Starting phenix.real_space_refine on Tue May 14 06:13:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1c_37990/05_2024/8x1c_37990_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1c_37990/05_2024/8x1c_37990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1c_37990/05_2024/8x1c_37990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1c_37990/05_2024/8x1c_37990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1c_37990/05_2024/8x1c_37990_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1c_37990/05_2024/8x1c_37990_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 316 5.49 5 S 254 5.16 5 C 34669 2.51 5 N 10022 2.21 5 O 11258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 741": "NH1" <-> "NH2" Residue "I TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 802": "OE1" <-> "OE2" Residue "I PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 860": "NH1" <-> "NH2" Residue "I TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 2032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 2078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 2086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 2105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 2114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 2137": "OD1" <-> "OD2" Residue "I ASP 2139": "OD1" <-> "OD2" Residue "I TYR 2164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 260": "NH1" <-> "NH2" Residue "J PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 36": "NH1" <-> "NH2" Residue "K TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "K TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 373": "OE1" <-> "OE2" Residue "K TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 139": "OE1" <-> "OE2" Residue "N TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 317": "OE1" <-> "OE2" Residue "O GLU 110": "OE1" <-> "OE2" Residue "O GLU 270": "OE1" <-> "OE2" Residue "O TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 110": "OE1" <-> "OE2" Residue "Q TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 255": "OD1" <-> "OD2" Residue "R PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 246": "OE1" <-> "OE2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 224": "OE1" <-> "OE2" Residue "U GLU 241": "OE1" <-> "OE2" Residue "U PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 120": "OE1" <-> "OE2" Residue "V PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 189": "OE1" <-> "OE2" Residue "V TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 40": "OE1" <-> "OE2" Residue "W ASP 41": "OD1" <-> "OD2" Residue "W TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 56519 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 898 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "B" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "C" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 808 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "H" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "I" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 7031 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 52, 'TRANS': 799} Chain breaks: 3 Chain: "J" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1114 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 12, 'TRANS': 122} Chain breaks: 2 Chain: "K" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3209 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 823 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain breaks: 1 Chain: "M" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3293 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3223 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 10, 'TRANS': 404} Chain breaks: 2 Chain: "O" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3287 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3368 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 422} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3293 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 10, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "T" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3146 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 1 Chain: "U" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2802 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Chain: "V" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1757 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain breaks: 1 Chain: "W" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1542 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "X" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3034 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "Y" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2990 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.01, per 1000 atoms: 0.37 Number of scatterers: 56519 At special positions: 0 Unit cell: (186.76, 189.428, 224.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 254 16.00 P 316 15.00 O 11258 8.00 N 10022 7.00 C 34669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 51879 O4' DC X 80 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.03 Conformation dependent library (CDL) restraints added in 6.5 seconds 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 273 helices and 48 sheets defined 43.2% alpha, 10.3% beta 130 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 19.59 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 47 through 73 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'B' and resid 35 through 45 removed outlier: 3.693A pdb=" N LYS B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 80 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 101 through 119 removed outlier: 3.651A pdb=" N ALA B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS B 105 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS B 106 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 116 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 119 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 64 through 76 Processing helix chain 'C' and resid 86 through 114 removed outlier: 3.512A pdb=" N ALA C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'D' and resid 25 through 28 Processing helix chain 'D' and resid 31 through 40 Processing helix chain 'D' and resid 50 through 76 removed outlier: 3.516A pdb=" N ALA D 76 " --> pdb=" O TYR D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'E' and resid 17 through 20 No H-bonds generated for 'chain 'E' and resid 17 through 20' Processing helix chain 'E' and resid 27 through 36 Processing helix chain 'E' and resid 47 through 73 Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'F' and resid 35 through 45 removed outlier: 3.533A pdb=" N TYR F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 80 Processing helix chain 'F' and resid 88 through 98 Processing helix chain 'F' and resid 102 through 120 Processing helix chain 'G' and resid 45 through 54 Processing helix chain 'G' and resid 64 through 77 removed outlier: 3.749A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 113 removed outlier: 3.577A pdb=" N LEU G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 130 Processing helix chain 'H' and resid 26 through 28 No H-bonds generated for 'chain 'H' and resid 26 through 28' Processing helix chain 'H' and resid 31 through 41 Processing helix chain 'H' and resid 48 through 75 removed outlier: 4.007A pdb=" N TYR H 51 " --> pdb=" O GLY H 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU H 52 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG H 55 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE H 66 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS H 75 " --> pdb=" O TYR H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 Processing helix chain 'I' and resid 95 through 115 removed outlier: 4.683A pdb=" N ALA I 100 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS I 101 " --> pdb=" O GLU I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 250 removed outlier: 3.782A pdb=" N GLN I 204 " --> pdb=" O LYS I 200 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE I 205 " --> pdb=" O ASP I 201 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP I 206 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS I 216 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS I 227 " --> pdb=" O GLU I 223 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR I 243 " --> pdb=" O GLN I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 620 through 634 Processing helix chain 'I' and resid 649 through 662 Processing helix chain 'I' and resid 676 through 689 removed outlier: 4.765A pdb=" N LEU I 680 " --> pdb=" O THR I 676 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN I 681 " --> pdb=" O SER I 677 " (cutoff:3.500A) Processing helix chain 'I' and resid 702 through 709 Processing helix chain 'I' and resid 725 through 728 No H-bonds generated for 'chain 'I' and resid 725 through 728' Processing helix chain 'I' and resid 732 through 736 Processing helix chain 'I' and resid 748 through 751 Processing helix chain 'I' and resid 759 through 763 Processing helix chain 'I' and resid 783 through 792 removed outlier: 3.502A pdb=" N PHE I 791 " --> pdb=" O SER I 787 " (cutoff:3.500A) Processing helix chain 'I' and resid 801 through 815 Proline residue: I 810 - end of helix removed outlier: 3.941A pdb=" N ILE I 815 " --> pdb=" O LEU I 811 " (cutoff:3.500A) Processing helix chain 'I' and resid 825 through 834 Processing helix chain 'I' and resid 842 through 845 No H-bonds generated for 'chain 'I' and resid 842 through 845' Processing helix chain 'I' and resid 863 through 873 removed outlier: 3.726A pdb=" N LEU I 868 " --> pdb=" O ARG I 864 " (cutoff:3.500A) Processing helix chain 'I' and resid 890 through 902 Processing helix chain 'I' and resid 904 through 906 No H-bonds generated for 'chain 'I' and resid 904 through 906' Processing helix chain 'I' and resid 928 through 930 No H-bonds generated for 'chain 'I' and resid 928 through 930' Processing helix chain 'I' and resid 932 through 934 No H-bonds generated for 'chain 'I' and resid 932 through 934' Processing helix chain 'I' and resid 937 through 939 No H-bonds generated for 'chain 'I' and resid 937 through 939' Processing helix chain 'I' and resid 943 through 945 No H-bonds generated for 'chain 'I' and resid 943 through 945' Processing helix chain 'I' and resid 949 through 951 No H-bonds generated for 'chain 'I' and resid 949 through 951' Processing helix chain 'I' and resid 957 through 961 Processing helix chain 'I' and resid 971 through 977 Processing helix chain 'I' and resid 1887 through 1911 Processing helix chain 'I' and resid 1921 through 1926 Processing helix chain 'I' and resid 1946 through 1950 removed outlier: 3.898A pdb=" N THR I1950 " --> pdb=" O THR I1947 " (cutoff:3.500A) Processing helix chain 'I' and resid 1953 through 1958 Processing helix chain 'I' and resid 1962 through 1976 removed outlier: 5.725A pdb=" N GLU I1971 " --> pdb=" O ASP I1967 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE I1972 " --> pdb=" O GLN I1968 " (cutoff:3.500A) Processing helix chain 'I' and resid 1997 through 2029 Proline residue: I2001 - end of helix removed outlier: 3.701A pdb=" N GLU I2013 " --> pdb=" O GLN I2009 " (cutoff:3.500A) Proline residue: I2016 - end of helix Proline residue: I2020 - end of helix removed outlier: 4.366A pdb=" N ARG I2023 " --> pdb=" O ARG I2019 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE I2024 " --> pdb=" O PRO I2020 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN I2027 " --> pdb=" O ARG I2023 " (cutoff:3.500A) Processing helix chain 'I' and resid 2037 through 2040 No H-bonds generated for 'chain 'I' and resid 2037 through 2040' Processing helix chain 'I' and resid 2043 through 2057 removed outlier: 3.550A pdb=" N GLN I2054 " --> pdb=" O VAL I2050 " (cutoff:3.500A) Processing helix chain 'I' and resid 2070 through 2082 removed outlier: 3.825A pdb=" N VAL I2074 " --> pdb=" O ARG I2070 " (cutoff:3.500A) Processing helix chain 'I' and resid 2095 through 2105 Processing helix chain 'I' and resid 2144 through 2151 Processing helix chain 'I' and resid 2172 through 2191 Processing helix chain 'J' and resid 172 through 198 removed outlier: 5.169A pdb=" N ILE J 178 " --> pdb=" O ARG J 174 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N THR J 179 " --> pdb=" O GLU J 175 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 278 removed outlier: 3.566A pdb=" N TRP J 277 " --> pdb=" O PHE J 274 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE J 278 " --> pdb=" O GLU J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 329 removed outlier: 3.821A pdb=" N LYS J 317 " --> pdb=" O ALA J 313 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS J 325 " --> pdb=" O GLU J 321 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR J 326 " --> pdb=" O ALA J 322 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 35 No H-bonds generated for 'chain 'K' and resid 33 through 35' Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 69 through 78 Processing helix chain 'K' and resid 127 through 138 Processing helix chain 'K' and resid 167 through 169 No H-bonds generated for 'chain 'K' and resid 167 through 169' Processing helix chain 'K' and resid 177 through 189 Processing helix chain 'K' and resid 201 through 208 removed outlier: 3.567A pdb=" N ASP K 208 " --> pdb=" O VAL K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 223 Processing helix chain 'K' and resid 252 through 254 No H-bonds generated for 'chain 'K' and resid 252 through 254' Processing helix chain 'K' and resid 273 through 276 No H-bonds generated for 'chain 'K' and resid 273 through 276' Processing helix chain 'K' and resid 278 through 281 Processing helix chain 'K' and resid 294 through 303 removed outlier: 4.789A pdb=" N ILE K 302 " --> pdb=" O ILE K 298 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLN K 303 " --> pdb=" O VAL K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 313 Proline residue: K 311 - end of helix No H-bonds generated for 'chain 'K' and resid 307 through 313' Processing helix chain 'K' and resid 322 through 325 removed outlier: 3.633A pdb=" N LEU K 325 " --> pdb=" O GLY K 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 322 through 325' Processing helix chain 'K' and resid 329 through 340 removed outlier: 3.555A pdb=" N CYS K 339 " --> pdb=" O SER K 335 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU K 340 " --> pdb=" O GLU K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 369 Processing helix chain 'K' and resid 379 through 385 Processing helix chain 'K' and resid 387 through 393 Processing helix chain 'L' and resid 21 through 36 removed outlier: 3.661A pdb=" N GLU L 36 " --> pdb=" O LEU L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 92 Processing helix chain 'L' and resid 138 through 145 Processing helix chain 'M' and resid 43 through 58 removed outlier: 3.601A pdb=" N GLU M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU M 55 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 87 Processing helix chain 'M' and resid 98 through 101 Processing helix chain 'M' and resid 108 through 119 removed outlier: 3.967A pdb=" N ALA M 119 " --> pdb=" O ASN M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 182 removed outlier: 4.087A pdb=" N GLU M 178 " --> pdb=" O