 91.49 % Rotamer: Outliers : 3.07 % Allowed : 19.86 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.11), residues: 5407 helix: 0.48 (0.13), residues: 1834 sheet: -0.33 (0.19), residues: 695 loop : -1.65 (0.11), residues: 2878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 24 HIS 0.010 0.001 HIS Q 117 PHE 0.029 0.001 PHE P 185 TYR 0.033 0.001 TYR Y 20 ARG 0.010 0.000 ARG Q 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 472 time to evaluate : 5.061 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: A 31 MET cc_start: 0.4238 (mtt) cc_final: 0.3912 (ttm) REVERT: A 133 TRP cc_start: 0.8096 (t60) cc_final: 0.7782 (t60) REVERT: A 198 MET cc_start: 0.7224 (mmt) cc_final: 0.6868 (tmm) REVERT: A 209 MET cc_start: 0.7495 (ptt) cc_final: 0.7097 (ppp) REVERT: C 10 ARG cc_start: 0.6518 (mmp-170) cc_final: 0.6174 (mmm160) REVERT: C 20 PHE cc_start: 0.6603 (m-10) cc_final: 0.6008 (m-80) REVERT: C 39 GLU cc_start: 0.6222 (pm20) cc_final: 0.5894 (pm20) REVERT: C 49 ARG cc_start: 0.7630 (ptp-170) cc_final: 0.7373 (mtt180) REVERT: C 54 LEU cc_start: 0.7532 (mm) cc_final: 0.7162 (mm) REVERT: C 67 ARG cc_start: 0.6807 (tpt90) cc_final: 0.6452 (tpt90) REVERT: C 75 GLU cc_start: 0.7026 (mp0) cc_final: 0.6785 (mp0) REVERT: C 78 GLU cc_start: 0.7179 (tp30) cc_final: 0.6760 (tp30) REVERT: F 29 ASP cc_start: 0.8430 (m-30) cc_final: 0.8229 (m-30) REVERT: G 46 LYS cc_start: 0.9376 (mppt) cc_final: 0.9029 (mppt) REVERT: H 83 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: I 23 TYR cc_start: 0.8137 (m-80) cc_final: 0.7846 (m-80) REVERT: I 48 LEU cc_start: 0.9457 (tp) cc_final: 0.9171 (tp) REVERT: I 57 LYS cc_start: 0.9422 (tptp) cc_final: 0.9143 (tptp) REVERT: J 42 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8286 (mt-10) REVERT: J 45 TYR cc_start: 0.6305 (m-80) cc_final: 0.5483 (m-80) REVERT: J 106 ASN cc_start: 0.7503 (t0) cc_final: 0.7265 (t0) REVERT: J 107 ASN cc_start: 0.7838 (p0) cc_final: 0.7588 (p0) REVERT: K 295 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8667 (mmtt) REVERT: L 165 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7612 (p) REVERT: L 183 MET cc_start: 0.5760 (ppp) cc_final: 0.5498 (ppp) REVERT: L 335 MET cc_start: 0.8623 (ppp) cc_final: 0.8278 (ptm) REVERT: M 1 MET cc_start: 0.7045 (tpp) cc_final: 0.6751 (tpp) REVERT: M 335 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8040 (ppp) REVERT: N 54 MET cc_start: 0.8784 (tpp) cc_final: 0.8006 (tpp) REVERT: O 1 MET cc_start: 0.8473 (mmm) cc_final: 0.8071 (tpp) REVERT: O 183 MET cc_start: 0.6961 (pmm) cc_final: 0.6468 (pmm) REVERT: Q 83 ARG cc_start: 0.7459 (mmm160) cc_final: 0.7170 (mmm160) REVERT: Q 90 TYR cc_start: 0.8647 (t80) cc_final: 0.8382 (t80) REVERT: Q 122 MET cc_start: 0.6746 (ppp) cc_final: 0.6416 (ppp) REVERT: Q 145 PHE cc_start: 0.8676 (t80) cc_final: 0.8236 (t80) REVERT: R 30 THR cc_start: 0.9351 (m) cc_final: 0.8997 (p) REVERT: R 332 LEU cc_start: 0.9444 (mt) cc_final: 0.9200 (mp) REVERT: S 84 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9004 (mt) REVERT: S 109 MET cc_start: 0.7491 (mmm) cc_final: 0.7245 (mmm) REVERT: T 14 HIS cc_start: 0.8773 (p-80) cc_final: 0.7425 (p-80) REVERT: T 54 MET cc_start: 0.7808 (mmp) cc_final: 0.6951 (mmp) REVERT: T 58 TRP cc_start: 0.6744 (m-90) cc_final: 0.5713 (m100) REVERT: V 231 ARG cc_start: 0.7439 (mmm160) cc_final: 0.7083 (mmt90) REVERT: V 235 ILE cc_start: 0.9377 (mm) cc_final: 0.8866 (pt) REVERT: V 236 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8438 (mm-30) REVERT: V 253 ASN cc_start: 0.6526 (t0) cc_final: 0.6002 (t0) REVERT: V 307 PHE cc_start: 0.8381 (m-80) cc_final: 0.7974 (m-80) REVERT: W 60 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.5688 (m-10) REVERT: W 229 ASN cc_start: 0.8496 (m-40) cc_final: 0.8093 (p0) REVERT: W 236 GLU cc_start: 0.8762 (mp0) cc_final: 0.8384 (mm-30) REVERT: W 290 ASN cc_start: 0.7591 (m-40) cc_final: 0.7327 (m110) REVERT: W 336 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7726 (m) REVERT: Y 7 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6458 (p) REVERT: Y 65 MET cc_start: 0.9057 (ttt) cc_final: 0.8846 (mtp) REVERT: Y 199 SER cc_start: 0.9408 (t) cc_final: 0.9204 (p) REVERT: Y 222 ARG cc_start: 0.8146 (tpp-160) cc_final: 0.7352 (tpp80) REVERT: Y 307 ILE cc_start: 0.7570 (mm) cc_final: 0.7297 (tp) outliers start: 137 outliers final: 83 residues processed: 573 average time/residue: 0.5478 time to fit residues: 521.7184 Evaluate side-chains 531 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 439 time to evaluate : 5.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 295 LYS Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 335 MET Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 140 PHE Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 334 LYS Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 201 ASP Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 303 ASN Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 333 VAL Chi-restraints excluded: chain W residue 3 VAL Chi-restraints excluded: chain W residue 60 PHE Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 230 GLU Chi-restraints excluded: chain W residue 246 LEU Chi-restraints excluded: chain W residue 287 ILE Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 317 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 336 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 54 PHE Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 178 THR Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 502 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 297 optimal weight: 4.9990 chunk 380 optimal weight: 0.5980 chunk 295 optimal weight: 0.8980 chunk 438 optimal weight: 10.0000 chunk 291 optimal weight: 0.4980 chunk 519 optimal weight: 7.9990 chunk 325 optimal weight: 0.0770 chunk 316 optimal weight: 0.7980 chunk 239 optimal weight: 7.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN M 17 ASN P 17 ASN ** Q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 44924 Z= 0.161 Angle : 0.624 12.398 61210 Z= 0.309 Chirality : 0.044 0.327 7034 Planarity : 0.004 0.058 7612 Dihedral : 12.071 159.189 6969 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.97 % Favored : 91.84 % Rotamer: Outliers : 2.57 % Allowed : 20.98 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.11), residues: 5407 helix: 0.51 (0.13), residues: 1821 sheet: -0.25 (0.19), residues: 695 loop : -1.61 (0.11), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 275 HIS 0.012 0.001 HIS Q 117 PHE 0.023 0.001 PHE P 185 TYR 0.031 0.001 TYR Y 20 ARG 0.011 0.000 ARG W 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 457 time to evaluate : 4.942 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: A 31 MET cc_start: 0.4231 (mtt) cc_final: 0.3912 (ttm) REVERT: A 133 TRP cc_start: 0.8078 (t60) cc_final: 0.7746 (t60) REVERT: A 198 MET cc_start: 0.7195 (mmt) cc_final: 0.6873 (tmm) REVERT: C 10 ARG cc_start: 0.6471 (mmp-170) cc_final: 0.6108 (mmm160) REVERT: C 20 PHE cc_start: 0.6758 (m-10) cc_final: 0.6395 (m-80) REVERT: C 67 ARG cc_start: 0.6962 (tpt90) cc_final: 0.6504 (tpt90) REVERT: C 78 GLU cc_start: 0.7166 (tp30) cc_final: 0.6877 (tp30) REVERT: F 29 ASP cc_start: 0.8469 (m-30) cc_final: 0.8194 (m-30) REVERT: G 46 LYS cc_start: 0.9381 (mppt) cc_final: 0.9053 (mppt) REVERT: H 83 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: I 23 