Starting phenix.real_space_refine on Tue Feb 13 19:42:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/02_2024/8ea3_27971_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/02_2024/8ea3_27971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/02_2024/8ea3_27971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/02_2024/8ea3_27971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/02_2024/8ea3_27971_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/02_2024/8ea3_27971_updated.pdb" } resolution = 3.7 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= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 529 5.49 5 Mg 14 5.21 5 S 170 5.16 5 C 33408 2.51 5 N 10159 2.21 5 O 11675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G GLU 238": "OE1" <-> "OE2" Residue "H GLU 19": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "H ASP 264": "OD1" <-> "OD2" Residue "H GLU 270": "OE1" <-> "OE2" Residue "I ASP 144": "OD1" <-> "OD2" Residue "I GLU 250": "OE1" <-> "OE2" Residue "J TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 250": "OE1" <-> "OE2" Residue "O TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 130": "OE1" <-> "OE2" Residue "O TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 230": "OE1" <-> "OE2" Residue "O PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 289": "OE1" <-> "OE2" Residue "O PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 384": "OE1" <-> "OE2" Residue "O PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 525": "NH1" <-> "NH2" Residue "O TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 572": "OE1" <-> "OE2" Residue "O TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 77": "OD1" <-> "OD2" Residue "Q GLU 113": "OE1" <-> "OE2" Residue "Q PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 26": "OE1" <-> "OE2" Residue "S TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 30": "OE1" <-> "OE2" Residue "W ASP 57": "OD1" <-> "OD2" Residue "W TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 360": "OE1" <-> "OE2" Residue "W ARG 367": "NH1" <-> "NH2" Residue "W TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 416": "NH1" <-> "NH2" Residue "W PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 30": "OE1" <-> "OE2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X ASP 57": "OD1" <-> "OD2" Residue "X PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 235": "NH1" <-> "NH2" Residue "X TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 362": "OE1" <-> "OE2" Residue "X TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 462": "OE1" <-> "OE2" Residue "X GLU 480": "OE1" <-> "OE2" Residue "X GLU 525": "OE1" <-> "OE2" Residue "X ARG 526": "NH1" <-> "NH2" Residue "Y TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ARG 380": "NH1" <-> "NH2" Residue "Y TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 478": "OE1" <-> "OE2" Residue "Y ARG 523": "NH1" <-> "NH2" Residue "Z TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 55955 Number of models: 1 Model: "" Number of chains: 44 Chain: "1" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2031 Classifications: {'DNA': 99} Link IDs: {'rna3p': 98} Chain: "3" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1022 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "7" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 4896 Classifications: {'RNA': 230} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 24, 'rna3p_pur': 97, 'rna3p_pyr': 89} Link IDs: {'rna2p': 43, 'rna3p': 186} Chain breaks: 2 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "K" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "L" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "O" Number of atoms: 4865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4865 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 582} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Q" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1306 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 13, 'TRANS': 150} Chain: "S" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "w" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "x" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "y" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "z" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "W" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4122 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 19, 'TRANS': 494} Chain: "X" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4068 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 19, 'TRANS': 487} Chain breaks: 1 Chain: "Y" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2453 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 11, 'TRANS': 292} Chain breaks: 3 Chain: "Z" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2426 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 289} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "2" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 593 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "4" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 941 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "5" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 573 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "6" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.82, per 1000 atoms: 0.37 Number of scatterers: 55955 At special positions: 0 Unit cell: (144.045, 146.179, 314.765, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 170 16.00 P 529 15.00 Mg 14 11.99 O 11675 8.00 N 10159 7.00 C 33408 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 54776 O5' DT 5 3 .*. O " rejected from bonding due to valence issues. Atom "ATOM 1473 O4' DC 1 42 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.59 Conformation dependent library (CDL) restraints added in 6.6 seconds 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 264 helices and 26 sheets defined 50.7% alpha, 9.1% beta 181 base pairs and 326 stacking pairs defined. Time for finding SS restraints: 18.79 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 37 through 51 removed outlier: 3.510A pdb=" N LYS A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.570A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.759A pdb=" N PHE A 154 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.176A pdb=" N ARG A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.727A pdb=" N ARG A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.851A pdb=" N GLU A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.915A pdb=" N GLU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 28 Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 66 through 74 Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.609A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.779A pdb=" N PHE B 154 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE B 160 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP B 163 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 184 through 187 No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 201 through 214 removed outlier: 3.993A pdb=" N