SER M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 246 Processing helix chain 'M' and resid 257 through 261 Processing helix chain 'M' and resid 276 through 289 Processing helix chain 'M' and resid 304 through 306 No H-bonds generated for 'chain 'M' and resid 304 through 306' Processing helix chain 'M' and resid 309 through 318 removed outlier: 4.094A pdb=" N ARG M 317 " --> pdb=" O THR M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 349 No H-bonds generated for 'chain 'M' and resid 347 through 349' Processing helix chain 'M' and resid 352 through 355 No H-bonds generated for 'chain 'M' and resid 352 through 355' Processing helix chain 'M' and resid 368 through 382 Processing helix chain 'M' and resid 388 through 400 removed outlier: 3.536A pdb=" N HIS M 393 " --> pdb=" O GLU M 389 " (cutoff:3.500A) Processing helix chain 'M' and resid 403 through 419 removed outlier: 3.984A pdb=" N VAL M 407 " --> pdb=" O LEU M 403 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN M 408 " --> pdb=" O ARG M 404 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR M 411 " --> pdb=" O VAL M 407 " (cutoff:3.500A) Proline residue: M 412 - end of helix Processing helix chain 'M' and resid 427 through 436 removed outlier: 3.575A pdb=" N GLU M 431 " --> pdb=" O LYS M 427 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU M 432 " --> pdb=" O GLU M 428 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU M 435 " --> pdb=" O GLU M 431 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU M 436 " --> pdb=" O GLU M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 440 through 449 removed outlier: 5.267A pdb=" N ASP M 449 " --> pdb=" O LYS M 445 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 65 Processing helix chain 'N' and resid 83 through 94 removed outlier: 3.828A pdb=" N ALA N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 126 Processing helix chain 'N' and resid 176 through 184 Processing helix chain 'N' and resid 244 through 250 Processing helix chain 'N' and resid 259 through 261 No H-bonds generated for 'chain 'N' and resid 259 through 261' Processing helix chain 'N' and resid 274 through 283 Processing helix chain 'N' and resid 301 through 303 No H-bonds generated for 'chain 'N' and resid 301 through 303' Processing helix chain 'N' and resid 306 through 317 removed outlier: 4.004A pdb=" N ARG N 314 " --> pdb=" O SER N 310 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLU N 317 " --> pdb=" O ASN N 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 345 No H-bonds generated for 'chain 'N' and resid 343 through 345' Processing helix chain 'N' and resid 348 through 353 removed outlier: 4.127A pdb=" N ARG N 353 " --> pdb=" O ASP N 349 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 377 Processing helix chain 'N' and resid 384 through 396 Processing helix chain 'N' and resid 399 through 415 removed outlier: 4.315A pdb=" N THR N 407 " --> pdb=" O ILE N 403 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA N 408 " --> pdb=" O GLN N 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 423 through 432 Processing helix chain 'N' and resid 436 through 441 Processing helix chain 'O' and resid 43 through 58 removed outlier: 3.794A pdb=" N VAL O 51 " --> pdb=" O GLU O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 87 Processing helix chain 'O' and resid 98 through 101 removed outlier: 3.892A pdb=" N VAL O 101 " --> pdb=" O GLY O 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 98 through 101' Processing helix chain 'O' and resid 108 through 118 removed outlier: 3.767A pdb=" N LEU O 112 " --> pdb=" O LYS O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 183 Processing helix chain 'O' and resid 208 through 211 removed outlier: 4.178A pdb=" N THR O 211 " --> pdb=" O THR O 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 208 through 211' Processing helix chain 'O' and resid 240 through 248 Processing helix chain 'O' and resid 256 through 263 removed outlier: 4.184A pdb=" N LEU O 263 " --> pdb=" O MET O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 272 through 275 No H-bonds generated for 'chain 'O' and resid 272 through 275' Processing helix chain 'O' and resid 278 through 288 Processing helix chain 'O' and resid 304 through 306 No H-bonds generated for 'chain 'O' and resid 304 through 306' Processing helix chain 'O' and resid 309 through 320 removed outlier: 3.697A pdb=" N HIS O 316 " --> pdb=" O PHE O 312 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 347 through 349 No H-bonds generated for 'chain 'O' and resid 347 through 349' Processing helix chain 'O' and resid 352 through 357 removed outlier: 4.214A pdb=" N ARG O 357 " --> pdb=" O ASP O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 368 through 381 removed outlier: 3.534A pdb=" N THR O 381 " --> pdb=" O ILE O 377 " (cutoff:3.500A) Processing helix chain 'O' and resid 388 through 399 Processing helix chain 'O' and resid 403 through 406 No H-bonds generated for 'chain 'O' and resid 403 through 406' Processing helix chain 'O' and resid 411 through 419 Processing helix chain 'O' and resid 427 through 436 Processing helix chain 'O' and resid 440 through 449 removed outlier: 3.581A pdb=" N LYS O 445 " --> pdb=" O LYS O 441 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE O 446 " --> pdb=" O SER O 442 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 453 No H-bonds generated for 'chain 'O' and resid 451 through 453' Processing helix chain 'P' and resid 43 through 45 No H-bonds generated for 'chain 'P' and resid 43 through 45' Processing helix chain 'P' and resid 50 through 63 Processing helix chain 'P' and resid 83 through 94 Processing helix chain 'P' and resid 105 through 108 removed outlier: 3.966A pdb=" N ILE P 108 " --> pdb=" O GLY P 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 105 through 108' Processing helix chain 'P' and resid 115 through 126 removed outlier: 3.761A pdb=" N SER P 126 " --> pdb=" O ALA P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 185 Processing helix chain 'P' and resid 244 through 250 Processing helix chain 'P' and resid 273 through 286 Processing helix chain 'P' and resid 301 through 303 No H-bonds generated for 'chain 'P' and resid 301 through 303' Processing helix chain 'P' and resid 306 through 315 removed outlier: 4.069A pdb=" N ARG P 314 " --> pdb=" O SER P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 345 No H-bonds generated for 'chain 'P' and resid 343 through 345' Processing helix chain 'P' and resid 350 through 352 No H-bonds generated for 'chain 'P' and resid 350 through 352' Processing helix chain 'P' and resid 364 through 377 Processing helix chain 'P' and resid 384 through 396 Processing helix chain 'P' and resid 399 through 415 removed outlier: 3.623A pdb=" N ILE P 406 " --> pdb=" O ALA P 402 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR P 407 " --> pdb=" O ILE P 403 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA P 408 " --> pdb=" O GLN P 404 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL P 412 " --> pdb=" O ALA P 408 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS P 413 " --> pdb=" O ALA P 409 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG P 414 " --> pdb=" O SER P 410 " (cutoff:3.500A) Processing helix chain 'P' and resid 423 through 432 Processing helix chain 'P' and resid 437 through 440 No H-bonds generated for 'chain 'P' and resid 437 through 440' Processing helix chain 'Q' and resid 43 through 58 removed outlier: 3.553A pdb=" N GLY Q 50 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE Q 52 " --> pdb=" O ALA Q 48 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL Q 53 " --> pdb=" O CYS Q 49 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU Q 54 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 87 removed outlier: 3.516A pdb=" N ALA Q 82 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE Q 83 " --> pdb=" O LEU Q 79 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN Q 85 " --> pdb=" O LEU Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 100 No H-bonds generated for 'chain 'Q' and resid 98 through 100' Processing helix chain 'Q' and resid 108 through 119 removed outlier: 3.747A pdb=" N LEU Q 112 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET Q 113 " --> pdb=" O THR Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 183 Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 256 through 259 No H-bonds generated for 'chain 'Q' and resid 256 through 259' Processing helix chain 'Q' and resid 272 through 276 Processing helix chain 'Q' and resid 280 through 287 removed outlier: 4.087A pdb=" N ASN Q 284 " --> pdb=" O ASN Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 304 through 306 No H-bonds generated for 'chain 'Q' and resid 304 through 306' Processing helix chain 'Q' and resid 309 through 318 removed outlier: 3.587A pdb=" N HIS Q 316 " --> pdb=" O PHE Q 312 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG Q 317 " --> pdb=" O THR Q 313 " (cutoff:3.500A) Processing helix chain 'Q' and resid 347 through 349 No H-bonds generated for 'chain 'Q' and resid 347 through 349' Processing helix chain 'Q' and resid 352 through 357 removed outlier: 3.818A pdb=" N ARG Q 357 " --> pdb=" O ASP Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 382 Processing helix chain 'Q' and resid 388 through 400 removed outlier: 3.645A pdb=" N LYS Q 400 " --> pdb=" O GLU Q 396 " (cutoff:3.500A) Processing helix chain 'Q' and resid 403 through 408 Processing helix chain 'Q' and resid 411 through 419 Processing helix chain 'Q' and resid 427 through 436 removed outlier: 3.553A pdb=" N GLU Q 431 " --> pdb=" O LYS Q 427 " (cutoff:3.500A) Processing helix chain 'Q' and resid 440 through 449 Processing helix chain 'R' and resid 24 through 26 No H-bonds generated for 'chain 'R' and resid 24 through 26' Processing helix chain 'R' and resid 50 through 65 Processing helix chain 'R' and resid 83 through 93 Processing helix chain 'R' and resid 117 through 126 removed outlier: 3.683A pdb=" N SER R 126 " --> pdb=" O ALA R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 184 Processing helix chain 'R' and resid 244 through 249 removed outlier: 4.009A pdb=" N ILE R 247 " --> pdb=" O LEU R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 260 Processing helix chain 'R' and resid 269 through 286 removed outlier: 4.900A pdb=" N ALA R 278 " --> pdb=" O GLU R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 303 No H-bonds generated for 'chain 'R' and resid 301 through 303' Processing helix chain 'R' and resid 306 through 317 removed outlier: 3.735A pdb=" N ARG R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU R 317 " --> pdb=" O ASN R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 345 No H-bonds generated for 'chain 'R' and resid 343 through 345' Processing helix chain 'R' and resid 348 through 353 removed outlier: 3.870A pdb=" N ARG R 353 " --> pdb=" O ASP R 349 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 377 removed outlier: 3.559A pdb=" N LYS R 368 " --> pdb=" O GLU R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 396 Processing helix chain 'R' and resid 399 through 415 removed outlier: 3.558A pdb=" N ILE R 406 " --> pdb=" O ALA R 402 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR R 407 " --> pdb=" O ILE R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 423 through 432 removed outlier: 3.604A pdb=" N LEU R 432 " --> pdb=" O ARG R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 441 Processing helix chain 'S' and resid 55 through 60 removed outlier: 3.877A pdb=" N SER S 60 " --> pdb=" O GLU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 91 Processing helix chain 'S' and resid 98 through 100 No H-bonds generated for 'chain 'S' and resid 98 through 100' Processing helix chain 'S' and resid 113 through 125 Processing helix chain 'S' and resid 137 through 145 Processing helix chain 'S' and resid 172 through 174 No H-bonds generated for 'chain 'S' and resid 172 through 174' Processing helix chain 'S' and resid 182 through 196 Processing helix chain 'S' and resid 203 through 216 Processing helix chain 'S' and resid 223 through 232 Processing helix chain 'S' and resid 252 through 261 removed outlier: 3.758A pdb=" N ARG S 256 " --> pdb=" O GLU S 253 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N CYS S 257 " --> pdb=" O ARG S 254 " (cutoff:3.500A) Proline residue: S 258 - end of helix Processing helix chain 'S' and resid 264 through 267 Processing helix chain 'S' and resid 274 through 283 Processing helix chain 'S' and resid 287 through 295 removed outlier: 4.487A pdb=" N LYS S 291 " --> pdb=" O VAL S 287 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASP S 292 " --> pdb=" O ASP S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 302 through 305 Processing helix chain 'S' and resid 309 through 320 Processing helix chain 'S' and resid 335 through 348 removed outlier: 5.195A pdb=" N VAL S 339 " --> pdb=" O LYS S 336 " (cutoff:3.500A) Processing helix chain 'S' and resid 351 through 355 removed outlier: 3.900A pdb=" N GLN S 354 " --> pdb=" O THR S 351 " (cutoff:3.500A) Processing helix chain 'S' and resid 359 through 365 Processing helix chain 'S' and resid 367 through 373 Processing helix chain 'T' and resid 72 through 75 No H-bonds generated for 'chain 'T' and resid 72 through 75' Processing helix chain 'T' and resid 96 through 108 Processing helix chain 'T' and resid 115 through 117 No H-bonds generated for 'chain 'T' and resid 115 through 117' Processing helix chain 'T' and resid 130 through 140 Processing helix chain 'T' and resid 154 through 162 Processing helix chain 'T' and resid 189 through 191 No H-bonds generated for 'chain 'T' and resid 189 through 191' Processing helix chain 'T' and resid 199 through 212 Processing helix chain 'T' and resid 220 through 222 No H-bonds generated for 'chain 'T' and resid 220 through 222' Processing helix chain 'T' and resid 248 through 266 Processing helix chain 'T' and resid 276 through 281 removed outlier: 3.778A pdb=" N GLN T 281 " --> pdb=" O GLN T 277 " (cutoff:3.500A) Processing helix chain 'T' and resid 300 through 309 removed outlier: 3.692A pdb=" N ILE T 304 " --> pdb=" O GLU T 300 " (cutoff:3.500A) Proline residue: T 305 - end of helix removed outlier: 4.432A pdb=" N LEU T 308 " --> pdb=" O ILE T 304 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE T 309 " --> pdb=" O PRO T 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 300 through 309' Processing helix chain 'T' and resid 325 through 334 Processing helix chain 'T' and resid 338 through 346 Proline residue: T 342 - end of helix Processing helix chain 'T' and resid 354 through 356 No H-bonds generated for 'chain 'T' and resid 354 through 356' Processing helix chain 'T' and resid 360 through 371 Processing helix chain 'T' and resid 386 through 390 Processing helix chain 'T' and resid 392 through 400 Processing helix chain 'T' and resid 404 through 409 removed outlier: 3.553A pdb=" N GLN T 408 " --> pdb=" O THR T 405 " (cutoff:3.500A) Processing helix chain 'T' and resid 413 through 419 Processing helix chain 'T' and resid 421 through 427 removed outlier: 4.137A pdb=" N LYS T 427 " --> pdb=" O VAL T 424 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 6 No H-bonds generated for 'chain 'U' and resid 3 through 6' Processing