TYR cc_start: 0.8117 (m-80) cc_final: 0.7829 (m-80) REVERT: I 46 LYS cc_start: 0.9483 (mmmt) cc_final: 0.8901 (mptt) REVERT: I 48 LEU cc_start: 0.9460 (tp) cc_final: 0.9156 (tp) REVERT: I 57 LYS cc_start: 0.9413 (tptp) cc_final: 0.9201 (tptp) REVERT: J 42 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8226 (mt-10) REVERT: J 45 TYR cc_start: 0.6130 (m-80) cc_final: 0.5540 (m-80) REVERT: J 106 ASN cc_start: 0.7437 (t0) cc_final: 0.7209 (t0) REVERT: K 295 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8554 (mmtt) REVERT: L 165 VAL cc_start: 0.7574 (OUTLIER) cc_final: 0.7351 (p) REVERT: L 335 MET cc_start: 0.8635 (ppp) cc_final: 0.8289 (ptm) REVERT: M 1 MET cc_start: 0.6963 (tpp) cc_final: 0.6702 (tpp) REVERT: M 335 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8080 (ppp) REVERT: O 183 MET cc_start: 0.6860 (pmm) cc_final: 0.6327 (pmm) REVERT: Q 83 ARG cc_start: 0.7519 (mmm160) cc_final: 0.7184 (mmm160) REVERT: Q 90 TYR cc_start: 0.8657 (t80) cc_final: 0.8447 (t80) REVERT: Q 145 PHE cc_start: 0.8502 (t80) cc_final: 0.8116 (t80) REVERT: Q 192 ARG cc_start: 0.6571 (tpt-90) cc_final: 0.6276 (tpp80) REVERT: R 30 THR cc_start: 0.9322 (m) cc_final: 0.9030 (p) REVERT: R 332 LEU cc_start: 0.9434 (mt) cc_final: 0.9164 (mp) REVERT: S 84 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8993 (mt) REVERT: S 105 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7180 (ptmm) REVERT: S 109 MET cc_start: 0.7445 (mmm) cc_final: 0.7156 (mmm) REVERT: T 14 HIS cc_start: 0.8652 (p-80) cc_final: 0.7344 (p90) REVERT: T 54 MET cc_start: 0.7797 (mmp) cc_final: 0.6929 (mmp) REVERT: T 58 TRP cc_start: 0.6826 (m-90) cc_final: 0.5804 (m100) REVERT: T 265 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: V 68 LYS cc_start: 0.8129 (pttt) cc_final: 0.7832 (pttt) REVERT: V 235 ILE cc_start: 0.9377 (mm) cc_final: 0.8906 (pt) REVERT: V 236 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8516 (mm-30) REVERT: V 253 ASN cc_start: 0.6525 (t0) cc_final: 0.6002 (t0) REVERT: V 307 PHE cc_start: 0.8360 (m-80) cc_final: 0.7988 (m-80) REVERT: W 60 PHE cc_start: 0.6290 (OUTLIER) cc_final: 0.5741 (m-10) REVERT: W 229 ASN cc_start: 0.8412 (m-40) cc_final: 0.8024 (p0) REVERT: W 236 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8376 (mm-30) REVERT: W 290 ASN cc_start: 0.7644 (m-40) cc_final: 0.7375 (m110) REVERT: W 295 LYS cc_start: 0.8583 (ptmm) cc_final: 0.7960 (mttp) REVERT: W 336 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7634 (m) REVERT: Y 7 THR cc_start: 0.7054 (OUTLIER) cc_final: 0.6426 (p) REVERT: Y 65 MET cc_start: 0.9067 (ttt) cc_final: 0.8781 (mmm) REVERT: Y 131 MET cc_start: 0.6830 (mmm) cc_final: 0.6617 (tpp) REVERT: Y 222 ARG cc_start: 0.7979 (tpp-160) cc_final: 0.7525 (tpp80) REVERT: Y 307 ILE cc_start: 0.7578 (mm) cc_final: 0.7122 (tt) outliers start: 115 outliers final: 86 residues processed: 543 average time/residue: 0.5591 time to fit residues: 500.1764 Evaluate side-chains 529 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 432 time to evaluate : 4.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 295 LYS Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 335 MET Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 201 ASP Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 140 PHE Chi-restraints excluded: chain T residue 265 GLU Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 313 LEU Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 334 LYS Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 201 ASP Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 303 ASN Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 333 VAL Chi-restraints excluded: chain W residue 3 