GLU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.978A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 258 removed outlier: 3.654A pdb=" N ARG B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 removed outlier: 4.001A pdb=" N GLU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 removed outlier: 3.514A pdb=" N GLU C 24 " --> pdb=" O TRP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 66 through 75 Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.875A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.761A pdb=" N PHE C 154 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 160 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.219A pdb=" N ARG C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.954A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 214 removed outlier: 3.632A pdb=" N GLU C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 241 through 258 removed outlier: 4.053A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 274 removed outlier: 3.811A pdb=" N GLU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 28 Processing helix chain 'D' and resid 37 through 52 removed outlier: 4.111A pdb=" N LEU D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 75 Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 151 through 163 removed outlier: 3.594A pdb=" N PHE D 154 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP D 163 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 3.577A pdb=" N ALA D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 187 No H-bonds generated for 'chain 'D' and resid 184 through 187' Processing helix chain 'D' and resid 201 through 214 removed outlier: 3.692A pdb=" N GLU D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 removed outlier: 4.357A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 258 removed outlier: 3.768A pdb=" N GLU D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 274 removed outlier: 3.792A pdb=" N GLU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 29 removed outlier: 3.526A pdb=" N GLU E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 removed outlier: 3.833A pdb=" N GLY E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 76 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 151 through 163 removed outlier: 3.759A pdb=" N PHE E 154 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP E 163 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.196A pdb=" N ARG E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 removed outlier: 3.958A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 214 removed outlier: 3.544A pdb=" N GLU E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 237 removed outlier: 3.802A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 258 Processing helix chain 'E' and resid 265 through 274 removed outlier: 4.139A pdb=" N GLU E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 28 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'F' and resid 66 through 76 removed outlier: 3.835A pdb=" N ARG F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.872A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.759A pdb=" N PHE F 154 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG F 158 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE F 160 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.318A pdb=" N ARG F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.622A pdb=" N GLU F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 184 through 189' Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.764A pdb=" N GLU F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 removed outlier: 4.357A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 258 removed outlier: 3.697A pdb=" N ARG F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 274 removed outlier: 4.208A pdb=" N GLU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 37 through 52 removed outlier: 3.572A pdb=" N GLY G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.744A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 151 through 163 removed outlier: 3.800A pdb=" N PHE G 154 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE G 160 " --> pdb=" O VAL G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 182 removed outlier: 4.194A pdb=" N ARG G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 187 No H-bonds generated for 'chain 'G' and resid 184 through 187' Processing helix chain 'G' and resid 201 through 214 removed outlier: 3.526A pdb=" N LYS G 205 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN G 206 " --> pdb=" O ASP G 203 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU G 212 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN G 213 " --> pdb=" O MET G 210 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET G 214 " --> pdb=" O TRP G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 237 removed outlier: 3.550A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 258 removed outlier: 3.801A pdb=" N ARG G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 274 removed outlier: 4.216A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 28 Processing helix chain 'H' and resid 37 through 51 Processing helix chain 'H' and resid 66 through 76 removed outlier: 3.555A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 151 through 163 removed outlier: 3.759A pdb=" N PHE H 154 " --> pdb=" O PRO H 151 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG H 158 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP H 163 " --> pdb=" O ILE H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 182 removed outlier: 4.230A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 removed outlier: 3.883A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 214 removed outlier: 3.664A pdb=" N GLU H 209 " --> pdb=" O LYS H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 237 removed outlier: 3.707A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 258 removed outlier: 3.561A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.893A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 29 removed outlier: 3.508A pdb=" N GLU I 24 " --> pdb=" O TRP I 20 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS I 29 " --> pdb=" O ILE I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 52 removed outlier: 3.611A pdb=" N LYS I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 76 removed outlier: 3.778A pdb=" N ARG I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 112 removed outlier: 3.602A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 151 through 163 removed outlier: 3.548A pdb=" N PHE I 154 " --> pdb=" O PRO I 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA I 155 " --> pdb=" O GLU I 152 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP I 159 " --> pdb=" O ASP I 156 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP I 163 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 4.021A pdb=" N ARG I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 removed outlier: 3.555A pdb=" N GLU I 188 " --> pdb=" O GLU I 184 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 184 through 189' Processing helix chain 'I' and resid 201 through 214 Processing helix chain 'I' and resid 227 through 237 