helix chain 'U' and resid 56 through 60 Processing helix chain 'U' and resid 81 through 92 removed outlier: 4.046A pdb=" N TYR U 91 " --> pdb=" O HIS U 87 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN U 92 " --> pdb=" O HIS U 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 99 No H-bonds generated for 'chain 'U' and resid 97 through 99' Processing helix chain 'U' and resid 112 through 127 removed outlier: 3.762A pdb=" N LYS U 118 " --> pdb=" O ALA U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 137 through 144 removed outlier: 3.999A pdb=" N ALA U 144 " --> pdb=" O LEU U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 166 through 168 No H-bonds generated for 'chain 'U' and resid 166 through 168' Processing helix chain 'U' and resid 183 through 192 Processing helix chain 'U' and resid 206 through 213 removed outlier: 3.825A pdb=" N ILE U 212 " --> pdb=" O ILE U 208 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS U 213 " --> pdb=" O VAL U 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 231 No H-bonds generated for 'chain 'U' and resid 228 through 231' Processing helix chain 'U' and resid 252 through 254 No H-bonds generated for 'chain 'U' and resid 252 through 254' Processing helix chain 'U' and resid 264 through 266 No H-bonds generated for 'chain 'U' and resid 264 through 266' Processing helix chain 'U' and resid 274 through 283 Processing helix chain 'U' and resid 290 through 294 removed outlier: 3.578A pdb=" N TYR U 294 " --> pdb=" O ARG U 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 290 through 294' Processing helix chain 'U' and resid 302 through 304 No H-bonds generated for 'chain 'U' and resid 302 through 304' Processing helix chain 'U' and resid 307 through 320 removed outlier: 3.890A pdb=" N ALA U 310 " --> pdb=" O PRO U 307 " (cutoff:3.500A) Processing helix chain 'U' and resid 335 through 347 removed outlier: 5.517A pdb=" N VAL U 339 " --> pdb=" O LYS U 336 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY U 342 " --> pdb=" O VAL U 339 " (cutoff:3.500A) Processing helix chain 'U' and resid 350 through 355 removed outlier: 4.564A pdb=" N GLN U 354 " --> pdb=" O THR U 351 " (cutoff:3.500A) Processing helix chain 'U' and resid 359 through 364 Processing helix chain 'V' and resid 55 through 62 Processing helix chain 'V' and resid 117 through 119 No H-bonds generated for 'chain 'V' and resid 117 through 119' Processing helix chain 'V' and resid 125 through 128 Processing helix chain 'V' and resid 140 through 146 Processing helix chain 'V' and resid 154 through 166 removed outlier: 4.214A pdb=" N HIS V 159 " --> pdb=" O ALA V 155 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU V 160 " --> pdb=" O GLU V 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 171 through 174 No H-bonds generated for 'chain 'V' and resid 171 through 174' Processing helix chain 'V' and resid 188 through 204 Processing helix chain 'V' and resid 220 through 232 Processing helix chain 'V' and resid 243 through 274 removed outlier: 4.458A pdb=" N ILE V 254 " --> pdb=" O LEU V 251 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG V 257 " --> pdb=" O ILE V 254 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LYS V 258 " --> pdb=" O GLU V 255 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS V 263 " --> pdb=" O GLU V 260 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG V 264 " --> pdb=" O ARG V 261 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 61 No H-bonds generated for 'chain 'W' and resid 59 through 61' Processing helix chain 'W' and resid 124 through 128 Processing helix chain 'W' and resid 149 through 156 Processing helix chain 'W' and resid 173 through 203 removed outlier: 3.828A pdb=" N VAL W 177 " --> pdb=" O ALA W 173 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS W 182 " --> pdb=" O LYS W 178 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA W 185 " --> pdb=" O GLU W 181 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU W 197 " --> pdb=" O GLU W 193 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU W 199 " --> pdb=" O ALA W 195 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG W 200 " --> pdb=" O GLU W 196 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'I' and resid 639 through 641 removed outlier: 3.779A pdb=" N GLY I 639 " --> pdb=" O ARG I 770 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU I 772 " --> pdb=" O GLY I 639 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 852 through 859 removed outlier: 6.460A pdb=" N VAL I2161 " --> pdb=" O TYR I 853 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N HIS I 855 " --> pdb=" O VAL I2161 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE I2163 " --> pdb=" O HIS I 855 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE I 857 " --> pdb=" O ILE I2163 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ARG I2165 " --> pdb=" O ILE I 857 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N CYS I 859 " --> pdb=" O ARG I2165 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE I2167 " --> pdb=" O CYS I 859 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 213 through 217 Processing sheet with id= D, first strand: chain 'K' and resid 4 through 6 Processing sheet with id= E, first strand: chain 'K' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'K' and resid 29 through 31 Processing sheet with id= G, first strand: chain 'K' and resid 145 through 150 Processing sheet with id= H, first strand: chain 'M' and resid 359 through 363 removed outlier: 6.844A pdb=" N VAL M 327 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU M 68 " --> pdb=" O VAL M 327 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE M 329 " --> pdb=" O LEU M 68 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLY M 70 " --> pdb=" O PHE M 329 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER M 331 " --> pdb=" O GLY M 70 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU M 299 " --> pdb=" O ILE M 328 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ALA M 330 " --> pdb=" O LEU M 299 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL M 301 " --> pdb=" O ALA M 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 237 through 239 Processing sheet with id= J, first strand: chain 'M' and resid 229 through 231 removed outlier: 3.627A pdb=" N GLY M 133 " --> pdb=" O ILE M 191 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE M 191 " --> pdb=" O GLY M 133 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR M 192 " --> pdb=" O ARG M 202 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG M 202 " --> pdb=" O TYR M 192 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'M' and resid 166 through 171 removed outlier: 3.932A pdb=" N GLU M 137 " --> pdb=" O GLY M 160 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS M 162 " --> pdb=" O VAL M 135 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL M 135 " --> pdb=" O LYS M 162 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 355 through 359 removed outlier: 6.659A pdb=" N LEU N 324 " --> pdb=" O VAL N 73 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE N 75 " --> pdb=" O LEU N 324 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET N 326 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY N 77 " --> pdb=" O MET N 326 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU N 296 " --> pdb=" O VAL N 323 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA N 327 " --> pdb=" O ILE N 298 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 289 through 293 Processing sheet with id= N, first strand: chain 'N' and resid 233 through 235 removed outlier: 3.513A pdb=" N LYS N 234 " --> pdb=" O ILE N 137 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'N' and resid 169 through 174 removed outlier: 3.654A pdb=" N GLY N 159 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LYS N 164 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL N 142 " --> pdb=" O LYS N 164 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'N' and resid 332 through 334 Processing sheet with id= Q, first strand: chain 'O' and resid 327 through 331 Processing sheet with id= R, first strand: chain 'O' and resid 93 through 97 removed outlier: 6.869A pdb=" N VAL O 298 " --> pdb=" O CYS O 94 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N MET O 96 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE O 300 " --> pdb=" O MET O 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'O' and resid 229 through 239 removed outlier: 3.567A pdb=" N GLN O 236 " --> pdb=" O ILE O 124 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL O 295 " --> pdb=" O GLY O 121 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 131 through 134 removed outlier: 3.676A pdb=" N GLY O 133 " --> pdb=" O ILE O 191 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 167 through 172 removed outlier: 3.638A pdb=" N VAL O 157 " --> pdb=" O LEU O 172 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N CYS O 141 " --> pdb=" O SER O 155 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL O 157 " --> pdb=" O THR O 139 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR O 139 " --> pdb=" O VAL O 157 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 335 through 337 removed outlier: 3.639A pdb=" N CYS O 336 " --> pdb=" O SER O 346 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 355 through 359 removed outlier: 3.575A pdb=" N LEU P 355 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU P 324 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE P 75 " --> pdb=" O LEU P 324 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N MET P 326 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY P 77 " --> pdb=" O MET P 326 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR P 328 " --> pdb=" O GLY P 77 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA P 327 " --> pdb=" O ILE P 298 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 128 through 133 Processing sheet with id= Y, first strand: chain 'P' and resid 233 through 235 removed outlier: 3.734A pdb=" N ILE P 137 " --> pdb=" O LYS P 234 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY P 206 " --> pdb=" O VAL P 192 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR P 194 " --> pdb=" O LYS P 204 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYS P 204 " --> pdb=" O THR P 194 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASP P 196 " --> pdb=" O ILE P 202 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE P 202 " --> pdb=" O ASP P 196 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 169 through 172 removed outlier: 3.699A pdb=" N GLU P 144 " --> pdb=" O THR P 162 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS P 164 " --> pdb=" O VAL P 142 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL P 142 " --> pdb=" O LYS P 164 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Q' and resid 359 through 362 removed outlier: 6.118A pdb=" N VAL Q 327 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU Q 68 " --> pdb=" O VAL Q 327 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE Q 329 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA Q 330 " --> pdb=" O VAL Q 301 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Q' and resid 292 through 296 Processing sheet with id= AC, first strand: chain 'Q' and resid 229 through 231 removed outlier: 3.690A pdb=" N ILE Q 193 " --> pdb=" O TYR Q 131 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY Q 133 " --> pdb=" O ILE Q 191 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE Q 191 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 167 through 172 removed outlier: 3.848A pdb=" N HIS Q 156 " --> pdb=" O CYS Q 141 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU Q 137 " --> pdb=" O GLY Q 160 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LYS Q 162 " --> pdb=" O VAL Q 135 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL Q 135 " --> pdb=" O LYS Q 162 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'R' and resid 356 through 359 removed outlier: 7.508A pdb=" N VAL R 357 " --> pdb=" O ALA R 72 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU R 74 " --> pdb=" O VAL R 357 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR R 359 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA R 76 " --> pdb=" O THR R 359 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU R 324 " --> pdb=" O VAL R 73 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE R 75 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N MET R 326 " --> pdb=" O ILE R 75 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLY R 77 " --> pdb=" O MET R 326 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR R 328 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA R 327 " --> pdb=" O ILE R 298 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 291 through 293 removed outlier: 3.510A pdb=" N THR R 135 " --> pdb=" O LYS R 236 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'R' and resid 169 through 173 removed outlier: 3.754A pdb=" N GLU R 144 " --> pdb=" O THR R 162 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS R 164 " --> pdb=" O VAL R 142 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N VAL R 142 " --> pdb=" O LYS R 164 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR R 194 " --> pdb=" O SER R 203 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N SER R 203 " --> pdb=" O THR R 194 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'R' and resid 332 through 334 Processing sheet with id= AI, first strand: chain 'S' and resid 132 through 136 removed outlier: 6.695A pdb=" N VAL S 103 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA S 135 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU S 105 " --> pdb=" O ALA S 135 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU S 8 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR S 106 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL S 10 " --> pdb=" O THR S 106 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'S' and resid 35 through 38 Processing sheet with id= AK, first strand: chain 'S' and resid 297 through 300 removed outlier: 6.324A pdb=" N ILE S 151 " --> pdb=" O VAL S 298 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N SER S 300 " --> pdb=" O ILE S 151 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N MET S 153 " --> pdb=" O SER S 300 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'S' and resid 238 through 241 Processing sheet with id= AM, first strand: chain 'T' and resid 35 through 38 removed outlier: 7.469A pdb=" N PHE T 16 " --> pdb=" O PRO T 119 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU T 121 " --> pdb=" O PHE T 16 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE T 18 " --> pdb=" O LEU T 121 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER T 123 " --> pdb=" O ILE T 18 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'T' and resid 42 through 44 removed outlier: 4.127A pdb=" N GLY T 42 " --> pdb=" O TYR T 69 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'T' and resid 348 through 351 removed outlier: 6.250A pdb=" N LEU T 168 " --> pdb=" O ILE T 349 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA T 351 " --> pdb=" O LEU T 168 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU T 170 " --> pdb=" O ALA T 351 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'T' and resid 285 through 288 removed outlier: 3.608A pdb=" N TYR T 287 " --> pdb=" O CYS T 295 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'T' and resid 223 through 227 removed outlier: 6.583A pdb=" N LYS T 238 " --> pdb=" O ALA T 224 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS T 226 " --> pdb=" O ASN T 236 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN T 236 " --> pdb=" O LYS T 226 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'U' and resid 8 through 11 removed outlier: 3.500A pdb=" N VAL U 9 " --> pdb=" O GLY U 20 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE U 31 " --> pdb=" O CYS U 17 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA U 19 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA U 29 " --> pdb=" O ALA U 19 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'U' and resid 104 through 107 removed outlier: 7.935A pdb=" N TYR U 133 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLU U 107 " --> pdb=" O TYR U 133 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA U 135 " --> pdb=" O GLU U 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'V' and resid 96 through 101 removed outlier: 3.658A pdb=" N LYS V 96 " --> pdb=" O ARG V 115 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG V 115 " --> pdb=" O LYS V 96 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'W' and resid 133 through 145 Processing sheet with id= AV, first strand: chain 'W' and resid 78 through 81 removed outlier: 6.932A pdb=" N PHE W 103 " --> pdb=" O LYS W 64 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE W 66 " --> pdb=" O LYS W 101 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS W 101 " --> pdb=" O ILE W 66 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE W 68 " --> pdb=" O ILE W 99 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE W 99 " --> pdb=" O PHE W 68 " (cutoff:3.500A) 1877 hydrogen bonds defined for protein. 