VAL Chi-restraints excluded: chain W residue 60 PHE Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 230 GLU Chi-restraints excluded: chain W residue 246 LEU Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 317 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 336 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 10 ILE Chi-restraints excluded: chain Y residue 54 PHE Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 178 THR Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 321 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 310 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 chunk 353 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 408 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN N 17 ASN ** Q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44924 Z= 0.170 Angle : 0.628 13.236 61210 Z= 0.311 Chirality : 0.044 0.316 7034 Planarity : 0.004 0.061 7612 Dihedral : 12.037 158.585 6969 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.21 % Favored : 91.58 % Rotamer: Outliers : 2.64 % Allowed : 21.38 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.98 (0.11), residues: 5407 helix: 0.53 (0.13), residues: 1835 sheet: -0.23 (0.19), residues: 698 loop : -1.59 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 275 HIS 0.014 0.001 HIS Q 117 PHE 0.024 0.001 PHE Q 155 TYR 0.030 0.001 TYR Y 20 ARG 0.008 0.000 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 441 time to evaluate : 4.939 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: A 31 MET cc_start: 0.4230 (mtt) cc_final: 0.3909 (ttm) REVERT: A 198 MET cc_start: 0.7196 (mmt) cc_final: 0.6870 (tmm) REVERT: A 209 MET cc_start: 0.7460 (ptt) cc_final: 0.7042 (ppp) REVERT: C 20 PHE cc_start: 0.6988 (m-10) cc_final: 0.6679 (m-80) REVERT: C 67 ARG cc_start: 0.6869 (tpt90) cc_final: 0.6359 (tpt90) REVERT: C 78 GLU cc_start: 0.7125 (tp30) cc_final: 0.6859 (tp30) REVERT: F 29 ASP cc_start: 0.8449 (m-30) cc_final: 0.8199 (m-30) REVERT: G 46 LYS cc_start: 0.9368 (mppt) cc_final: 0.9042 (mppt) REVERT: H 83 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: I 23 TYR cc_start: 0.8128 (m-80) cc_final: 0.7830 (m-80) REVERT: I 48 LEU cc_start: 0.9461 (tp) cc_final: 0.9138 (tp) REVERT: I 57 LYS cc_start: 0.9416 (tptp) cc_final: 0.9195 (tptp) REVERT: K 295 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8556 (mmtt) REVERT: L 165 VAL cc_start: 0.7557 (OUTLIER) cc_final: 0.7336 (p) REVERT: L 335 MET cc_start: 0.8631 (ppp) cc_final: 0.8282 (ptm) REVERT: M 1 MET cc_start: 0.6980 (tpp) cc_final: 0.6721 (tpp) REVERT: M 335 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8021 (ppp) REVERT: O 183 MET cc_start: 0.6858 (pmm) cc_final: 0.6328 (pmm) REVERT: Q 83 ARG cc_start: 0.7951 (mmm160) cc_final: 0.7387 (mmm160) REVERT: Q 145 PHE cc_start: 0.8459 (t80) cc_final: 0.8096 (t80) REVERT: R 30 THR cc_start: 0.9297 (m) cc_final: 0.9000 (p) REVERT: R 332 LEU cc_start: 0.9394 (mt) cc_final: 0.9098 (mp) REVERT: S 84 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9011 (mt) REVERT: S 89 PHE cc_start: 0.8774 (m-80) cc_final: 0.8367 (m-80) REVERT: S 105 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7137 (ptmm) REVERT: S 109 MET cc_start: 0.7166 (mmm) cc_final: 0.6855 (mmm) REVERT: T 14 HIS cc_start: 0.8679 (p-80) cc_final: 0.7458 (p90) REVERT: T 54 MET cc_start: 0.7792 (mmp) cc_final: 0.6874 (mmp) REVERT: T 58 TRP cc_start: 0.6887 (m-90) cc_final: 0.5794 (m100) REVERT: T 265 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7248 (pm20) REVERT: V 68 LYS cc_start: 0.8043 (pttt) cc_final: 0.7724 (pmtt) REVERT: V 196 PHE cc_start: 0.8771 (p90) cc_final: 0.8500 (p90) REVERT: V 235 ILE cc_start: 0.9332 (mm) cc_final: 0.8866 (pt) REVERT: V 236 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8405 (mm-30) REVERT: V 253 ASN cc_start: 0.6415 (t0) cc_final: 0.5900 (t0) REVERT: V 286 TYR cc_start: 0.7581 (p90) cc_final: 0.7222 (p90) REVERT: V 307 PHE cc_start: 0.8420 (m-80) cc_final: 0.8044 (m-80) REVERT: W 60 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.5759 (m-10) REVERT: W 229 ASN cc_start: 0.8434 (m-40) cc_final: 0.7999 (p0) REVERT: W 236 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8407 (mm-30) REVERT: W 295 LYS cc_start: 0.8655 (ptmm) cc_final: 0.7947 (mttp) REVERT: W 336 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7651 (m) REVERT: Y 7 THR cc_start: 0.7021 (OUTLIER) cc_final: 0.6354 (p) REVERT: Y 65 MET cc_start: 0.9078 (ttt) cc_final: 0.8807 (mmm) REVERT: Y 111 MET cc_start: 0.7739 (mmp) cc_final: 0.7490 (mmp) REVERT: Y 131 MET cc_start: 0.7049 (mmm) cc_final: 0.6763 (tpp) REVERT: Y 222 ARG cc_start: 0.7988 (tpp-160) cc_final: 0.7349 (tpp80) REVERT: Y 271 MET cc_start: 0.5560 (ptt) cc_final: 0.4923 (ppp) REVERT: Y 307 ILE cc_start: 0.7581 (mm) cc_final: 0.7187 (tt) REVERT: Y 308 MET cc_start: 0.8395 (mmp) cc_final: 0.8184 (mmm) outliers start: 118 outliers final: 90 residues processed: 531 average time/residue: 0.5572 time to fit residues: 486.9091 Evaluate side-chains 521 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 420 time to evaluate : 5.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 295 LYS Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain M residue 335 MET Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 140 PHE Chi-restraints excluded: chain T residue 265 GLU Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 313 LEU Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 334 LYS Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 201 ASP Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 303 ASN Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 333 VAL Chi-restraints excluded: chain V residue 335 MET Chi-restraints excluded: chain W residue 3 VAL Chi-restraints excluded: chain W residue 60 PHE Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 230 GLU Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 317 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 336 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 10 ILE Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 178 THR Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 472 optimal weight: 5.9990 chunk 497 optimal weight: 3.9990 chunk 454 optimal weight: 8.9990 chunk 484 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 chunk 210 optimal weight: 0.0000 chunk 380 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 437 optimal weight: 6.9990 chunk 457 optimal weight: 5.9990 chunk 482 optimal weight: 7.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN N 17 ASN P 17 ASN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 44924 Z= 0.327 Angle : 0.690 11.837 61210 Z= 0.348 Chirality : 0.046 0.317 7034 Planarity : 0.004 0.065 7612 Dihedral : 12.077 159.116 6969 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.32 % Favored : 90.49 % Rotamer: Outliers : 2.60 % Allowed : 21.83 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.15 (0.11), residues: 5407 helix: 0.44 (0.13), residues: 1838 sheet: -0.57 (0.18), residues: 777 loop : -1.67 (0.12), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP V 58 HIS 0.015 0.002 HIS Q 117 PHE 0.024 0.002 PHE K 258 TYR 0.035 0.001 TYR Y 20 ARG 0.008 0.001 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 422 time to evaluate : 5.079 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: A 31 MET cc_start: 0.4279 (mtt) cc_final: 