Processing helix chain 'I' and resid 241 through 258 removed outlier: 3.786A pdb=" N GLU I 246 " --> pdb=" O GLY I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 274 removed outlier: 3.758A pdb=" N GLU I 270 " --> pdb=" O ALA I 266 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU I 274 " --> pdb=" O GLU I 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 29 removed outlier: 3.630A pdb=" N GLU J 24 " --> pdb=" O TRP J 20 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE J 25 " --> pdb=" O LEU J 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 26 " --> pdb=" O GLN J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 52 removed outlier: 3.693A pdb=" N GLY J 48 " --> pdb=" O ASP J 44 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 75 Processing helix chain 'J' and resid 102 through 112 removed outlier: 3.612A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 135 removed outlier: 3.658A pdb=" N ASP J 127 " --> pdb=" O SER J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 151 through 163 removed outlier: 3.786A pdb=" N PHE J 154 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG J 158 " --> pdb=" O ALA J 155 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP J 159 " --> pdb=" O ASP J 156 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU J 162 " --> pdb=" O ASP J 159 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP J 163 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 3.571A pdb=" N ALA J 178 " --> pdb=" O ASP J 174 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 removed outlier: 3.571A pdb=" N GLU J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 184 through 189' Processing helix chain 'J' and resid 201 through 214 removed outlier: 3.501A pdb=" N LYS J 205 " --> pdb=" O GLY J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 237 removed outlier: 4.004A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 257 Processing helix chain 'J' and resid 265 through 274 removed outlier: 4.398A pdb=" N GLU J 274 " --> pdb=" O GLU J 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 29 removed outlier: 3.699A pdb=" N GLU K 24 " --> pdb=" O TRP K 20 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA K 26 " --> pdb=" O GLN K 22 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU K 28 " --> pdb=" O GLU K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 52 Processing helix chain 'K' and resid 66 through 76 removed outlier: 3.857A pdb=" N ARG K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 112 Processing helix chain 'K' and resid 122 through 133 Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 154 through 163 Processing helix chain 'K' and resid 174 through 182 removed outlier: 4.109A pdb=" N ARG K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 189 removed outlier: 3.553A pdb=" N GLU K 188 " --> pdb=" O GLU K 184 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 189' Processing helix chain 'K' and resid 201 through 214 Processing helix chain 'K' and resid 227 through 237 removed outlier: 3.695A pdb=" N ILE K 232 " --> pdb=" O GLU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 257 Processing helix chain 'K' and resid 265 through 274 removed outlier: 3.632A pdb=" N GLU K 274 " --> pdb=" O GLU K 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 29 removed outlier: 3.521A pdb=" N ALA L 26 " --> pdb=" O GLN L 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 52 removed outlier: 4.029A pdb=" N GLY L 48 " --> pdb=" O ASP L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 76 Processing helix chain 'L' and resid 102 through 112 Processing helix chain 'L' and resid 122 through 133 Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 151 through 163 removed outlier: 3.784A pdb=" N PHE L 154 " --> pdb=" O PRO L 151 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG L 158 " --> pdb=" O ALA L 155 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE L 160 " --> pdb=" O VAL L 157 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP L 163 " --> pdb=" O ILE L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 182 removed outlier: 4.057A pdb=" N ARG L 182 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 removed outlier: 3.764A pdb=" N ARG L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 214 Processing helix chain 'L' and resid 227 through 237 removed outlier: 3.721A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 258 Processing helix chain 'L' and resid 265 through 274 removed outlier: 4.094A pdb=" N GLU L 274 " --> pdb=" O GLU L 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 39 removed outlier: 3.885A pdb=" N THR O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Proline residue: O 30 - end of helix removed outlier: 3.912A pdb=" N LEU O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 51 Processing helix chain 'O' and resid 58 through 66 Proline residue: O 65 - end of helix Processing helix chain 'O' and resid 77 through 114 removed outlier: 3.906A pdb=" N ALA O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG O 100 " --> pdb=" O ALA O 96 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TRP O 111 " --> pdb=" O GLY O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 125 Processing helix chain 'O' and resid 129 through 143 Processing helix chain 'O' and resid 174 through 183 Processing helix chain 'O' and resid 190 through 199 removed outlier: 3.724A pdb=" N LYS O 199 " --> pdb=" O TYR O 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 232 Processing helix chain 'O' and resid 245 through 256 Processing helix chain 'O' and resid 262 through 272 Processing helix chain 'O' and resid 288 through 290 No H-bonds generated for 'chain 'O' and resid 288 through 290' Processing helix chain 'O' and resid 322 through 338 removed outlier: 3.580A pdb=" N LEU O 329 " --> pdb=" O PHE O 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 344 through 346 No H-bonds generated for 'chain 'O' and resid 344 through 346' Processing helix chain 'O' and resid 365 through 368 No H-bonds generated for 'chain 'O' and resid 365 through 368' Processing helix chain 'O' and resid 379 through 381 No H-bonds generated for 'chain 'O' and resid 379 through 381' Processing helix chain 'O' and resid 384 through 405 removed outlier: 3.670A pdb=" N ILE O 389 " --> pdb=" O GLU O 385 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 430 removed outlier: 4.074A pdb=" N ALA O 417 " --> pdb=" O ASP O 413 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN O 430 " --> pdb=" O LEU O 426 " (cutoff:3.500A) Processing helix chain 'O' and resid 477 through 480 No H-bonds generated for 'chain 'O' and resid 477 through 480' Processing helix chain 'O' and resid 482 through 508 removed outlier: 4.752A pdb=" N GLU O 486 " --> pdb=" O ASP O 483 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN O 495 " --> pdb=" O ARG O 492 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU O 498 " --> pdb=" O GLN O 495 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER O 499 " --> pdb=" O GLN O 496 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS O 507 " --> pdb=" O LYS O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 