5094 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 25.33 Time building geometry restraints manager: 20.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14881 1.33 - 1.46: 16498 1.46 - 1.59: 25769 1.59 - 1.72: 581 1.72 - 1.84: 424 Bond restraints: 58153 Sorted by residual: bond pdb=" C3' DC X 21 " pdb=" C2' DC X 21 " ideal model delta sigma weight residual 1.525 1.844 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" O3' DA X 60 " pdb=" P DA X 61 " ideal model delta sigma weight residual 1.607 1.427 0.180 1.50e-02 4.44e+03 1.44e+02 bond pdb=" C4 ATP T 501 " pdb=" C5 ATP T 501 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.62e+01 bond pdb=" C4 ATP U 401 " pdb=" C5 ATP U 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.62e+01 bond pdb=" C4 ATP K 401 " pdb=" C5 ATP K 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.55e+01 ... (remaining 58148 not shown) Histogram of bond angle deviations from ideal: 87.64 - 97.43: 5 97.43 - 107.21: 3737 107.21 - 116.99: 39582 116.99 - 126.77: 35200 126.77 - 136.56: 1307 Bond angle restraints: 79831 Sorted by residual: angle pdb=" PB ATP U 401 " pdb=" O3B ATP U 401 " pdb=" PG ATP U 401 " ideal model delta sigma weight residual 139.87 120.03 19.84 1.00e+00 1.00e+00 3.94e+02 angle pdb=" PB ATP T 501 " pdb=" O3B ATP T 501 " pdb=" PG ATP T 501 " ideal model delta sigma weight residual 139.87 120.74 19.13 1.00e+00 1.00e+00 3.66e+02 angle pdb=" PB ATP K 401 " pdb=" O3B ATP K 401 " pdb=" PG ATP K 401 " ideal model delta sigma weight residual 139.87 120.85 19.02 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP T 501 " pdb=" O3A ATP T 501 " pdb=" PB ATP T 501 " ideal model delta sigma weight residual 136.83 120.68 16.15 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PA ATP K 401 " pdb=" O3A ATP K 401 " pdb=" PB ATP K 401 " ideal model delta sigma weight residual 136.83 121.37 15.46 1.00e+00 1.00e+00 2.39e+02 ... (remaining 79826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 32442 33.38 - 66.75: 2214 66.75 - 100.13: 86 100.13 - 133.50: 8 133.50 - 166.88: 6 Dihedral angle restraints: 34756 sinusoidal: 16380 harmonic: 18376 Sorted by residual: dihedral pdb=" CA GLU Q 278 " pdb=" C GLU Q 278 " pdb=" N ILE Q 279 " pdb=" CA ILE Q 279 " ideal model delta harmonic sigma weight residual 180.00 -132.44 -47.56 0 5.00e+00 4.00e-02 9.05e+01 dihedral pdb=" CD ARG J 260 " pdb=" NE ARG J 260 " pdb=" CZ ARG J 260 " pdb=" NH1 ARG J 260 " ideal model delta sinusoidal sigma weight residual 0.00 84.08 -84.08 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CA CYS U 257 " pdb=" C CYS U 257 " pdb=" N PRO U 258 " pdb=" CA PRO U 258 " ideal model delta harmonic sigma weight residual 180.00 133.86 46.14 0 5.00e+00 4.00e-02 8.52e+01 ... (remaining 34753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 8514 0.108 - 0.216: 282 0.216 - 0.323: 16 0.323 - 0.431: 44 0.431 - 0.539: 137 Chirality restraints: 8993 Sorted by residual: chirality pdb=" P DT Y-138 " pdb=" OP1 DT Y-138 " pdb=" OP2 DT Y-138 " pdb=" O5' DT Y-138 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.54 2.00e-01 2.50e+01 7.26e+00 chirality pdb=" P DA X 89 " pdb=" OP1 DA X 89 " pdb=" OP2 DA X 89 " pdb=" O5' DA X 89 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" P DG X 37 " pdb=" OP1 DG X 37 " pdb=" OP2 DG X 37 " pdb=" O5' DG X 37 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.93e+00 ... (remaining 8990 not shown) Planarity restraints: 9191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 260 " 1.078 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARG J 260 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG J 260 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG J 260 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG J 260 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 263 " -1.077 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARG J 263 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG J 263 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG J 263 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG J 263 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I2029 " 0.985 9.50e-02 1.11e+02 4.41e-01 1.18e+02 pdb=" NE ARG I2029 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG I2029 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG I2029 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I2029 " 0.023 2.00e-02 2.50e+03 ... (remaining 9188 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 14 1.82 - 2.59: 753 2.59 - 3.36: 75761 3.36 - 4.13: 146422 4.13 - 4.90: 257188 Nonbonded interactions: 480138 Sorted by model distance: nonbonded pdb=" N GLU W 40 " pdb=" OP1 DA Y -82 " model vdw 1.051 2.520 nonbonded pdb=" OD1 ASN I 902 " pdb=" OD2 ASP I2137 " model vdw 1.075 3.040 nonbonded pdb=" NH2 ARG I 898 " pdb=" OE1 GLN I2067 " model vdw 1.168 2.520 nonbonded pdb=" OH TYR F 37 " pdb=" OP1 DG X 121 " model vdw 1.299 2.440 nonbonded pdb=" NH2 ARG E 32 " pdb=" OP1 DA Y-117 " model vdw 1.366 2.520 ... (remaining 480133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 118) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 28 through 121) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 41 through 134) selection = (chain 'G' and resid 41 through 134) } ncs_group { reference = (chain 'D' and resid 23 through 102) selection = chain 'H' } ncs_group { reference = (chain 'M' and (resid 15 through 451 or resid 501)) selection = (chain 'O' and (resid 15 through 141 or resid 153 through 451 or resid 501)) selection = (chain 'Q' and (resid 15 through 141 or resid 153 through 451 or resid 501)) } ncs_group { reference = (chain 'N' and (resid 18 through 148 or resid 157 through 210 or (resid 223 and \ (name N or name CA or name C or name O or name CB )) or resid 224 through 447 or \ resid 501)) selection = (chain 'P' and (resid 18 through 148 or resid 157 through 210 or resid 223 throu \ gh 447 or resid 501)) selection = (chain 'R' and (resid 18 through 210 or (resid 223 and (name N or name CA or nam \ e C or name O or name CB )) or resid 224 through 447 or resid 501)) } ncs_group { reference = (chain 'S' and (resid 2 through 40 or resid 52 through 371)) selection = (chain 'U' and resid 2 through 371) } 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=0.01 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: 2.400 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: 0.030 Extract box with map and model: 14.520 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 131.330 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5327 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 : 0.005 0.319 58153 Z= 0.279 Angle : 0.894 24.392 79831 Z= 0.533 Chirality : 0.077 0.539 8993 Planarity : 0.009 0.483 9191 Dihedral : 18.429 166.879 22892 Min Nonbonded Distance : 1.051 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.45 % Favored : 95.18 % Rotamer: Outliers : 5.29 % Allowed : 7.09 % Favored : 87.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.10), residues: 6271 helix: -0.98 (0.09), residues: 2812 sheet: -1.54 (0.18), residues: 760 loop : -2.23 (0.11), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 206 HIS 0.004 0.001 HIS K 194 PHE 0.013 0.001 PHE P 257 TYR 0.011 0.001 TYR W 86 ARG 0.004 0.000 ARG J 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1069 time to evaluate : 4.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.6244 (m-80) cc_final: 0.6027 (m-80) REVERT: E 118 LYS cc_start: 0.3843 (tmmm) cc_final: 0.3642 (tttm) REVERT: I 120 SER cc_start: 0.0672 (OUTLIER) cc_final: 0.0347 (p) REVERT: I 144 MET cc_start: -0.0067 (OUTLIER) cc_final: -0.0671 (ttt) REVERT: I 225 ARG cc_start: 0.7059 (tpp-160) cc_final: 0.6762 (ttm-80) REVERT: I 227 LYS cc_start: 0.5460 (tttt) cc_final: 0.5135 (ttpt) REVERT: I 784 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: I 943 MET cc_start: 0.8740 (mmp) cc_final: 0.8254 (mmt) REVERT: I 1936 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8347 (pt) REVERT: I 2015 TRP cc_start: 0.7698 (OUTLIER) cc_final: 0.6616 (m-90) REVERT: I 2051 LEU cc_start: 0.7272 (tp) cc_final: 0.6920 (tp) REVERT: I 2126 ASN cc_start: 0.4150 (m-40) cc_final: 0.3900 (t0) REVERT: K 71 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: K 88 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6544 (t80) REVERT: K 106 GLN cc_start: 0.6439 (mt0) cc_final: 0.5749 (tt0) REVERT: L 35 LEU cc_start: 0.8025 (mt) cc_final: 0.7499 (mt) REVERT: M 192 TYR cc_start: 0.5087 (m-80) cc_final: 0.4857 (m-10) REVERT: N 88 MET cc_start: 0.7481 (mmm) cc_final: 0.7273 (mmt) REVERT: N 209 PHE cc_start: 0.4845 (OUTLIER) cc_final: 0.4062 (m-80) REVERT: N 269 LYS cc_start: 0.8068 (tptt) cc_final: 0.6924 (tptt) REVERT: N 274 GLU cc_start: 0.7291 (pt0) cc_final: 0.6711 (pt0) REVERT: N 338 THR cc_start: 0.6866 (p) cc_final: 0.6648 (p) REVERT: O 55 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7328 (tp) REVERT: O 171 LYS cc_start: 0.7110 (mttt) cc_final: 0.6570 (tttt) REVERT: O 272 THR cc_start: 0.8081 (m) cc_final: 0.7776 (p) REVERT: O 371 MET cc_start: 0.8244 (ttp) cc_final: 0.7982 (ttp) REVERT: O 455 MET cc_start: 0.6929 (tpt) cc_final: 0.6455 (tpt) REVERT: P 269 LYS cc_start: 0.8610 (tttm) cc_final: 0.7842 (tttm) REVERT: P 441 GLN cc_start: 0.8988 (tt0) cc_final: 0.8633 (tp40) REVERT: P 448 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6144 (t0) REVERT: Q 129 GLU cc_start: 0.7453 (pm20) cc_final: 0.6758 (pm20) REVERT: Q 196 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7366 (m-40) REVERT: Q 228 VAL cc_start: 0.9077 (p) cc_final: 0.8795 (t) REVERT: Q 259 MET cc_start: 0.6489 (tpp) cc_final: 0.6061 (tpp) REVERT: Q 289 GLN cc_start: 0.7561 (tt0) cc_final: 0.7274 (mt0) REVERT: Q 362 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7571 (ptm-80) REVERT: Q 431 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7697 (mt-10) REVERT: Q 450 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.6488 (pt0) REVERT: R 88 MET cc_start: 0.7741 (mmm) cc_final: 0.7172 (mmt) REVERT: R 90 MET cc_start: 0.8467 (mtp) cc_final: 0.8094 (mtp) REVERT: R 117 GLU cc_start: 0.5485 (mm-30) cc_final: 0.5188 (mt-10) REVERT: R 171 ILE cc_start: 0.8578 (mt) cc_final: 0.8361 (tt) REVERT: R 193 ILE cc_start: 0.8233 (tp) cc_final: 0.7726 (pt) REVERT: R 253 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7498 (ttp-170) REVERT: R 269 LYS cc_start: 0.7876 (mptt) cc_final: 0.7241 (mtmt) REVERT: S 1 MET cc_start: 0.0376 (mtt) cc_final: -0.1340 (tpt) REVERT: S 44 MET cc_start: -0.2109 (mtt) cc_final: -0.2811 (ptt) REVERT: T 10 GLU cc_start: 0.0196 (OUTLIER) cc_final: -0.1222 (pp20) REVERT: T 77 VAL cc_start: 0.1326 (OUTLIER) cc_final: 0.1037 (t) REVERT: T 79 ARG cc_start: -0.0674 (OUTLIER) cc_final: -0.0992 (mtt90) REVERT: T 399 ILE cc_start: 0.4265 (OUTLIER) cc_final: 0.3944 (tt) REVERT: U 78 ASN cc_start: 0.1331 (OUTLIER) cc_final: 0.0967 (p0) REVERT: U 165 ILE cc_start: 0.1373 (OUTLIER) cc_final: 0.0859 (tt) REVERT: U 175 ILE cc_start: 0.1369 (OUTLIER) cc_final: 0.0817 (mt) REVERT: U 270 GLU cc_start: 0.1826 (OUTLIER) cc_final: 0.0450 (tt0) REVERT: U 359 LYS cc_start: 0.3138 (OUTLIER) cc_final: 0.2258 (tttp) REVERT: V 229 GLN cc_start: 0.1874 (OUTLIER) cc_final: 0.1477 (pt0) REVERT: V 255 GLU cc_start: 0.3251 (OUTLIER) cc_final: 0.2227 (mt-10) REVERT: W 98 ILE cc_start: 0.1994 (mt) cc_final: 0.1162 (pt) REVERT: W 151 MET cc_start: 0.0289 (tpt) cc_final: 0.0030 (mmm) outliers start: 288 outliers final: 46 residues processed: 1301 average time/residue: 0.5958 time to fit residues: 1241.8643 Evaluate side-chains 595 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 526 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 726 LYS Chi-restraints excluded: chain I residue 732 HIS Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 864 ARG Chi-restraints excluded: chain I residue 966 ARG Chi-restraints excluded: chain I residue 988 LYS Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 2015 TRP Chi-restraints excluded: chain I residue 2176 ILE Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 124 ARG Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 256 ILE Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 325 ILE Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 273 ASP Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 261 PHE Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 196 ASN Chi-restraints excluded: chain Q residue 450 GLN Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain T residue 10 GLU Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 399 ILE Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 85 ILE Chi-restraints excluded: chain U residue 165 ILE Chi-restraints excluded: chain U residue 175 ILE Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 270 GLU Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 229 GLN Chi-restraints excluded: chain V residue 245 GLU Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 38 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 550 optimal weight: 9.9990 chunk 494 optimal weight: 9.9990 chunk 274 optimal weight: 0.8980 chunk 168 optimal weight: 7.9990 chunk 333 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 511 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 310 optimal weight: 0.5980 chunk 380 optimal weight: 0.7980 chunk 592 optimal weight: 6.