0.3941 (ttm) REVERT: A 133 TRP cc_start: 0.8058 (t60) cc_final: 0.6504 (t-100) REVERT: A 198 MET cc_start: 0.7221 (mmt) cc_final: 0.6797 (tmm) REVERT: A 209 MET cc_start: 0.7617 (ptt) cc_final: 0.7182 (ppp) REVERT: C 67 ARG cc_start: 0.7041 (tpt90) cc_final: 0.6597 (tpt90) REVERT: F 29 ASP cc_start: 0.8481 (m-30) cc_final: 0.8265 (m-30) REVERT: G 46 LYS cc_start: 0.9423 (mppt) cc_final: 0.9069 (mppt) REVERT: H 83 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: H 88 LYS cc_start: 0.9207 (mmmt) cc_final: 0.8398 (tptt) REVERT: I 23 TYR cc_start: 0.8128 (m-80) cc_final: 0.7826 (m-80) REVERT: I 46 LYS cc_start: 0.9492 (mmmt) cc_final: 0.9115 (mptt) REVERT: I 48 LEU cc_start: 0.9464 (tp) cc_final: 0.9138 (tp) REVERT: K 295 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8714 (tppt) REVERT: L 165 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7394 (p) REVERT: L 335 MET cc_start: 0.8644 (ppp) cc_final: 0.8283 (ptm) REVERT: M 335 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7854 (ptt) REVERT: N 19 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: N 54 MET cc_start: 0.8714 (tpp) cc_final: 0.8425 (tpp) REVERT: O 183 MET cc_start: 0.7264 (pmm) cc_final: 0.6690 (pmm) REVERT: Q 83 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7562 (mmm160) REVERT: Q 145 PHE cc_start: 0.8547 (t80) cc_final: 0.8184 (t80) REVERT: Q 192 ARG cc_start: 0.7299 (tpp80) cc_final: 0.6696 (tpp-160) REVERT: R 332 LEU cc_start: 0.9442 (mt) cc_final: 0.9193 (mp) REVERT: S 84 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9102 (mt) REVERT: S 109 MET cc_start: 0.7056 (mmm) cc_final: 0.6762 (mmm) REVERT: T 14 HIS cc_start: 0.8772 (p-80) cc_final: 0.7663 (p-80) REVERT: T 58 TRP cc_start: 0.6906 (m-90) cc_final: 0.6481 (m100) REVERT: V 68 LYS cc_start: 0.8122 (pttt) cc_final: 0.7759 (pttt) REVERT: V 235 ILE cc_start: 0.9356 (mm) cc_final: 0.8813 (pt) REVERT: V 236 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8366 (mm-30) REVERT: V 286 TYR cc_start: 0.7549 (p90) cc_final: 0.7184 (p90) REVERT: V 307 PHE cc_start: 0.8407 (m-80) cc_final: 0.7988 (m-80) REVERT: W 60 PHE cc_start: 0.6042 (OUTLIER) cc_final: 0.5461 (m-10) REVERT: W 229 ASN cc_start: 0.8380 (m-40) cc_final: 0.7985 (p0) REVERT: W 236 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8442 (mm-30) REVERT: W 290 ASN cc_start: 0.7749 (m-40) cc_final: 0.7424 (m-40) REVERT: W 336 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7706 (m) REVERT: Y 7 THR cc_start: 0.6835 (OUTLIER) cc_final: 0.6031 (p) REVERT: Y 65 MET cc_start: 0.9145 (ttt) cc_final: 0.8679 (mmm) REVERT: Y 111 MET cc_start: 0.7850 (mmp) cc_final: 0.7648 (mmp) REVERT: Y 131 MET cc_start: 0.7238 (mmm) cc_final: 0.6915 (tpp) REVERT: Y 222 ARG cc_start: 0.7975 (tpp-160) cc_final: 0.7471 (tpp80) REVERT: Y 271 MET cc_start: 0.5873 (ptt) cc_final: 0.5132 (ppp) REVERT: Y 307 ILE cc_start: 0.7651 (mm) cc_final: 0.7149 (tt) outliers start: 116 outliers final: 94 residues processed: 510 average time/residue: 0.5655 time to fit residues: 476.7460 Evaluate side-chains 518 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 414 time to evaluate : 5.