517 through 537 Processing helix chain 'O' and resid 551 through 565 removed outlier: 4.033A pdb=" N GLN O 565 " --> pdb=" O ALA O 561 " (cutoff:3.500A) Processing helix chain 'O' and resid 571 through 575 Processing helix chain 'O' and resid 579 through 586 Processing helix chain 'O' and resid 590 through 604 Processing helix chain 'O' and resid 619 through 634 removed outlier: 3.839A pdb=" N ARG O 634 " --> pdb=" O ALA O 630 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 32 Processing helix chain 'Q' and resid 37 through 44 Processing helix chain 'Q' and resid 47 through 55 removed outlier: 4.051A pdb=" N VAL Q 50 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU Q 54 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 74 removed outlier: 3.589A pdb=" N VAL Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 84 removed outlier: 3.653A pdb=" N GLN Q 83 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET Q 84 " --> pdb=" O ARG Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 115 Processing helix chain 'Q' and resid 143 through 145 No H-bonds generated for 'chain 'Q' and resid 143 through 145' Processing helix chain 'Q' and resid 158 through 163 removed outlier: 3.869A pdb=" N ALA Q 162 " --> pdb=" O ALA Q 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 15 removed outlier: 3.527A pdb=" N GLU S 14 " --> pdb=" O LYS S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 45 removed outlier: 3.558A pdb=" N GLY S 41 " --> pdb=" O ASN S 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS S 42 " --> pdb=" O HIS S 38 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU S 45 " --> pdb=" O GLY S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 73 removed outlier: 3.521A pdb=" N ARG S 72 " --> pdb=" O ASP S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 85 Processing helix chain 'w' and resid 575 through 581 Processing helix chain 'x' and resid 575 through 581 Processing helix chain 'y' and resid 575 through 581 Processing helix chain 'z' and resid 575 through 581 removed outlier: 3.629A pdb=" N ARG z 579 " --> pdb=" O TYR z 575 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 52 Processing helix chain 'W' and resid 58 through 72 Processing helix chain 'W' and resid 76 through 88 Processing helix chain 'W' and resid 91 through 93 No H-bonds generated for 'chain 'W' and resid 91 through 93' Processing helix chain 'W' and resid 109 through 123 Processing helix chain 'W' and resid 131 through 145 Processing helix chain 'W' and resid 153 through 159 Processing helix chain 'W' and resid 161 through 172 removed outlier: 4.049A pdb=" N GLN W 167 " --> pdb=" O ILE W 163 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN W 168 " --> pdb=" O LEU W 164 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS W 169 " --> pdb=" O GLU W 165 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER W 172 " --> pdb=" O GLN W 168 " (cutoff:3.500A) Processing helix chain 'W' and resid 249 through 260 Processing helix chain 'W' and resid 267 through 269 No H-bonds generated for 'chain 'W' and resid 267 through 269' Processing helix chain 'W' and resid 295 through 304 Processing helix chain 'W' and resid 314 through 330 removed outlier: 3.669A pdb=" N GLY W 318 " --> pdb=" O SER W 315 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL W 319 " --> pdb=" O GLU W 316 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG W 322 " --> pdb=" O VAL W 319 " (cutoff:3.500A) Proline residue: W 323 - end of helix removed outlier: 3.700A pdb=" N GLN W 330 " --> pdb=" O LEU W 327 " (cutoff:3.500A) Processing helix chain 'W' and resid 332 through 334 No H-bonds generated for 'chain 'W' and resid 332 through 334' Processing helix chain 'W' and resid 343 through 345 No H-bonds generated for 'chain 'W' and resid 343 through 345' Processing helix chain 'W' and resid 358 through 371 Processing helix chain 'W' and resid 373 through 375 No H-bonds generated for 'chain 'W' and resid 373 through 375' Processing helix chain 'W' and resid 386 through 393 Processing helix chain 'W' and resid 403 through 409 removed outlier: 3.917A pdb=" N ILE W 408 " --> pdb=" O ASP W 405 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 422 No H-bonds generated for 'chain 'W' and resid 420 through 422' Processing helix chain 'W' and resid 436 through 439 Processing helix chain 'W' and resid 484 through 497 Processing helix chain 'W' and resid 503 through 519 Processing helix chain 'W' and resid 526 through 540 Processing helix chain 'X' and resid 39 through 52 removed outlier: 6.015A pdb=" N VAL X 44 " --> pdb=" O GLU X 40 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS X 45 " --> pdb=" O GLU X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 71 removed outlier: 4.177A pdb=" N GLY X 62 " --> pdb=" O ARG X 58 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN X 63 " --> pdb=" O THR X 59 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU X 70 " --> pdb=" O ARG X 66 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS X 71 " --> pdb=" O GLU X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 94 removed outlier: 8.134A pdb=" N LEU X 91 " --> pdb=" O GLU X 87 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL X 92 " --> pdb=" O GLN X 88 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY X 93 " --> pdb=" O ASP X 89 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU X 94 " --> pdb=" O GLY X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 109 through 123 Processing helix chain 'X' and resid 131 through 144 Processing helix chain 'X' and resid 153 through 172 Proline residue: X 162 - end of helix removed outlier: 4.021A pdb=" N GLN X 167 " --> pdb=" O ILE X 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 260 Processing helix chain 'X' and resid 267 through 269 No H-bonds generated for 'chain 'X' and resid 267 through 269' Processing helix chain 'X' and resid 295 through 304 Processing helix chain 'X' and resid 318 through 330 Proline residue: X 323 - end of helix Processing helix chain 'X' and resid 332 through 334 No H-bonds generated for 'chain 'X' and resid 332 through 334' Processing helix chain 'X' and resid 358 through 371 removed outlier: 3.821A pdb=" N ARG X 367 " --> pdb=" O GLN X 363 " (cutoff:3.500A) Processing helix chain 'X' and resid 373 through 375 No H-bonds generated for 'chain 'X' and resid 373 through 375' Processing helix chain 'X' and resid 386 through 393 Processing helix chain 'X' and resid 403 through 409 removed outlier: 3.527A pdb=" N ILE X 408 " --> pdb=" O ASP X 405 " (cutoff:3.500A) Processing helix chain 'X' and resid 436 through 439 Processing helix chain 'X' and resid 484 through 497 Processing helix chain 'X' and resid 503 through 515 removed outlier: 3.785A pdb=" N ASP X 512 " --> pdb=" O GLN X 508 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ARG X 513 " --> pdb=" O GLU X 509 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 540 Processing helix chain 'Y' and resid 252 through 260 Processing helix chain 'Y' and resid 267 through 269 No H-bonds generated for 'chain 'Y' and resid 267 through 269' Processing helix chain 'Y' and resid 296 through 304 Processing helix