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS D 25 ASN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 93 GLN G 108 ASN G 113 HIS I 178 GLN ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 ASN I 652 GLN ** I 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 790 HIS I 800 HIS I 819 GLN I 905 ASN I1896 GLN ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2084 HIS ** I2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2175 ASN ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 304 ASN K 310 GLN L 45 HIS M 203 GLN M 236 GLN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN M 414 ASN N 240 HIS N 245 HIS N 275 GLN N 277 ASN N 302 HIS N 447 GLN O 18 HIS O 20 HIS O 34 GLN O 348 HIS O 393 HIS P 25 HIS P 27 HIS P 44 GLN P 313 ASN P 422 GLN P 447 GLN Q 18 HIS ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 203 GLN Q 229 HIS Q 236 GLN Q 393 HIS ** Q 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 GLN R 233 GLN R 313 ASN ** S 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 408 GLN U 12 ASN U 78 ASN U 280 ASN V 54 HIS V 235 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 58153 Z= 0.413 Angle : 0.789 13.787 79831 Z= 0.409 Chirality : 0.049 0.245 8993 Planarity : 0.006 0.118 9191 Dihedral : 22.029 173.367 10488 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.71 % Favored : 94.13 % Rotamer: Outliers : 4.12 % Allowed : 13.34 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.10), residues: 6271 helix: -0.13 (0.10), residues: 2835 sheet: -1.13 (0.17), residues: 819 loop : -1.64 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 68 HIS 0.009 0.002 HIS O 305 PHE 0.032 0.002 PHE D 61 TYR 0.030 0.002 TYR C 54 ARG 0.022 0.001 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 543 time to evaluate : 4.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 118 LYS cc_start: 0.4414 (tmmm) cc_final: 0.3765 (tttm) REVERT: I 225 ARG cc_start: 0.7083 (tpp-160) cc_final: 0.6731 (ttm-80) REVERT: I 227 LYS cc_start: 0.5987 (tttt) cc_final: 0.5662 (ttpt) REVERT: I 613 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6438 (tt) REVERT: I 679 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8324 (ttm) REVERT: I 784 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: I 814 MET cc_start: 0.7487 (mmt) cc_final: 0.6759 (mmt) REVERT: I 861 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7727 (mp) REVERT: I 864 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7897 (ttt180) REVERT: I 943 MET cc_start: 0.8815 (mmp) cc_final: 0.8350 (mmt) REVERT: I 1884 PHE cc_start: 0.6810 (m-80) cc_final: 0.6576 (m-10) REVERT: I 1936 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8907 (pt) REVERT: I 2144 MET cc_start: 0.7265 (mmm) cc_final: 0.7001 (mmm) REVERT: J 131 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6650 (mttp) REVERT: K 3 THR cc_start: 0.4602 (OUTLIER) cc_final: 0.4274 (m) REVERT: K 88 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6499 (t80) REVERT: K 109 MET cc_start: 0.5161 (mtm) cc_final: 0.4566 (mtp) REVERT: K 196 MET cc_start: 0.7262 (ppp) cc_final: 0.6298 (ptm) REVERT: L 35 LEU cc_start: 0.8276 (mt) cc_final: 0.7831 (mt) REVERT: M 26 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8593 (mp) REVERT: M 106 ILE cc_start: 0.7048 (mm) cc_final: 0.6836 (tt) REVERT: M 182 LYS cc_start: 0.8818 (tppt) cc_final: 0.8526 (mtpt) REVERT: M 293 GLU cc_start: 0.8121 (tp30) cc_final: 0.7845 (tp30) REVERT: M 323 ILE cc_start: 0.8778 (pt) cc_final: 0.8417 (mt) REVERT: M 359 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7452 (mtt) REVERT: M 410 LEU cc_start: 0.8403 (tt) cc_final: 0.8133 (tt) REVERT: N 46 MET cc_start: 0.7347 (mtp) cc_final: 0.7106 (tpp) REVERT: N 88 MET cc_start: 0.7519 (mmm) cc_final: 0.7187 (mmt) REVERT: N 178 MET cc_start: 0.8558 (mmp) cc_final: 0.8214 (mmt) REVERT: N 209 PHE cc_start: 0.5354 (OUTLIER) cc_final: 0.4249 (m-80) REVERT: N 261 PHE cc_start: 0.7739 (p90) cc_final: 0.7515 (p90) REVERT: N 319 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: O 18 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.6025 (t70) REVERT: O 100 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: O 371 MET cc_start: 0.8546 (ttp) cc_final: 0.8231 (ttp) REVERT: P 46 MET cc_start: 0.8627 (mmm) cc_final: 0.7687 (mmm) REVERT: P 255 GLN cc_start: 0.5378 (OUTLIER) cc_final: 0.4557 (mp10) REVERT: P 269 LYS cc_start: 0.8677 (tttm) cc_final: 0.8190 (tttm) REVERT: P 441 GLN cc_start: 0.8958 (tt0) cc_final: 0.8567 (tp40) REVERT: Q 137 GLU cc_start: 0.7312 (pp20) cc_final: 0.6967 (pp20) REVERT: Q 236 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: Q 345 THR cc_start: 0.7085 (OUTLIER) cc_final: 0.6771 (t) REVERT: Q 346 SER cc_start: 0.8652 (p) cc_final: 0.8290 (t) REVERT: R 90 MET cc_start: 0.8772 (mtp) cc_final: 0.8383 (mtp) REVERT: R 253 ARG cc_start: 0.8134 (ttm170) cc_final: 0.7834 (ttm170) REVERT: R 261 PHE cc_start: 0.5590 (p90) cc_final: 0.5387 (p90) REVERT: R 269 LYS cc_start: 0.8228 (mptt) cc_final: 0.7709 (tmtt) REVERT: R 273 ARG cc_start: 0.7101 (mpt180) cc_final: 0.6860 (mmt-90) REVERT: R 284 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7714 (mtp180) REVERT: R 435 ASP cc_start: 0.7691 (t0) cc_final: 0.7358 (p0) REVERT: R 444 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7343 (ptpp) REVERT: S 1 MET cc_start: 0.0139 (mtt) cc_final: -0.1494 (tpt) REVERT: S 44 MET cc_start: -0.1766 (mtt) cc_final: -0.3000 (ptp) REVERT: S 47 MET cc_start: 0.2386 (tmm) cc_final: 0.2162 (tmt) REVERT: S 82 MET cc_start: 0.4099 (mmm) cc_final: 0.3850 (tpp) REVERT: S 123 MET cc_start: 0.5624 (ttm) cc_final: 0.5371 (ttm) REVERT: S 161 HIS cc_start: 0.2827 (OUTLIER) cc_final: 0.2396 (t-90) REVERT: S 227 MET cc_start: 0.2387 (mmm) cc_final: 0.1937 (mmp) REVERT: T 251 HIS cc_start: 0.2234 (t-170) cc_final: 0.2016 (t-170) REVERT: T 399 ILE cc_start: 0.4234 (OUTLIER) cc_final: 0.4028 (tt) REVERT: U 190 MET cc_start: 0.0568 (ttt) cc_final: 0.0270 (ttp) REVERT: U 359 LYS cc_start: 0.2915 (OUTLIER) cc_final: 0.1991 (tttp) REVERT: V 53 MET cc_start: 0.2944 (ttm) cc_final: 0.2394 (ttm) REVERT: V 62 TYR cc_start: 0.3392 (t80) cc_final: 0.3035 (t80) REVERT: V 98 MET cc_start: 0.1455 (ppp) cc_final: 0.0932 (ttp) REVERT: V 154 LYS cc_start: 0.3456 (tttm) cc_final: 0.3219 (tmtt) REVERT: V 248 LEU cc_start: 0.3751 (OUTLIER) cc_final: 0.3104 (tp) REVERT: V 255 GLU cc_start: 0.3123 (OUTLIER) cc_final: 0.2109 (mt-10) REVERT: W 151 MET cc_start: 0.0377 (tpt) cc_final: 0.0002 (mmm) outliers start: 224 outliers final: 106 residues processed: 731 average time/residue: 0.5743 time to fit residues: 707.5013 Evaluate side-chains 559 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 429 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 679 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 776 THR Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 811 LEU Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 864 ARG Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 2015 TRP Chi-restraints excluded: chain I residue 2068 MET Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2115 ILE Chi-restraints excluded: chain I residue 2120 SER Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 306 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 226 LYS Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 254 GLN Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 283 TRP Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 319 ASP Chi-restraints excluded: chain N residue 325 ILE Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 44 ASN Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 271 ILE Chi-restraints excluded: chain O residue 273 ASP Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 345 THR Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 255 GLN Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 261 PHE Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 209 TYR Chi-restraints excluded: chain Q residue 236 GLN Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 345 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 53 TYR Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 285 CYS Chi-restraints excluded: chain T residue 399 ILE Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 85 ILE Chi-restraints excluded: chain U residue 165 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 58 TYR Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 248 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 329 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 492 optimal weight: 7.9990 chunk 403 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 593 optimal weight: 8.9990 chunk 640 optimal weight: 6.9990 chunk 528 optimal weight: 20.0000 chunk 588 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 475 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN G 85 GLN H 75 HIS ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 702 GLN ** I 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 892 ASN I 902 ASN ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN ** K 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN L 29 ASN L 83 ASN L 91 GLN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 429 HIS ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 373 GLN O 392 ASN ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 HIS Q 203 GLN ** Q 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 241 HIS Q 348 HIS Q 380 GLN ** Q 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 HIS R 240 HIS ** T 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 12 ASN ** U 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.235 58153 Z= 0.536 Angle : 0.803 11.093 79831 Z= 0.418 Chirality : 0.050 0.233 8993 Planarity : 0.006 0.095 9191 Dihedral : 21.825 170.963 10415 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.43 % Favored : 93.41 % Rotamer: Outliers : 5.20 % Allowed : 14.09 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.12 % 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: -1.36 (0.10), residues: 6271 helix: -0.19 (0.09), residues: 2874 sheet: -0.99 (0.18), residues: 790 loop : -1.60 (0.12), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP S 356 HIS 0.038 0.002 HIS B 46 PHE 0.027 0.003 PHE J 265 TYR 0.028 0.002 TYR O 192 ARG 0.015 0.001 ARG P 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 441 time to evaluate : 4.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.6108 (m-80) cc_final: 0.5737 (m-10) REVERT: E 118 LYS cc_start: 0.4854 (tmmm) cc_final: 0.4127 (mttm) REVERT: I 182 ARG cc_start: 0.4603 (OUTLIER) cc_final: 0.4336 (tpp80) REVERT: I 225 ARG cc_start: 0.7092 (tpp-160) cc_final: 0.6749 (ttm-80) REVERT: I 227 LYS cc_start: 0.5488 (tttt) cc_final: 0.5286 (ttpt) REVERT: I 729 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8594 (tp) REVERT: I 784 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: I 814 MET cc_start: 0.7517 (mmt) cc_final: 0.7003 (mmt) REVERT: I 861 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7585 (mp) REVERT: I 864 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8390 (ttt-90) REVERT: I 867 CYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8104 (m) REVERT: I 943 MET cc_start: 0.8755 (mmp) cc_final: 0.8298 (mmt) REVERT: I 992 MET cc_start: 0.4640 (OUTLIER) cc_final: 0.4416 (mpp) REVERT: I 1884 PHE cc_start: 0.6866 (m-80) cc_final: 0.6539 (m-10) REVERT: I 1901 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8355 (mt) REVERT: I 2028 MET cc_start: 0.9096 (mtp) cc_final: 0.8863 (mtm) REVERT: J 131 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6719 (mttp) REVERT: J 133 MET cc_start: 0.5381 (mpp) cc_final: 0.5129 (mpp) REVERT: K 88 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6450 (t80) REVERT: K 109 MET cc_start: 0.5445 (mtm) cc_final: 0.5074 (mtp) REVERT: K 279 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: M 182 LYS cc_start: 0.8911 (tppt) cc_final: 0.8607 (mtpt) REVERT: M 184 ARG cc_start: 0.8322 (mtp85) cc_final: 0.8098 (mtt-85) REVERT: M 262 GLN cc_start: 0.5734 (OUTLIER) cc_final: 0.5317 (mp10) REVERT: M 323 ILE cc_start: 0.8640 (pt) cc_final: 0.8429 (mt) REVERT: N 88 MET cc_start: 0.7684 (mmm) cc_final: 0.7346 (mmt) REVERT: N 320 MET cc_start: 0.8673 (mmt) cc_final: 0.8010 (mmt) REVERT: N 326 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7757 (mtp) REVERT: N 354 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8477 (pp) REVERT: N 411 LEU cc_start: 0.8179 (mt) cc_final: 0.7928 (mt) REVERT: O 18 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.5344 (t70) REVERT: O 100 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6529 (mp0) REVERT: O 113 MET cc_start: 0.7889 (tpt) cc_final: 0.7405 (tpp) REVERT: O 237 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7615 (p0) REVERT: O 371 MET cc_start: 0.8543 (ttp) cc_final: 0.8236 (ttp) REVERT: P 46 MET cc_start: 0.8974 (mmm) cc_final: 0.8295 (mmm) REVERT: P 168 MET cc_start: 0.8599 (ptm) cc_final: 0.8380 (ptp) REVERT: P 269 LYS cc_start: 0.8424 (tttm) cc_final: 0.7840 (tptp) REVERT: P 392 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7674 (ttp80) REVERT: P 441 GLN cc_start: 0.8810 (tt0) cc_final: 0.8471 (tp40) REVERT: P 448 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: Q 209 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.5580 (p90) REVERT: Q 249 ARG cc_start: 0.6647 (mtm180) cc_final: 0.5961 (mtm180) REVERT: Q 345 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7860 (t) REVERT: Q 346 SER cc_start: 0.8732 (p) cc_final: 0.8503 (t) REVERT: Q 352 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8549 (mt) REVERT: Q 404 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6239 (mtt90) REVERT: R 17 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7483 (p) REVERT: R 139 GLU cc_start: 0.7846 (pt0) cc_final: 0.7325 (pp20) REVERT: R 207 ARG cc_start: 0.6332 (ttm170) cc_final: 0.5987 (ttp-170) REVERT: R 246 GLU cc_start: 0.5491 (OUTLIER) cc_final: 0.5099 (pt0) REVERT: R 267 GLU cc_start: 0.4176 (OUTLIER) cc_final: 0.3832 (tt0) REVERT: R 269 LYS cc_start: 0.8236 (mptt) cc_final: 0.7870 (tmtt) REVERT: R 273 ARG cc_start: 0.7111 (mpt180) cc_final: 0.6698 (mmt-90) REVERT: R 326 MET cc_start: 0.8810 (mtt) cc_final: 0.8585 (mtm) REVERT: S 1 MET cc_start: 0.0338 (mtt) cc_final: -0.1111 (tpt) REVERT: S 47 MET cc_start: 0.2571 (tmm) cc_final: 0.2282 (tmm) REVERT: S 161 HIS cc_start: 0.3336 (OUTLIER) cc_final: 0.2330 (t-90) REVERT: S 227 MET cc_start: 0.2953 (mmm) cc_final: 0.2174 (mmp) REVERT: T 109 MET cc_start: 0.1200 (tmm) cc_final: 0.0361 (tpt) REVERT: U 190 MET cc_start: 0.1077 (ttt) cc_final: 0.0831 (ttp) REVERT: U 283 MET cc_start: 0.5112 (mtp) cc_final: 0.4899 (mtp) REVERT: U 359 LYS cc_start: 0.3503 (OUTLIER) cc_final: 0.2226 (tttp) REVERT: V 53 MET cc_start: 0.3530 (ttm) cc_final: 0.3078 (ttm) REVERT: W 151 MET cc_start: 0.0088 (tpt) cc_final: -0.0483 (mmm) outliers start: 283 outliers final: 155 residues processed: 680 average time/residue: 0.5373 time to fit residues: 618.1275 Evaluate side-chains 555 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 373 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 629 LEU Chi-restraints excluded: chain I residue 660 LEU Chi-restraints excluded: chain I residue 723 THR Chi-restraints excluded: chain I residue 729 LEU Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 776 THR Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 799 SER Chi-restraints excluded: chain I residue 811 