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 295 LYS Chi-restraints excluded: chain K residue 303 ASN Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain M residue 335 MET Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain N residue 227 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 185 PHE Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 140 PHE Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 312 ASP Chi-restraints excluded: chain T residue 313 LEU Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 334 LYS Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 201 ASP Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 303 ASN Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 333 VAL Chi-restraints excluded: chain W residue 3 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 60 PHE Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 317 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 336 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 10 ILE Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 178 THR Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 317 optimal weight: 3.9990 chunk 511 optimal weight: 0.6980 chunk 312 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 355 optimal weight: 1.9990 chunk 536 optimal weight: 8.9990 chunk 494 optimal weight: 5.9990 chunk 427 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 330 optimal weight: 9.9990 chunk 262 optimal weight: 0.0670 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN N 17 ASN P 17 ASN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 GLN ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 84 ASN ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44924 Z= 0.176 Angle : 0.655 13.353 61210 Z= 0.323 Chirality : 0.045 0.324 7034 Planarity : 0.004 0.064 7612 Dihedral : 12.049 160.302 6969 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.27 % Favored : 91.55 % Rotamer: Outliers : 2.37 % Allowed : 22.18 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.03 (0.11), residues: 5407 helix: 0.51 (0.13), residues: 1830 sheet: -0.31 (0.19), residues: 702 loop : -1.62 (0.11), residues: 2875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP V 58 HIS 0.014 0.001 HIS Q 117 PHE 0.027 0.001 PHE S 89 TYR 0.027 0.001 TYR Y 20 ARG 0.010 0.000 ARG Q 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 433 time to evaluate : 4.715 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: A 31 MET cc_start: 0.4257 (mtt) cc_final: 0.3904 (ttm) REVERT: A 133 TRP cc_start: 0.8036 (t60) cc_final: 0.7778 (t60) REVERT: A 169 MET cc_start: 0.7470 (ttt) cc_final: 0.6977 (tpp) REVERT: A 198 MET cc_start: 0.7258 (mmt) cc_final: 0.6883 (tmm) REVERT: A 209 MET cc_start: 0.7600 (ptt) cc_final: 0.7169 (ppp) REVERT: C 20 PHE cc_start: 0.6854 (m-80) cc_final: 0.6645 (m-80) REVERT: C 67 ARG cc_start: 0.6999 (tpt90) cc_final: 0.6558 (tpt90) REVERT: E 91 ARG cc_start: 0.6668 (mmm160) cc_final: 0.6003 (mmm160) REVERT: F 29 ASP cc_start: 0.8449 (m-30) cc_final: 0.8185 (m-30) REVERT: G 46 LYS cc_start: 0.9393 (mppt) cc_final: 0.9049 (mppt) REVERT: H 83 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: I 23 TYR cc_start: 0.8147 (m-80) cc_final: 0.7863 (m-80) REVERT: I 46 LYS cc_start: 0.9440 (mmmt) cc_final: 0.9031 (mptt) REVERT: I 48 LEU cc_start: 0.9449 (tp) cc_final: 0.9120 (tp) REVERT: K 295 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8574 (mmtt) REVERT: L 335 MET cc_start: 0.8596 (ppp) cc_final: 0.8225 (ptm) REVERT: M 335 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7746 (ptt) REVERT: O 183 MET cc_start: 0.7060 (pmm) cc_final: 0.6523 (pmm) REVERT: Q 83 ARG cc_start: 0.7873 (mmm160) cc_final: 0.7469 (mmm160) REVERT: Q 145 PHE cc_start: 0.8404 (t80) cc_final: 0.8086 (t80) REVERT: R 266 LEU cc_start: 0.8693 (pt) cc_final: 0.8184 (pp) REVERT: S 84 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9062 (mt) REVERT: S 105 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6880 (ptmm) REVERT: S 109 MET cc_start: 0.6870 (mmm) cc_final: 0.6535 (mmm) REVERT: T 14 HIS cc_start: 0.8702 (p-80) cc_final: 0.7619 (p-80) REVERT: T 54 MET cc_start: 0.7728 (mmp) cc_final: 0.6985 (mmp) REVERT: T 58 TRP cc_start: 0.6894 (m-90) cc_final: 0.5888 (m100) REVERT: V 68 LYS cc_start: 0.8107 (pttt) cc_final: 0.7756 (pttt) REVERT: V 141 ILE cc_start: 0.9277 (mt) cc_final: 0.9062 (mm) REVERT: V 235 ILE cc_start: 0.9309 (mm) cc_final: 0.8817 (pt) REVERT: V 236 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8351 (mm-30) REVERT: V 286 TYR cc_start: 0.7564 (p90) cc_final: 0.7183 (p90) REVERT: V 307 PHE cc_start: 0.8392 (m-80) cc_final: 0.7981 (m-80) REVERT: W 60 PHE cc_start: 0.6016 (OUTLIER) cc_final: 0.5448 (m-10) REVERT: W 236 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8433 (mm-30) REVERT: W 246 LEU cc_start: 0.8390 (mt) cc_final: 0.8105 (mm) REVERT: W 290 ASN cc_start: 0.7700 (m-40) cc_final: 0.7438 (m110) REVERT: W 336 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7679 (m) REVERT: Y 7 THR cc_start: 0.6796 (OUTLIER) cc_final: 0.6034 (p) REVERT: Y 65 MET cc_start: 0.9108 (ttt) cc_final: 0.8790 (mmm) REVERT: Y 111 MET cc_start: 0.7762 (mmp) cc_final: 0.7558 (mmp) REVERT: Y 222 ARG cc_start: 0.7921 (tpp-160) cc_final: 0.7478 (tpp80) REVERT: Y 271 MET cc_start: 0.5717 (ptt) cc_final: 0.5076 (ppp) REVERT: Y 307 ILE cc_start: 0.7661 (mm) cc_final: 0.7204 (tt) REVERT: Y 308 MET cc_start: 0.8559 (mmp) cc_final: 0.8256 (mmm) outliers start: 106 outliers final: 86 residues processed: 515 average time/residue: 0.5587 time to fit residues: 475.7481 Evaluate side-chains 515 residues out of total 4590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 420 time to evaluate : 4.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 295 LYS Chi-restraints excluded: chain K residue 303 ASN Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain M residue 335 MET Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 140 PHE Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain T residue 334 LYS Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 303 ASN Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 333 VAL Chi-restraints excluded: chain W residue 3 VAL Chi-restraints excluded: chain W residue 60 PHE Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 317 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 336 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 10 ILE Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 178 THR Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 339 optimal weight: 20.0000 chunk 455 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 394 optimal weight: 0.0980 chunk 63 optimal weight: 0.2980 chunk 118 optimal weight: 7.9990 chunk 428 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 439 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN M 53 ASN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 GLN ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.118591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.088728 restraints weight = 182957.250| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 4.49 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44924 Z= 0.182 Angle : 0.642 11.527 61210 Z= 0.317 Chirality : 0.044 0.323 7034 Planarity : 0.004 0.061 7612 Dihedral : 11.990 160.559 6969 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.66 % Favored : 91.18 % Rotamer: Outliers : 2.42 % Allowed : 22.32 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.99 (0.12), residues: 5407 helix: 0.52 (0.13), residues: 1832 sheet: -0.34 (0.19), residues: 693 loop : -1.56 (0.11), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP V 58 HIS 0.014 0.001 HIS Q 117 PHE 0.023 0.001 PHE O 185 TYR 0.026 0.001 TYR Y 20 ARG 0.010 0.000 ARG Q 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9842.90 seconds wall clock time: 179 minutes 38.60 seconds (10778.60 seconds total)