chain 'Y' and resid 324 through 330 Processing helix chain 'Y' and resid 332 through 334 No H-bonds generated for 'chain 'Y' and resid 332 through 334' Processing helix chain 'Y' and resid 358 through 371 Processing helix chain 'Y' and resid 379 through 381 No H-bonds generated for 'chain 'Y' and resid 379 through 381' Processing helix chain 'Y' and resid 386 through 392 Processing helix chain 'Y' and resid 403 through 409 removed outlier: 4.342A pdb=" N ILE Y 408 " --> pdb=" O ASP Y 405 " (cutoff:3.500A) Processing helix chain 'Y' and resid 436 through 439 Processing helix chain 'Y' and resid 484 through 500 Processing helix chain 'Y' and resid 505 through 517 removed outlier: 5.071A pdb=" N VAL Y 510 " --> pdb=" O LEU Y 507 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP Y 512 " --> pdb=" O GLU Y 509 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP Y 514 " --> pdb=" O VAL Y 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL Y 517 " --> pdb=" O ASP Y 514 " (cutoff:3.500A) Processing helix chain 'Z' and resid 249 through 260 Processing helix chain 'Z' and resid 267 through 269 No H-bonds generated for 'chain 'Z' and resid 267 through 269' Processing helix chain 'Z' and resid 296 through 304 Processing helix chain 'Z' and resid 324 through 330 Processing helix chain 'Z' and resid 332 through 334 No H-bonds generated for 'chain 'Z' and resid 332 through 334' Processing helix chain 'Z' and resid 358 through 371 Processing helix chain 'Z' and resid 373 through 375 No H-bonds generated for 'chain 'Z' and resid 373 through 375' Processing helix chain 'Z' and resid 386 through 392 Processing helix chain 'Z' and resid 403 through 409 removed outlier: 4.564A pdb=" N ILE Z 408 " --> pdb=" O ASP Z 405 " (cutoff:3.500A) Processing helix chain 'Z' and resid 437 through 439 No H-bonds generated for 'chain 'Z' and resid 437 through 439' Processing helix chain 'Z' and resid 484 through 501 Processing helix chain 'Z' and resid 504 through 523 removed outlier: 3.576A pdb=" N GLU Z 509 " --> pdb=" O LEU Z 506 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP Z 514 " --> pdb=" O VAL Z 511 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL Z 517 " --> pdb=" O ASP Z 514 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.727A pdb=" N ARG A 57 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE A 196 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 59 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 193 through 196 removed outlier: 6.729A pdb=" N ARG B 57 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE B 196 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 59 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 193 through 196 removed outlier: 6.727A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE C 196 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL C 59 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 193 through 196 removed outlier: 6.810A pdb=" N ARG D 57 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE D 196 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL D 59 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 193 through 196 removed outlier: 6.577A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE E 196 " --> pdb=" O ARG E 57 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 59 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 193 through 196 removed outlier: 6.569A pdb=" N ARG F 57 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE F 196 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL F 59 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 193 through 196 removed outlier: 6.777A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE G 196 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL G 59 " --> pdb=" O PHE G 196 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.847A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 193 through 196 removed outlier: 6.729A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE I 196 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL I 59 " --> pdb=" O PHE I 196 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 193 through 196 removed outlier: 6.749A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE J 196 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL J 59 " --> pdb=" O PHE J 196 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 193 through 196 removed outlier: 6.780A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE K 196 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL K 59 " --> pdb=" O PHE K 196 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 193 through 196 removed outlier: 6.785A pdb=" N ARG L 57 " --> pdb=" O LEU L 194 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE L 196 " --> pdb=" O ARG L 57 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL L 59 " --> pdb=" O PHE L 196 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'O' and resid 314 through 316 removed outlier: 4.832A pdb=" N LEU O 371 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN O 351 " --> pdb=" O CYS O 376 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP O 378 " --> pdb=" O LEU O 349 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU O 349 " --> pdb=" O ASP O 378 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'O' and resid 291 through 295 Processing sheet with id= O, first strand: chain 'O' and resid 607 through 611 removed outlier: 3.583A pdb=" N GLY O 611 " --> pdb=" O LEU O 545 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER O 542 " --> pdb=" O ILE O 447 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA O 473 " --> pdb=" O VAL O 463 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP O 465 " --> pdb=" O VAL O 471 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL O 471 " --> pdb=" O ASP O 465 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'W' and resid 184 through 186 Processing sheet with id= Q, first strand: chain 'W' and resid 237 through 243 removed outlier: 6.602A pdb=" N VAL W 229 " --> pdb=" O MET W 238 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE W 240 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR W 227 " --> pdb=" O ILE W 240 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU W 242 " --> pdb=" O TRP W 225 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP W 225 " --> pdb=" O LEU W 242 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP W 205 " --> pdb=" O THR W 228 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS W 283 " --> pdb=" O TRP W 202 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N CYS W 204 " --> pdb=" O HIS W 283 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR W 285 " --> pdb=" O CYS W 204 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N HIS W 206 " --> pdb=" O TYR W 285 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL W 307 " --> pdb=" O PHE W 284 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N THR W 286 " --> pdb=" O VAL W 307 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS W 309 " --> pdb=" O THR W 286 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'W' and resid 411 through 413 removed outlier: 3.561A pdb=" N LEU