LEU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 864 ARG Chi-restraints excluded: chain I residue 867 CYS Chi-restraints excluded: chain I residue 894 LEU Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 969 LEU Chi-restraints excluded: chain I residue 992 MET Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1979 VAL Chi-restraints excluded: chain I residue 1991 HIS Chi-restraints excluded: chain I residue 2015 TRP Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2068 MET Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2120 SER Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain I residue 2185 MET Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 306 THR Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 272 ASN Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 148 ARG Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 254 GLN Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 283 TRP Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 325 ILE Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 44 ASN Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 237 ASP Chi-restraints excluded: chain O residue 271 ILE Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 362 ARG Chi-restraints excluded: chain O residue 419 ILE Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 137 ILE Chi-restraints excluded: chain P residue 255 GLN Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 161 LEU Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 209 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 235 ILE Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 345 THR Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain Q residue 404 ARG Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 267 GLU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 379 ASP Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 434 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 285 CYS Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 165 ILE Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 58 TYR Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 38 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 586 optimal weight: 10.0000 chunk 445 optimal weight: 0.0170 chunk 307 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 283 optimal weight: 0.9980 chunk 398 optimal weight: 0.9980 chunk 595 optimal weight: 20.0000 chunk 630 optimal weight: 5.9990 chunk 311 optimal weight: 0.6980 chunk 564 optimal weight: 0.8980 chunk 169 optimal weight: 7.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1964 GLN I2067 GLN ** I2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2153 HIS J 200 GLN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 HIS ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 GLN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 HIS ** O 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 429 HIS ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 251 HIS T 327 HIS T 407 GLN ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 58153 Z= 0.188 Angle : 0.620 10.406 79831 Z= 0.320 Chirality : 0.042 0.343 8993 Planarity : 0.004 0.090 9191 Dihedral : 21.478 170.007 10407 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 3.47 % Allowed : 15.89 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.07 % 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: -0.79 (0.11), residues: 6271 helix: 0.33 (0.10), residues: 2853 sheet: -0.82 (0.18), residues: 809 loop : -1.31 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP S 356 HIS 0.009 0.001 HIS S 173 PHE 0.039 0.001 PHE N 261 TYR 0.020 0.001 TYR I 821 ARG 0.005 0.000 ARG J 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 442 time to evaluate : 4.566 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: E 118 LYS cc_start: 0.4952 (tmmm) cc_final: 0.4302 (mttm) REVERT: I 225 ARG cc_start: 0.7067 (tpp-160) cc_final: 0.6849 (ttm-80) REVERT: I 627 ASP cc_start: 0.7163 (m-30) cc_final: 0.6749 (m-30) REVERT: I 861 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7475 (mp) REVERT: I 864 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7328 (mtm180) REVERT: I 2144 MET cc_start: 0.6983 (mmm) cc_final: 0.6739 (mmm) REVERT: J 274 PHE cc_start: 0.5349 (OUTLIER) cc_final: 0.4879 (t80) REVERT: J 323 TYR cc_start: 0.7170 (t80) cc_final: 0.6857 (t80) REVERT: K 88 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6422 (t80) REVERT: K 196 MET cc_start: 0.7389 (ppp) cc_final: 0.6244 (ptm) REVERT: K 199 THR cc_start: 0.7113 (OUTLIER) cc_final: 0.6720 (m) REVERT: M 178 GLU cc_start: 0.7259 (mp0) cc_final: 0.6996 (mp0) REVERT: M 182 LYS cc_start: 0.8854 (tppt) cc_final: 0.8504 (mtpt) REVERT: M 254 GLN cc_start: 0.5284 (OUTLIER) cc_final: 0.4625 (pm20) REVERT: M 293 GLU cc_start: 0.8143 (tp30) cc_final: 0.7659 (tm-30) REVERT: M 323 ILE cc_start: 0.8719 (pt) cc_final: 0.8470 (mt) REVERT: M 408 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: N 88 MET cc_start: 0.7673 (mmm) cc_final: 0.7408 (mmt) REVERT: N 179 ILE cc_start: 0.8453 (tt) cc_final: 0.8126 (tp) REVERT: N 354 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8426 (pp) REVERT: N 442 TYR cc_start: 0.8441 (m-80) cc_final: 0.7994 (m-80) REVERT: O 100 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: O 371 MET cc_start: 0.8543 (ttp) cc_final: 0.8296 (ttp) REVERT: O 378 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8206 (tpt-90) REVERT: P 257 PHE cc_start: 0.6428 (OUTLIER) cc_final: 0.6149 (p90) REVERT: P 269 LYS cc_start: 0.8337 (tttm) cc_final: 0.7702 (tptp) REVERT: P 441 GLN cc_start: 0.8843 (tt0) cc_final: 0.8480 (tp40) REVERT: P 448 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7158 (m-30) REVERT: Q 168 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6816 (ttpt) REVERT: Q 196 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.7125 (m-40) REVERT: R 17 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7453 (p) REVERT: R 139 GLU cc_start: 0.7777 (pt0) cc_final: 0.7324 (pp20) REVERT: R 269 LYS cc_start: 0.8074 (mptt) cc_final: 0.7439 (tmtt) REVERT: R 273 ARG cc_start: 0.6875 (mpt180) cc_final: 0.6556 (mmt-90) REVERT: R 364 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7349 (tm-30) REVERT: R 435 ASP cc_start: 0.7833 (t0) cc_final: 0.7506 (p0) REVERT: R 444 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7132 (mmmt) REVERT: S 1 MET cc_start: 0.0428 (mtt) cc_final: -0.1038 (tpt) REVERT: S 161 HIS cc_start: 0.3097 (OUTLIER) cc_final: 0.2545 (t-90) REVERT: S 227 MET cc_start: 0.3551 (mmm) cc_final: 0.2983 (mmp) REVERT: S 305 MET cc_start: 0.5001 (mmm) cc_final: 0.4679 (mmp) REVERT: T 109 MET cc_start: 0.1427 (tmm) cc_final: 0.0523 (tpt) REVERT: U 359 LYS cc_start: 0.3551 (OUTLIER) cc_final: 0.2361 (tttp) REVERT: V 53 MET cc_start: 0.3288 (ttm) cc_final: 0.3013 (ttm) REVERT: V 255 GLU cc_start: 0.3119 (OUTLIER) cc_final: 0.2803 (mm-30) REVERT: W 59 MET cc_start: -0.0908 (OUTLIER) cc_final: -0.1248 (tpp) REVERT: W 151 MET cc_start: 0.0153 (tpt) cc_final: -0.0459 (mmm) outliers start: 189 outliers final: 114 residues processed: 593 average time/residue: 0.5459 time to fit residues: 546.3167 Evaluate side-chains 530 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 396 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 776 THR Chi-restraints excluded: chain I residue 857 ILE Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 864 ARG Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 949 ILE Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 2015 TRP Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2120 SER Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 306 THR Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 254 GLN Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 332 ASN Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 319 ASP Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 44 ASN Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 362 ARG Chi-restraints excluded: chain O residue 378 ARG Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 326 MET Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 196 ASN Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 434 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain T residue 251 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 58 TYR Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 524 optimal weight: 20.0000 chunk 357 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 469 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 537 optimal weight: 30.0000 chunk 435 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 321 optimal weight: 3.9990 chunk 565 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 HIS ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 623 HIS I 865 GLN ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 408 GLN ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 316 HIS ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 344 HIS ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 404 GLN S 128 ASN ** S 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 100 GLN U 12 ASN U 225 GLN V 235 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.246 58153 Z= 0.667 Angle : 0.841 14.232 79831 Z= 0.434 Chirality : 0.052 0.297 8993 Planarity : 0.007 0.095 9191 Dihedral : 21.741 174.332 10396 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.35 % Favored : 92.47 % Rotamer: Outliers : 5.03 % Allowed : 15.71 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.13 % 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: -1.32 (0.10), residues: 6271 helix: -0.18 (0.09), residues: 2866 sheet: -1.02 (0.17), residues: 836 loop : -1.53 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP S 356 HIS 0.025 0.002 HIS T 251 PHE 0.041 0.003 PHE L 84 TYR 0.034 0.003 TYR K 217 ARG 0.013 0.001 ARG P 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 368 time to evaluate : 4.563 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: D 93 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7774 (mm110) REVERT: E 118 LYS cc_start: 0.5246 (tmmm) cc_final: 0.4452 (mttm) REVERT: I 627 ASP cc_start: 0.7472 (m-30) cc_final: 0.6894 (m-30) REVERT: I 861 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7621 (mp) REVERT: J 274 PHE cc_start: 0.5602 (OUTLIER) cc_final: 0.5096 (t80) REVERT: K 1 MET cc_start: 0.5665 (tmm) cc_final: 0.4893 (tmm) REVERT: K 88 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6230 (t80) REVERT: K 199 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7065 (m) REVERT: K 279 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: M 172 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7716 (mp) REVERT: M 182 LYS cc_start: 0.8883 (tppt) cc_final: 0.8571 (mtpt) REVERT: M 254 GLN cc_start: 0.5466 (OUTLIER) cc_final: 0.4800 (pm20) REVERT: N 88 MET cc_start: 0.7687 (mmm) cc_final: 0.7338 (mmt) REVERT: N 291 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8763 (pt) REVERT: N 354 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8525 (pp) REVERT: N 411 LEU cc_start: 0.8260 (mt) cc_final: 0.7971 (mt) REVERT: O 100 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: O 237 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7717 (p0) REVERT: O 267 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8096 (mttt) REVERT: O 371 MET cc_start: 0.8549 (ttp) cc_final: 0.8308 (ttp) REVERT: P 257 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6505 (p90) REVERT: P 269 LYS cc_start: 0.8453 (tttm) cc_final: 0.7813 (tptp) REVERT: P 354 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8757 (pp) REVERT: P 441 GLN cc_start: 0.8795 (tt0) cc_final: 0.8446 (tp40) REVERT: P 448 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7102 (m-30) REVERT: Q 105 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8531 (pt0) REVERT: Q 168 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7718 (ttpt) REVERT: Q 428 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: R 62 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8319 (ptp) REVERT: R 139 GLU cc_start: 0.7988 (pt0) cc_final: 0.7467 (pp20) REVERT: R 207 ARG cc_start: 0.6418 (ttm170) cc_final: 0.6100 (ttp-170) REVERT: R 214 ASP cc_start: 0.6371 (OUTLIER) cc_final: 0.5566 (p0) REVERT: R 269 LYS cc_start: 0.8195 (mptt) cc_final: 0.7784 (tmtt) REVERT: R 273 ARG cc_start: 0.7356 (mpt180) cc_final: 0.7100 (mpt180) REVERT: S 1 MET cc_start: 0.0187 (mtt) cc_final: -0.0960 (tpt) REVERT: S 161 HIS cc_start: 0.3867 (OUTLIER) cc_final: 0.3069 (t-90) REVERT: S 325 MET cc_start: 0.5100 (tpp) cc_final: 0.4856 (tpt) REVERT: T 109 MET cc_start: 0.1213 (tmm) cc_final: 0.0376 (tpt) REVERT: U 359 LYS cc_start: 0.4257 (OUTLIER) cc_final: 0.2855 (tttp) REVERT: V 169 LEU cc_start: 0.3757 (OUTLIER) cc_final: 0.3508 (tt) REVERT: V 255 GLU cc_start: 0.2965 (OUTLIER) cc_final: 0.2261 (mt-10) REVERT: W 59 MET cc_start: -0.0734 (OUTLIER) cc_final: -0.1053 (tpp) REVERT: W 151 MET cc_start: 0.0473 (tpt) cc_final: -0.0145 (mmm) outliers start: 274 outliers final: 187 residues processed: 600 average time/residue: 0.5310 time to fit residues: 543.2626 Evaluate side-chains 562 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 349 time to evaluate : 4.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 660 LEU Chi-restraints excluded: chain I residue 723 THR Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 776 THR Chi-restraints excluded: chain I residue 811 LEU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 894 LEU Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 929 VAL Chi-restraints excluded: chain I residue 1899 GLU Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1979 VAL Chi-restraints excluded: chain I residue 1991 HIS Chi-restraints excluded: chain I residue 2015 TRP Chi-restraints excluded: chain I residue 2034 ASP Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2120 SER Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 273 THR Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 306 THR Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 254 GLN Chi-restraints excluded: chain M residue 259 MET Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 332 ASN Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 319 ASP Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 44 ASN Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 237 ASP Chi-restraints excluded: chain O residue 257 LEU Chi-restraints excluded: chain O residue 267 LYS Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 345 THR Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 362 ARG Chi-restraints excluded: chain O residue 378 ARG Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 290 GLU Chi-restraints excluded: chain P residue 295 VAL Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 354 LEU Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 360 THR Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 161 LEU Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 207 ASP Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 235 ILE Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 346 SER Chi-restraints excluded: chain Q residue 399 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 428 GLU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 360 THR Chi-restraints excluded: chain R residue 379 ASP Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain R residue 434 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 285 CYS Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 43 MET Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain T residue 337 ASP Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 236 LEU Chi-restraints excluded: chain U residue 297 THR Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 58 TYR Chi-restraints excluded: chain V residue 169 LEU Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 212 optimal weight: 9.9990 chunk 567 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 370 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 630 optimal weight: 5.9990 chunk 523 optimal weight: 8.9990 chunk 292 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 331 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN I 178 GLN ** I 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 310 GLN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN M 408 GLN ** O 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 404 GLN ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 12 ASN ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 58153 Z= 0.188 Angle : 0.620 11.412 79831 Z= 0.320 Chirality : 0.042 0.178 8993 Planarity : 0.004 0.097 9191 Dihedral : 21.390 175.311 10392 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.59 % Rotamer: Outliers : 3.33 % Allowed : 16.98 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.05 % 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: -0.77 (0.11), residues: 6271 helix: 0.33 (0.10), residues: 2861 sheet: -0.84 (0.18), residues: 836 loop : -1.27 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP S 356 HIS 0.009 0.001 HIS M 316 PHE 0.040 0.001 PHE N 261 TYR 0.019 0.001 TYR K 17 ARG 0.010 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 404 time to evaluate : 4.515 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: D 53 GLU cc_start: 0.5373 (mp0) cc_final: 0.4924 (mp0) REVERT: D 93 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7348 (mm-40) REVERT: E 118 LYS cc_start: 0.5443 (tmmm) cc_final: 0.4650 (mttm) REVERT: F 80 TYR cc_start: 0.7147 (m-10) cc_final: 0.5286 (m-10) REVERT: I 627 ASP cc_start: 0.7315 (m-30) cc_final: 0.6845 (m-30) REVERT: I 684 MET cc_start: 0.8178 (mmm) cc_final: 0.7972 (mmp) REVERT: I 861 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7665 (mp) REVERT: J 274 PHE cc_start: 0.5704 (OUTLIER) cc_final: 0.5157 (t80) REVERT: K 1 MET cc_start: 0.5573 (tmm) cc_final: 0.4815 (tmm) REVERT: K 196 MET cc_start: 0.7240 (ppp) cc_final: 0.6263 (ptm) REVERT: K 199 THR cc_start: 0.7391 (OUTLIER) cc_final: 0.7000 (m) REVERT: K 279 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7583 (tp30) REVERT: L 36 GLU cc_start: 0.6428 (pp20) cc_final: 0.5987 (pp20) REVERT: M 182 LYS cc_start: 0.8866 (tppt) cc_final: 0.8506 (mtpt) REVERT: N 88 MET cc_start: 0.7659 (mmm) cc_final: 0.7350 (mmt) REVERT: N 258 LEU cc_start: 0.4805 (mt) cc_final: 0.4314 (mt) REVERT: N 320 MET cc_start: 0.8808 (mmt) cc_final: 0.8192 (mmt) REVERT: N 354 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8464 (pp) REVERT: N 442 TYR cc_start: 0.8547 (m-80) cc_final: 0.8307 (m-80) REVERT: O 100 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: O 371 MET cc_start: 0.8509 (ttp) cc_final: 0.8273 (ttp) REVERT: O 378 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8198 (tpt-90) REVERT: P 112 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: P 257 PHE cc_start: 0.6599 (OUTLIER) cc_final: 0.6132 (p90) REVERT: P 269 LYS cc_start: 0.8329 (tttm) cc_final: 0.7594 (tptp) REVERT: P 441 GLN cc_start: 0.8834 (tt0) cc_final: 0.8429 (tp40) REVERT: P 448 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6873 (m-30) REVERT: Q 168 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7255 (ttpt) REVERT: Q 172 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7485 (mt) REVERT: R 139 GLU cc_start: 0.7885 (pt0) cc_final: 0.7448 (pp20) REVERT: R 207 ARG cc_start: 0.6293 (ttm170) cc_final: 0.6019 (ttp-170) REVERT: R 269 LYS cc_start: 0.8050 (mptt) cc_final: 0.7391 (tmtt) REVERT: R 273 ARG cc_start: 0.6906 (mpt180) cc_final: 0.6676 (mpt180) REVERT: R 435 ASP cc_start: 0.7907 (t0) cc_final: 0.7686 (p0) REVERT: R 444 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7131 (mmmt) REVERT: S 1 MET cc_start: 0.0886 (mtt) cc_final: -0.0486 (tpt) REVERT: S 161 HIS cc_start: 0.3753 (OUTLIER) cc_final: 0.2993 (t-90) REVERT: S 227 MET cc_start: 0.2068 (mmm) cc_final: 0.1195 (mmp) REVERT: S 305 MET cc_start: 0.5128 (mmm) cc_final: 0.4701 (mmt) REVERT: T 109 MET cc_start: 0.1426 (tmm) cc_final: 0.0545 (tpt) REVERT: U 121 GLN cc_start: 0.5300 (tm-30) cc_final: 0.4955 (tm-30) REVERT: U 147 ARG cc_start: -0.0469 (OUTLIER) cc_final: -0.0888 (ptp90) REVERT: U 359 LYS cc_start: 0.4136 (OUTLIER) cc_final: 0.2824 (tttp) REVERT: V 169 LEU cc_start: 0.3786 (OUTLIER) cc_final: 0.3544 (tt) REVERT: V 255 GLU cc_start: 0.2940 (OUTLIER) cc_final: 0.2739 (mm-30) REVERT: V 261 ARG cc_start: 0.1606 (OUTLIER) cc_final: 0.0702 (ptp-170) REVERT: W 59 MET cc_start: -0.1088 (OUTLIER) cc_final: -0.1315 (tpp) REVERT: W 151 MET cc_start: 0.0486 (tpt) cc_final: -0.0207 (mmm) outliers start: 181 outliers final: 111 residues processed: 548 average time/residue: 0.5394 time to fit residues: 502.7385 Evaluate side-chains 511 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 379 time to evaluate : 4.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 776 THR Chi-restraints excluded: chain I residue 837 LEU Chi-restraints excluded: chain I residue 857 ILE Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 929 VAL Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 2034 ASP Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2120 SER Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 259 MET Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 332 ASN Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 225 VAL Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 44 ASN Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 362 ARG Chi-restraints excluded: chain O residue 378 ARG Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 434 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 147 ARG Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 169 LEU Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 608 optimal weight: 40.0000 chunk 71 optimal weight: 5.9990 chunk 359 optimal weight: 0.9980 chunk 460 optimal weight: 0.7980 chunk 356 optimal weight: 0.9990 chunk 531 optimal weight: 20.0000 chunk 352 optimal weight: 0.7980 chunk 628 optimal weight: 10.0000 chunk 393 optimal weight: 0.9990 chunk 383 optimal weight: 1.9990 chunk 290 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** I 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 865 GLN ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 58153 Z= 0.183 Angle : 0.599 9.983 79831 Z= 0.307 Chirality : 0.041 0.197 8993 Planarity : 0.004 0.096 9191 Dihedral : 21.178 174.422 10382 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.21 % Rotamer: Outliers : 3.12 % Allowed : 17.58 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.05 % 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: -0.55 (0.11), residues: 6271 helix: 0.52 (0.10), residues: 2860 sheet: -0.76 (0.18), residues: 832 loop : -1.16 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 356 HIS 0.009 0.001 HIS M 316 PHE 0.031 0.001 PHE P 257 TYR 0.042 0.001 TYR I 821 ARG 0.008 0.000 ARG Q 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 396 time to evaluate : 4.945 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: D 88 TYR cc_start: 0.6198 (m-10) cc_final: 0.5851 (m-10) REVERT: D 93 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7348 (mm-40) REVERT: E 118 LYS cc_start: 0.5428 (tmmm) cc_final: 0.4683 (mttm) REVERT: I 627 ASP cc_start: 0.7289 (m-30) cc_final: 0.6844 (m-30) REVERT: I 861 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7528 (mp) REVERT: I 930 LEU cc_start: 0.8384 (mp) cc_final: 0.8165 (mp) REVERT: J 274 PHE cc_start: 0.5576 (OUTLIER) cc_final: 0.4995 (t80) REVERT: K 199 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.7003 (m) REVERT: K 255 MET cc_start: 0.5319 (mtp) cc_final: 0.4950 (ptp) REVERT: K 279 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: L 36 GLU cc_start: 0.6664 (pp20) cc_final: 0.6342 (pp20) REVERT: L 92 ASN cc_start: 0.6359 (OUTLIER) cc_final: 0.5949 (m110) REVERT: M 178 GLU cc_start: 0.7189 (mp0) cc_final: 0.6936 (mp0) REVERT: M 182 LYS cc_start: 0.8827 (tppt) cc_final: 0.8486 (mtpt) REVERT: M 293 GLU cc_start: 0.8156 (tp30) cc_final: 0.7647 (tm-30) REVERT: N 88 MET cc_start: 0.7681 (mmm) cc_final: 0.7315 (mmt) REVERT: N 168 MET cc_start: 0.8894 (ptp) cc_final: 0.8600 (ptp) REVERT: N 258 LEU cc_start: 0.4359 (mt) cc_final: 0.4077 (mt) REVERT: N 320 MET cc_start: 0.8831 (mmt) cc_final: 0.8138 (mmt) REVERT: N 354 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8468 (pp) REVERT: N 395 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8426 (mm) REVERT: N 442 TYR cc_start: 0.8582 (m-80) cc_final: 0.8351 (m-80) REVERT: O 18 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.6276 (t-170) REVERT: O 44 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7599 (p0) REVERT: O 378 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7878 (tpt-90) REVERT: P 257 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6285 (p90) REVERT: P 269 LYS cc_start: 0.8285 (tttm) cc_final: 0.7560 (tptp) REVERT: P 441 GLN cc_start: 0.8852 (tt0) cc_final: 0.8472 (tp40) REVERT: P 448 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6979 (m-30) REVERT: Q 168 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7242 (tttt) REVERT: Q 172 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7785 (mt) REVERT: R 139 GLU cc_start: 0.7912 (pt0) cc_final: 0.7410 (pp20) REVERT: R 207 ARG cc_start: 0.6289 (ttm170) cc_final: 0.5959 (ttp-170) REVERT: R 258 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6417 (tp) REVERT: R 269 LYS cc_start: 0.7859 (mptt) cc_final: 0.7305 (tmtt) REVERT: R 273 ARG cc_start: 0.6969 (mpt180) cc_final: 0.6739 (mpt90) REVERT: R 435 ASP cc_start: 0.7878 (t0) cc_final: 0.7606 (p0) REVERT: R 444 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7244 (mmmt) REVERT: S 1 MET cc_start: 0.0850 (mtt) cc_final: -0.0538 (tpt) REVERT: S 161 HIS cc_start: 0.3607 (OUTLIER) cc_final: 0.2893 (t-90) REVERT: S 227 MET cc_start: 0.1955 (mmm) cc_final: 0.1678 (mmp) REVERT: S 305 MET cc_start: 0.5171 (mmm) cc_final: 0.4318 (mmt) REVERT: T 109 MET cc_start: 0.1325 (tmm) cc_final: 0.0322 (tpt) REVERT: U 121 GLN cc_start: 0.5500 (tm-30) cc_final: 0.5152 (tm-30) REVERT: U 132 MET cc_start: 0.0246 (tmm) cc_final: -0.0269 (tpt) REVERT: U 292 ASP cc_start: 0.2924 (OUTLIER) cc_final: 0.2532 (m-30) REVERT: U 359 LYS cc_start: 0.4012 (OUTLIER) cc_final: 0.2718 (tttt) REVERT: V 261 ARG cc_start: 0.1846 (OUTLIER) cc_final: 0.0935 (ptp-170) REVERT: W 151 MET cc_start: 0.0423 (tpt) cc_final: -0.0270 (mmm) outliers start: 170 outliers final: 116 residues processed: 528 average time/residue: 0.5296 time to fit residues: 476.3776 Evaluate side-chains 510 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 373 time to evaluate : 4.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 776 THR Chi-restraints excluded: chain I residue 837 LEU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 929 VAL Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 2034 ASP Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2075 LEU Chi-restraints excluded: chain I residue 2120 SER Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 259 MET Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 332 ASN Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 225 VAL Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 44 ASN Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 306 MET Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 362 ARG Chi-restraints excluded: chain O residue 378 ARG Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 434 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 292 ASP Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 388 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 375 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 399 optimal weight: 3.9990 chunk 428 optimal weight: 0.6980 chunk 310 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 493 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 800 HIS ** I 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 387 HIS M 332 ASN ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 58153 Z= 0.246 Angle : 0.624 14.325 79831 Z= 0.319 Chirality : 0.042 0.210 8993 Planarity : 0.004 0.104 9191 Dihedral : 21.095 166.924 10377 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.25 % Favored : 93.67 % Rotamer: Outliers : 3.36 % Allowed : 17.55 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.05 % 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: -0.52 (0.11), residues: 6271 helix: 0.53 (0.10), residues: 2863 sheet: -0.73 (0.18), residues: 847 loop : -1.14 (0.12), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 628 HIS 0.013 0.001 HIS I 800 PHE 0.029 0.001 PHE P 257 TYR 0.034 0.001 TYR I 821 ARG 0.012 0.000 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 382 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7336 (mm-40) REVERT: E 118 LYS cc_start: 0.5438 (tmmm) cc_final: 0.4702 (mttm) REVERT: F 80 TYR cc_start: 0.6814 (m-10) cc_final: 0.6558 (m-80) REVERT: I 627 ASP cc_start: 0.7204 (m-30) cc_final: 0.6812 (m-30) REVERT: I 861 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7693 (mp) REVERT: I 930 LEU cc_start: 0.8503 (mp) cc_final: 0.8286 (mp) REVERT: I 2144 MET cc_start: 0.6937 (mmm) cc_final: 0.6628 (mmm) REVERT: J 274 PHE cc_start: 0.5547 (OUTLIER) cc_final: 0.5007 (t80) REVERT: K 1 MET cc_start: 0.4968 (tmm) cc_final: 0.4088 (tmm) REVERT: K 196 MET cc_start: 0.7474 (ppp) cc_final: 0.6454 (ptm) REVERT: K 199 THR cc_start: 0.7752 (OUTLIER) cc_final: 0.7358 (m) REVERT: K 279 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: L 36 GLU cc_start: 0.6661 (pp20) cc_final: 0.6372 (pp20) REVERT: M 178 GLU cc_start: 0.7205 (mp0) cc_final: 0.6971 (mp0) REVERT: M 182 LYS cc_start: 0.8825 (tppt) cc_final: 0.8508 (mtpt) REVERT: N 88 MET cc_start: 0.7690 (mmm) cc_final: 0.7357 (mmt) REVERT: N 320 MET cc_start: 0.8860 (mmt) cc_final: 0.8183 (mmt) REVERT: N 354 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8374 (pp) REVERT: N 442 TYR cc_start: 0.8598 (m-80) cc_final: 0.8175 (m-80) REVERT: O 100 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: O 113 MET cc_start: 0.7637 (tpt) cc_final: 0.7421 (tpp) REVERT: O 378 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8002 (tpt-90) REVERT: P 255 GLN cc_start: 0.5853 (OUTLIER) cc_final: 0.5539 (mt0) REVERT: P 257 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.6376 (p90) REVERT: P 269 LYS cc_start: 0.8065 (tttm) cc_final: 0.7315 (tptp) REVERT: P 441 GLN cc_start: 0.8867 (tt0) cc_final: 0.8468 (tp40) REVERT: P 448 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7092 (m-30) REVERT: Q 168 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7379 (tttt) REVERT: Q 172 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7580 (mt) REVERT: Q 428 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: R 269 LYS cc_start: 0.7915 (mptt) cc_final: 0.7331 (tmtt) REVERT: R 273 ARG cc_start: 0.7040 (mpt180) cc_final: 0.6818 (mpt90) REVERT: R 358 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8552 (t) REVERT: R 435 ASP cc_start: 0.7907 (t0) cc_final: 0.7624 (p0) REVERT: R 444 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7501 (ptpp) REVERT: S 1 MET cc_start: 0.0527 (mtt) cc_final: -0.0674 (tpt) REVERT: S 161 HIS cc_start: 0.3652 (OUTLIER) cc_final: 0.2943 (t-90) REVERT: S 227 MET cc_start: 0.1880 (mmm) cc_final: 0.1410 (mmp) REVERT: S 305 MET cc_start: 0.4990 (mmm) cc_final: 0.4317 (mmt) REVERT: U 121 GLN cc_start: 0.5527 (tm-30) cc_final: 0.5202 (tm-30) REVERT: U 132 MET cc_start: 0.0137 (tmm) cc_final: -0.0379 (tpt) REVERT: U 147 ARG cc_start: -0.0817 (OUTLIER) cc_final: -0.1369 (ptp90) REVERT: U 292 ASP cc_start: 0.3484 (OUTLIER) cc_final: 0.2622 (m-30) REVERT: U 359 LYS cc_start: 0.3917 (OUTLIER) cc_final: 0.2694 (tttt) REVERT: V 261 ARG cc_start: 0.1891 (OUTLIER) cc_final: 0.0870 (ptp-170) REVERT: W 151 MET cc_start: 0.0435 (tpt) cc_final: -0.0210 (mmm) outliers start: 183 outliers final: 133 residues processed: 529 average time/residue: 0.5673 time to fit residues: 513.5120 Evaluate side-chains 528 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 374 time to evaluate : 4.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 660 LEU Chi-restraints excluded: chain I residue 713 THR Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 776 THR Chi-restraints excluded: chain I residue 837 LEU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 929 VAL Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 2034 ASP Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2075 LEU Chi-restraints excluded: chain I residue 2120 SER Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 259 MET Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 332 ASN Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 225 VAL Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 306 MET Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 378 ARG Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain P residue 254 THR Chi-restraints excluded: chain P residue 255 GLN Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 323 ILE Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 428 GLU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 434 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 147 ARG Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 292 ASP Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 571 optimal weight: 10.0000 chunk 602 optimal weight: 8.9990 chunk 549 optimal weight: 5.9990 chunk 585 optimal weight: 4.9990 chunk 601 optimal weight: 10.0000 chunk 352 optimal weight: 0.9990 chunk 255 optimal weight: 4.9990 chunk 459 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 chunk 529 optimal weight: 0.0040 chunk 553 optimal weight: 20.0000 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 58153 Z= 0.228 Angle : 0.613 9.979 79831 Z= 0.314 Chirality : 0.042 0.273 8993 Planarity : 0.004 0.108 9191 Dihedral : 21.006 166.865 10373 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.06 % Favored : 93.86 % Rotamer: Outliers : 3.14 % Allowed : 17.97 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.07 % 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: -0.49 (0.11), residues: 6271 helix: 0.54 (0.10), residues: 2867 sheet: -0.71 (0.18), residues: 844 loop : -1.11 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 628 HIS 0.010 0.001 HIS M 316 PHE 0.028 0.001 PHE P 257 TYR 0.034 0.001 TYR I 821 ARG 0.008 0.000 ARG I 615 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 382 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7330 (mm-40) REVERT: E 118 LYS cc_start: 0.5441 (tmmm) cc_final: 0.4710 (mttm) REVERT: F 37 TYR cc_start: 0.7597 (m-80) cc_final: 0.7270 (m-80) REVERT: I 684 MET cc_start: 0.8376 (mmp) cc_final: 0.8085 (mmp) REVERT: I 861 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7759 (mp) REVERT: I 930 LEU cc_start: 0.8497 (mp) cc_final: 0.8257 (mp) REVERT: I 2144 MET cc_start: 0.6952 (mmm) cc_final: 0.6441 (mmm) REVERT: J 274 PHE cc_start: 0.5578 (OUTLIER) cc_final: 0.5019 (t80) REVERT: K 1 MET cc_start: 0.5306 (tmm) cc_final: 0.4383 (tmm) REVERT: K 196 MET cc_start: 0.7472 (ppp) cc_final: 0.6443 (ptm) REVERT: K 199 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7383 (m) REVERT: K 279 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7652 (tp30) REVERT: L 36 GLU cc_start: 0.6684 (pp20) cc_final: 0.6434 (pp20) REVERT: M 178 GLU cc_start: 0.7206 (mp0) cc_final: 0.6974 (mp0) REVERT: M 182 LYS cc_start: 0.8821 (tppt) cc_final: 0.8500 (mtpt) REVERT: M 293 GLU cc_start: 0.8096 (tp30) cc_final: 0.7597 (tm-30) REVERT: N 88 MET cc_start: 0.7637 (mmm) cc_final: 0.7208 (mmt) REVERT: N 168 MET cc_start: 0.8881 (ptp) cc_final: 0.8625 (ptp) REVERT: N 320 MET cc_start: 0.8879 (mmt) cc_final: 0.8141 (mmt) REVERT: N 326 MET cc_start: 0.7669 (mtp) cc_final: 0.7455 (mtt) REVERT: N 354 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8466 (pp) REVERT: N 395 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8493 (mm) REVERT: N 411 LEU cc_start: 0.8234 (mt) cc_final: 0.7937 (mt) REVERT: N 442 TYR cc_start: 0.8607 (m-80) cc_final: 0.8397 (m-80) REVERT: O 100 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: O 113 MET cc_start: 0.7693 (tpt) cc_final: 0.7470 (tpp) REVERT: O 378 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7948 (tpt-90) REVERT: P 255 GLN cc_start: 0.5770 (OUTLIER) cc_final: 0.5413 (mt0) REVERT: P 269 LYS cc_start: 0.8109 (tttm) cc_final: 0.7139 (tptp) REVERT: P 441 GLN cc_start: 0.8865 (tt0) cc_final: 0.8464 (tp40) REVERT: P 448 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: Q 168 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7410 (tttt) REVERT: Q 172 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7591 (mt) REVERT: R 269 LYS cc_start: 0.7908 (mptt) cc_final: 0.7316 (tmtt) REVERT: R 273 ARG cc_start: 0.7027 (mpt180) cc_final: 0.6798 (mpt90) REVERT: R 358 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8529 (t) REVERT: R 435 ASP cc_start: 0.7898 (t0) cc_final: 0.7623 (p0) REVERT: R 444 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7479 (ptpp) REVERT: S 1 MET cc_start: 0.0562 (mtt) cc_final: -0.0640 (tpt) REVERT: S 119 MET cc_start: 0.4382 (mpp) cc_final: 0.3555 (mpp) REVERT: S 161 HIS cc_start: 0.3661 (OUTLIER) cc_final: 0.2959 (t-90) REVERT: S 227 MET cc_start: 0.1940 (mmm) cc_final: 0.1522 (mmp) REVERT: S 305 MET cc_start: 0.5005 (mmm) cc_final: 0.4360 (mmt) REVERT: U 121 GLN cc_start: 0.5752 (tm-30) cc_final: 0.5430 (tm-30) REVERT: U 132 MET cc_start: 0.0118 (tmm) cc_final: -0.0394 (tpt) REVERT: U 292 ASP cc_start: 0.3473 (OUTLIER) cc_final: 0.2609 (m-30) REVERT: U 359 LYS cc_start: 0.3890 (OUTLIER) cc_final: 0.2682 (tttt) REVERT: V 261 ARG cc_start: 0.1538 (OUTLIER) cc_final: 0.0686 (ptp-170) REVERT: W 151 MET cc_start: 0.0591 (tpt) cc_final: -0.0046 (mmm) outliers start: 171 outliers final: 129 residues processed: 516 average time/residue: 0.5243 time to fit residues: 471.8922 Evaluate side-chains 514 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 366 time to evaluate : 4.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 660 LEU Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 776 THR Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 929 VAL Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 2034 ASP Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2075 LEU Chi-restraints excluded: chain I residue 2120 SER Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 141 CYS Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 259 MET Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 332 ASN Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 225 VAL Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 306 MET Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 378 ARG Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain P residue 255 GLN Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 434 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 292 ASP Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 583 optimal weight: 7.9990 chunk 384 optimal weight: 0.9980 chunk 619 optimal weight: 8.9990 chunk 377 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 430 optimal weight: 0.7980 chunk 649 optimal weight: 10.0000 chunk 597 optimal weight: 4.9990 chunk 517 optimal weight: 0.0170 chunk 53 optimal weight: 9.9990 chunk 399 optimal weight: 1.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 HIS ** I 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN ** O 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.6280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 58153 Z= 0.189 Angle : 0.606 15.070 79831 Z= 0.309 Chirality : 0.041 0.237 8993 Planarity : 0.004 0.108 9191 Dihedral : 20.889 167.412 10373 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 2.85 % Allowed : 18.08 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.07 % 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: -0.41 (0.11), residues: 6271 helix: 0.62 (0.10), residues: 2858 sheet: -0.66 (0.18), residues: 837 loop : -1.07 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 628 HIS 0.010 0.001 HIS M 316 PHE 0.021 0.001 PHE R 257 TYR 0.035 0.001 TYR I 821 ARG 0.008 0.000 ARG F 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 387 time to evaluate : 5.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 118 LYS cc_start: 0.5297 (tmmm) cc_final: 0.4543 (mttm) REVERT: F 37 TYR cc_start: 0.7522 (m-80) cc_final: 0.7225 (m-80) REVERT: I 861 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7753 (mp) REVERT: I 930 LEU cc_start: 0.8456 (mp) cc_final: 0.8209 (mp) REVERT: I 2144 MET cc_start: 0.6998 (mmm) cc_final: 0.6610 (mmm) REVERT: J 274 PHE cc_start: 0.5559 (OUTLIER) cc_final: 0.4995 (t80) REVERT: K 1 MET cc_start: 0.5252 (tmm) cc_final: 0.4448 (tmm) REVERT: K 196 MET cc_start: 0.7711 (ppp) cc_final: 0.6388 (ptm) REVERT: K 199 THR cc_start: 0.7231 (OUTLIER) cc_final: 0.6818 (m) REVERT: K 279 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: L 36 GLU cc_start: 0.6694 (pp20) cc_final: 0.6445 (pp20) REVERT: M 178 GLU cc_start: 0.7294 (mp0) cc_final: 0.7048 (mp0) REVERT: M 182 LYS cc_start: 0.8809 (tppt) cc_final: 0.8486 (mtpt) REVERT: M 293 GLU cc_start: 0.8037 (tp30) cc_final: 0.7611 (tm-30) REVERT: M 308 ASP cc_start: 0.7109 (t0) cc_final: 0.6660 (t70) REVERT: N 88 MET cc_start: 0.7598 (mmm) cc_final: 0.7202 (mmt) REVERT: N 320 MET cc_start: 0.8885 (mmt) cc_final: 0.8169 (mmt) REVERT: N 326 MET cc_start: 0.7631 (mtp) cc_final: 0.7373 (mtm) REVERT: N 354 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8411 (pp) REVERT: N 395 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8452 (mm) REVERT: N 411 LEU cc_start: 0.8245 (mt) cc_final: 0.7959 (mt) REVERT: N 442 TYR cc_start: 0.8572 (m-80) cc_final: 0.8333 (m-80) REVERT: O 61 MET cc_start: 0.7976 (mmm) cc_final: 0.7764 (mmm) REVERT: O 113 MET cc_start: 0.7681 (tpt) cc_final: 0.7458 (tpp) REVERT: O 378 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7872 (tpt-90) REVERT: P 255 GLN cc_start: 0.5553 (OUTLIER) cc_final: 0.5248 (mt0) REVERT: P 269 LYS cc_start: 0.8118 (tttm) cc_final: 0.7276 (tptp) REVERT: P 441 GLN cc_start: 0.8867 (tt0) cc_final: 0.8458 (tp40) REVERT: P 448 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7097 (m-30) REVERT: Q 172 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7607 (mt) REVERT: Q 428 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: R 269 LYS cc_start: 0.7904 (mptt) cc_final: 0.7298 (tmtt) REVERT: R 273 ARG cc_start: 0.6988 (mpt180) cc_final: 0.6766 (mpt90) REVERT: R 358 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8484 (t) REVERT: R 435 ASP cc_start: 0.7882 (t0) cc_final: 0.7631 (p0) REVERT: R 444 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7245 (mmmt) REVERT: S 1 MET cc_start: 0.0551 (mtt) cc_final: -0.0757 (tpt) REVERT: S 119 MET cc_start: 0.4422 (mpp) cc_final: 0.3834 (mpp) REVERT: S 161 HIS cc_start: 0.3551 (OUTLIER) cc_final: 0.2878 (t-90) REVERT: S 227 MET cc_start: 0.1757 (mmm) cc_final: 0.1485 (mmp) REVERT: S 305 MET cc_start: 0.5090 (mmm) cc_final: 0.4207 (mmt) REVERT: U 121 GLN cc_start: 0.5753 (tm-30) cc_final: 0.5451 (tm-30) REVERT: U 132 MET cc_start: 0.0104 (tmm) cc_final: -0.0359 (tpt) REVERT: U 292 ASP cc_start: 0.3181 (OUTLIER) cc_final: 0.2657 (m-30) REVERT: U 355 MET cc_start: -0.0037 (mtm) cc_final: -0.0950 (mtt) REVERT: U 359 LYS cc_start: 0.3441 (OUTLIER) cc_final: 0.2280 (tttt) REVERT: W 151 MET cc_start: 0.0470 (tpt) cc_final: -0.0189 (mmm) outliers start: 155 outliers final: 128 residues processed: 509 average time/residue: 0.5165 time to fit residues: 450.3267 Evaluate side-chains 514 residues out of total 5462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 370 time to evaluate : 4.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 660 LEU Chi-restraints excluded: chain I residue 776 THR Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 929 VAL Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 2034 ASP Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2075 LEU Chi-restraints excluded: chain I residue 2120 SER Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 141 CYS Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 259 MET Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 332 ASN Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 225 VAL Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 306 MET Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 378 ARG Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain P residue 255 GLN Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 428 GLU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 413 CYS Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 434 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 292 ASP Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 317 optimal weight: 0.0980 chunk 410 optimal weight: 1.9990 chunk 550 optimal weight: 7.9990 chunk 158 optimal weight: 0.0370 chunk 476 optimal weight: 0.0770 chunk 76 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 518 optimal weight: 9.9990 chunk 216 optimal weight: 0.0000 chunk 531 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 830 HIS ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 373 GLN P 49 GLN ** P 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.131719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.088857 restraints weight = 150371.210| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.19 r_work: 0.3235 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 58153 Z= 0.151 Angle : 0.590 12.592 79831 Z= 0.301 Chirality : 0.040 0.229 8993 Planarity : 0.004 0.106 9191 Dihedral : 20.718 168.851 10368 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.57 % Favored : 94.35 % Rotamer: Outliers : 2.17 % Allowed : 18.87 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 6271 helix: 0.72 (0.10), residues: 2861 sheet: -0.59 (0.18), residues: 833 loop : -1.00 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 628 HIS 0.010 0.001 HIS T 105 PHE 0.025 0.001 PHE R 257 TYR 0.035 0.001 TYR I 821 ARG 0.011 0.000 ARG M 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12168.91 seconds wall clock time: 214 minutes 24.95 seconds (12864.95 seconds total)