W 446 " --> pdb=" O GLN W 413 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ARG W 460 " --> pdb=" O PHE W 468 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE W 468 " --> pdb=" O ARG W 460 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU W 462 " --> pdb=" O GLU W 466 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU W 466 " --> pdb=" O GLU W 462 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG W 432 " --> pdb=" O HIS W 473 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 184 through 186 Processing sheet with id= T, first strand: chain 'X' and resid 237 through 243 removed outlier: 6.517A pdb=" N VAL X 229 " --> pdb=" O MET X 238 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE X 240 " --> pdb=" O THR X 227 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR X 227 " --> pdb=" O ILE X 240 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU X 242 " --> pdb=" O TRP X 225 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP X 225 " --> pdb=" O LEU X 242 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR X 228 " --> pdb=" O ASP X 205 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP X 205 " --> pdb=" O THR X 228 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS X 283 " --> pdb=" O TRP X 202 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N CYS X 204 " --> pdb=" O HIS X 283 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR X 285 " --> pdb=" O CYS X 204 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N HIS X 206 " --> pdb=" O TYR X 285 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL X 307 " --> pdb=" O PHE X 284 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR X 286 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS X 309 " --> pdb=" O THR X 286 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 411 through 413 removed outlier: 6.011A pdb=" N ARG X 460 " --> pdb=" O PHE X 468 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N PHE X 468 " --> pdb=" O ARG X 460 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU X 462 " --> pdb=" O GLU X 466 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU X 466 " --> pdb=" O GLU X 462 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 423 through 426 Processing sheet with id= W, first strand: chain 'Y' and resid 236 through 243 removed outlier: 3.511A pdb=" N CYS Y 236 " --> pdb=" O ASP Y 231 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL Y 229 " --> pdb=" O MET Y 238 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE Y 240 " --> pdb=" O THR Y 227 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR Y 227 " --> pdb=" O ILE Y 240 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU Y 242 " --> pdb=" O TRP Y 225 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP Y 225 " --> pdb=" O LEU Y 242 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N HIS Y 283 " --> pdb=" O TRP Y 202 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N CYS Y 204 " --> pdb=" O HIS Y 283 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR Y 285 " --> pdb=" O CYS Y 204 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N HIS Y 206 " --> pdb=" O TYR Y 285 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL Y 307 " --> pdb=" O PHE Y 284 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Y' and resid 411 through 413 removed outlier: 3.597A pdb=" N MET Y 411 " --> pdb=" O PHE Y 448 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG Y 460 " --> pdb=" O PHE Y 468 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE Y 468 " --> pdb=" O ARG Y 460 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU Y 462 " --> pdb=" O GLU Y 466 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLU Y 466 " --> pdb=" O GLU Y 462 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N MET Y 430 " --> pdb=" O GLN Y 475 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 236 through 243 removed outlier: 7.025A pdb=" N VAL Z 229 " --> pdb=" O MET Z 238 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE Z 240 " --> pdb=" O THR Z 227 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR Z 227 " --> pdb=" O ILE Z 240 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU Z 242 " --> pdb=" O TRP Z 225 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP Z 225 " --> pdb=" O LEU Z 242 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS Z 283 " --> pdb=" O TRP Z 202 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N CYS Z 204 " --> pdb=" O HIS Z 283 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR Z 285 " --> pdb=" O CYS Z 204 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N HIS Z 206 " --> pdb=" O TYR Z 285 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL Z 307 " --> pdb=" O PHE Z 284 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 411 through 413 removed outlier: 3.502A pdb=" N THR Z 470 " --> pdb=" O VAL Z 458 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG Z 460 " --> pdb=" O PHE Z 468 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N PHE Z 468 " --> pdb=" O ARG Z 460 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N MET Z 430 " --> pdb=" O GLN Z 475 " (cutoff:3.500A) 1917 hydrogen bonds defined for protein. 5229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 434 hydrogen bonds 840 hydrogen bond angles 0 basepair planarities 181 basepair parallelities 326 stacking parallelities Total time for adding SS restraints: 20.25 Time building geometry restraints manager: 20.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 8148 1.29 - 1.42: 16959 1.42 - 1.56: 31542 1.56 - 1.69: 1043 1.69 - 1.83: 250 Bond restraints: 57942 Sorted by residual: bond pdb=" C ASN Z 463 " pdb=" N ASN Z 464 " ideal model delta sigma weight residual 1.332 1.220 0.112 1.40e-02 5.10e+03 6.44e+01 bond pdb=" C VAL B 186 " pdb=" O VAL B 186 " ideal model delta sigma weight residual 1.236 1.154 0.083 1.10e-02 8.26e+03 5.63e+01 bond pdb=" C ARG X 355 " pdb=" N LEU X 356 " ideal model delta sigma weight residual 1.330 1.228 0.103 1.38e-02 5.25e+03 5.52e+01 bond pdb=" C GLN A 38 " pdb=" O GLN A 38 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.19e-02 7.06e+03 5.23e+01 bond pdb=" C GLU B 184 " pdb=" O GLU B 184 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.18e-02 7.18e+03 5.11e+01 ... (remaining 57937 not shown) Histogram of bond angle deviations from ideal: 95.22 - 103.24: 1227 103.24 - 111.26: 23243 111.26 - 119.27: 27071 119.27 - 127.29: 27450 127.29 - 135.31: 1443 Bond angle restraints: 80434 Sorted by residual: angle pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " pdb=" PG ATP B 302 " ideal model delta sigma weight residual 139.87 113.42 26.45 1.00e+00 1.00e+00 7.00e+02 angle pdb=" PB ATP E 302 " pdb=" O3B ATP E 302 " pdb=" PG ATP E 302 " ideal model delta sigma weight residual 139.87 114.76 25.11 1.00e+00 1.00e+00 6.30e+02 angle pdb=" PB ATP F 302 " pdb=" O3B ATP F 302 " pdb=" PG ATP F 302 " ideal model delta sigma weight residual 139.87 115.25 24.62 1.00e+00 1.00e+00 6.06e+02 angle pdb=" PB ATP C 302 " pdb=" O3B ATP C 302 " pdb=" PG ATP C 302 " ideal model delta sigma weight residual 139.87 118.58 21.29 1.00e+00 1.00e+00 4.53e+02 angle pdb=" PB ATP I 302 " pdb=" O3B ATP I 302 " pdb=" PG ATP I 302 " ideal model delta sigma weight residual 139.87 119.92 19.95 1.00e+00 1.00e+00 3.98e+02 ... (remaining 80429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 33184 35.60 - 71.21: 1973 71.21 - 106.81: 158 106.81 - 142.41: 2 142.41 - 178.01: 11 Dihedral angle restraints: 35328 sinusoidal: 19034 harmonic: 16294 Sorted by residual: dihedral pdb=" O4' U 7 49 " pdb=" C2' U 7 49 " pdb=" C1' U 7 49 " pdb=" C3' U 7 49 " ideal model delta sinusoidal sigma weight residual -35.00 33.96 -68.96 1 8.00e+00 1.56e-02 9.62e+01 dihedral pdb=" CD ARG W 367 " pdb=" NE ARG W 367 " pdb=" CZ ARG W 367 " pdb=" NH1 ARG W 367 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" C4' U 7 49 " pdb=" C3' U 7 49 " pdb=" C2' U 7 49 " pdb=" C1' U 7 49 " ideal model delta sinusoidal sigma weight residual -35.00 29.48 -64.48 1 8.00e+00 1.56e-02 8.54e+01 ... (remaining 35325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 8947 0.216 - 0.431: 190 0.431 - 0.647: 14 0.647 - 0.862: 1 0.862 - 1.078: 1 Chirality restraints: 9153 Sorted by residual: chirality pdb=" CA GLU K 24 " pdb=" N GLU K 24 " pdb=" C GLU K 24 " pdb=" CB GLU K 24 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA GLN K 22 " pdb=" N GLN K 22 " pdb=" C GLN K 22 " pdb=" CB GLN K 22 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" P DT 1 35 " pdb=" OP1 DT 1 35 " pdb=" OP2 DT 1 35 " pdb=" O5' DT 1 35 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.55 2.00e-01 2.50e+01 7.47e+00 ... (remaining 9150 not shown) Planarity restraints: 8462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 20 " -0.216 2.00e-02 2.50e+03 1.07e-01 2.86e+02 pdb=" CG TRP G 20 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP G 20 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TRP G 20 " 0.091 2.00e-02 2.50e+03 pdb=" NE1 TRP G 20 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 TRP G 20 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP G 20 " 0.137 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 20 " -0.130 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 20 " 0.049 2.00e-02 2.50e+03 pdb=" CH2 TRP G 20 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG W 367 " -1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG W 367 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG W 367 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG W 367 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG W 367 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 526 " -1.087 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG Y 526 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG Y 526 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 526 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 526 " -0.018 2.00e-02 2.50e+03 ... (remaining 8459 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 65 1.91 - 2.66: 1479 2.66 - 3.40: 73457 3.40 - 4.15: 143944 4.15 - 4.90: 237264 Nonbonded interactions: 456209 Sorted by model distance: nonbonded pdb=" OE2 GLU B 162 " pdb=" NH1 ARG B 189 " model vdw 1.162 2.520 nonbonded pdb=" NH1 ARG X 322 " pdb=" N3 DA 2 4 " model vdw 1.188 2.600 nonbonded pdb=" CZ ARG K 191 " pdb=" NH2 ARG L 243 " model vdw 1.222 3.350 nonbonded pdb=" NH2 ARG W 380 " pdb=" O5' DT 5 3 " model vdw 1.232 2.520 nonbonded pdb=" OP2 DG 1 36 " pdb=" CE LYS I 119 " model vdw 1.236 3.440 ... (remaining 456204 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 '2' and (resid 1 through 11 or resid 13 through 18 or resid 20 through 25 \ or resid 27 or resid 29)) selection = (chain '5' and (resid 1 through 11 or resid 13 through 18 or resid 20 through 25 \ or resid 27 through 28)) } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'W' and (resid 29 through 516 or resid 524 through 542 or resid 600)) selection = chain 'X' } ncs_group { reference = (chain 'Y' and (resid 196 through 287 or resid 295 through 340 or resid 354 thro \ ugh 525 or (resid 526 and (name N or name CA or name C or name O or name CB )) o \ r resid 527)) selection = chain 'Z' } ncs_group { reference = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 31.580 Check model and map are aligned: 0.600 Set scattering table: 0.400 Process input model: 123.570 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 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 : 0.013 0.112 57942 Z= 0.842 Angle : 1.649 26.449 80434 Z= 1.166 Chirality : 0.086 1.078 9153 Planarity : 0.020 0.493 8462 Dihedral : 18.841 178.015 24792 Min Nonbonded Distance : 1.162 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.39 % Rotamer: Outliers : 0.29 % Allowed : 1.25 % Favored : 98.47 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.10), residues: 5554 helix: -1.16 (0.08), residues: 2863 sheet: 0.26 (0.21), residues: 559 loop : 0.06 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.216 0.022 TRP G 20 HIS 0.019 0.002 HIS X 258 PHE 0.074 0.009 PHE Q 56 TYR 0.159 0.017 TYR x 575 ARG 0.015 0.001 ARG J 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1323 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7977 (ttp80) REVERT: A 144 ASP cc_start: 0.8746 (t0) cc_final: 0.8542 (t0) REVERT: C 187 LEU cc_start: 0.9324 (tp) cc_final: 0.9062 (tp) REVERT: C 260 LEU cc_start: 0.5968 (mm) cc_final: 0.5685 (tp) REVERT: F 117 VAL cc_start: 0.8725 (t) cc_final: 0.8304 (m) REVERT: G 123 SER cc_start: 0.7790 (p) cc_final: 0.7098 (t) REVERT: G 229 MET cc_start: 0.7501 (mmm) cc_final: 0.7198 (mmt) REVERT: H 156 ASP cc_start: 0.7162 (m-30) cc_final: 0.6952 (m-30) REVERT: J 229 MET cc_start: 0.6539 (mmm) cc_final: 0.5983 (mmt) REVERT: L 64 THR cc_start: 0.8702 (p) cc_final: 0.8464 (p) REVERT: Q 156 MET cc_start: 0.6889 (ttp) cc_final: 0.6145 (ttt) REVERT: Z 233 TYR cc_start: 0.4961 (t80) cc_final: 0.4597 (t80) outliers start: 14 outliers final: 2 residues processed: 1335 average time/residue: 0.6626 time to fit residues: 1390.7406 Evaluate side-chains 546 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 543 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 251 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 502 optimal weight: 0.7980 chunk 450 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 466 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 283 optimal weight: 0.8980 chunk 347 optimal weight: 2.9990 chunk 540 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN D 38 GLN F 38 GLN G 77 HIS G 269 GLN H 38 GLN I 80 GLN I 213 GLN J 98 GLN J 185 GLN ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 GLN K 269 GLN L 213 GLN ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN O 269 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 369 HIS O 370 HIS O 420 GLN O 603 GLN O 613 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 135 ASN S 28 GLN S 37 ASN y 577 GLN W 88 GLN W 217 HIS W 272 HIS W 463 ASN X 217 HIS X 272 HIS X 363 GLN Y 296 HIS Y 309 HIS ** Y 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 463 ASN Z 203 GLN ** Z 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 283 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 428 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 57942 Z= 0.222 Angle : 0.633 11.266 80434 Z= 0.343 Chirality : 0.039 0.208 9153 Planarity : 0.005 0.079 8462 Dihedral : 21.028 176.241 13194 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.35 % Allowed : 8.72 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.11), residues: 5554 helix: 0.67 (0.09), residues: 2918 sheet: 0.28 (0.23), residues: 511 loop : 0.44 (0.14), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 20 HIS 0.008 0.001 HIS Q 94 PHE 0.024 0.002 PHE Q 158 TYR 0.036 0.002 TYR y 575 ARG 0.015 0.001 ARG L 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 587 time to evaluate : 4.346 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: C 235 SER cc_start: 0.8216 (t) cc_final: 0.8001 (p) REVERT: E 210 MET cc_start: 0.6929 (mtp) cc_final: 0.6648 (ttm) REVERT: F 64 THR cc_start: 0.8880 (p) cc_final: 0.8613 (p) REVERT: F 159 ASP cc_start: 0.6792 (t70) cc_final: 0.6481 (t0) REVERT: G 229 MET cc_start: 0.7636 (mmm) cc_final: 0.7169 (mmt) REVERT: I 183 ASP cc_start: 0.7048 (t0) cc_final: 0.6734 (t0) REVERT: I 269 GLN cc_start: 0.7929 (mm110) cc_final: 0.7678 (mm-40) REVERT: J 64 THR cc_start: 0.8656 (p) cc_final: 0.8450 (p) REVERT: L 64 THR cc_start: 0.8611 (p) cc_final: 0.8327 (p) REVERT: Q 70 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8839 (tt) REVERT: Q 72 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.8782 (t) REVERT: Q 75 GLU cc_start: 0.7758 (mp0) cc_final: 0.7548 (mp0) REVERT: Q 147 GLU cc_start: 0.7335 (tt0) cc_final: 0.6949 (tt0) REVERT: S 71 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8761 (ttmt) REVERT: w 574 ASP cc_start: 0.8115 (t0) cc_final: 0.7802 (t0) REVERT: w 581 GLU cc_start: 0.6541 (tt0) cc_final: 0.6144 (tt0) REVERT: X 178 TRP cc_start: 0.6293 (m100) cc_final: 0.5665 (m100) REVERT: X 341 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8374 (t) REVERT: X 426 PHE cc_start: 0.6844 (t80) cc_final: 0.5715 (t80) outliers start: 115 outliers final: 77 residues processed: 676 average time/residue: 0.5924 time to fit residues: 660.5239 Evaluate side-chains 490 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 409 time to evaluate : 4.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 235 SER Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 420 GLN Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 469 ASN Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 597 ILE Chi-restraints excluded: chain O residue 621 ASP Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain x residue 573 TRP Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 341 SER Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain X residue 411 MET Chi-restraints excluded: chain X residue 423 CYS Chi-restraints excluded: chain Y residue 210 ASP Chi-restraints excluded: chain Y residue 251 VAL Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 308 CYS Chi-restraints excluded: chain Z residue 265 TYR Chi-restraints excluded: chain Z residue 295 ASN Chi-restraints excluded: chain Z residue 308 CYS Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 491 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 300 optimal weight: 0.0980 chunk 167 optimal weight: 4.9990 chunk 449 optimal weight: 0.3980 chunk 367 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 541 optimal weight: 8.9990 chunk 584 optimal weight: 0.9980 chunk 482 optimal weight: 10.0000 chunk 536 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 434 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN B 223 ASN D 38 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 81 GLN I 22 GLN ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN K 269 GLN O 33 ASN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 420 GLN O 500 HIS ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 HIS y 577 GLN W 88 GLN W 272 HIS ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 375 GLN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 57942 Z= 0.263 Angle : 0.574 8.260 80434 Z= 0.311 Chirality : 0.039 0.218 9153 Planarity : 0.004 0.077 8462 Dihedral : 21.014 174.842 13188 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.61 % Allowed : 10.21 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.11), residues: 5554 helix: 1.15 (0.10), residues: 2914 sheet: 0.29 (0.23), residues: 510 loop : 0.47 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP Z 225 HIS 0.006 0.001 HIS O 586 PHE 0.018 0.002 PHE A 190 TYR 0.020 0.002 TYR W 61 ARG 0.017 0.000 ARG x 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 439 time to evaluate : 4.286 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: C 193 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.8277 (p-80) REVERT: D 64 THR cc_start: 0.8679 (p) cc_final: 0.8440 (p) REVERT: F 64 THR cc_start: 0.8992 (p) cc_final: 0.8728 (p) REVERT: G 111 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7365 (tm-30) REVERT: G 229 MET cc_start: 0.7731 (mmm) cc_final: 0.7235 (mmt) REVERT: K 37 GLN cc_start: 0.7294 (tp40) cc_final: 0.7091 (tp40) REVERT: K 214 MET cc_start: 0.7440 (mmm) cc_final: 0.7028 (mtp) REVERT: L 64 THR cc_start: 0.8710 (p) cc_final: 0.8450 (p) REVERT: L 269 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8084 (mt0) REVERT: O 81 MET cc_start: 0.7371 (mmm) cc_final: 0.7117 (mmm) REVERT: O 435 ARG cc_start: 0.3842 (OUTLIER) cc_final: 0.1844 (ttt90) REVERT: Q 72 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.8853 (t) REVERT: y 581 GLU cc_start: 0.7946 (pp20) cc_final: 0.7065 (pp20) REVERT: W 381 MET cc_start: 0.8235 (mmp) cc_final: 0.7707 (mmt) REVERT: Y 430 MET cc_start: 0.8258 (tpp) cc_final: 0.8045 (tpp) outliers start: 128 outliers final: 85 residues processed: 534 average time/residue: 0.5373 time to fit residues: 479.6118 Evaluate side-chains 462 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 374 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 235 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 435 ARG Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 469 ASN Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 597 ILE Chi-restraints excluded: chain O residue 621 ASP Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain w residue 570 ILE Chi-restraints excluded: chain x residue 573 TRP Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 199 ASN Chi-restraints excluded: chain Y residue 210 ASP Chi-restraints excluded: chain Y residue 251 VAL Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 308 CYS Chi-restraints excluded: chain Z residue 236 CYS Chi-restraints excluded: chain Z residue 265 TYR Chi-restraints excluded: chain Z residue 295 ASN Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Chi-restraints excluded: chain Z residue 491 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 534 optimal weight: 20.0000 chunk 406 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 258 optimal weight: 2.9990 chunk 363 optimal weight: 9.9990 chunk 543 optimal weight: 2.9990 chunk 575 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 514 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS E 37 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS H 38 GLN ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 HIS O 304 HIS O 521 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 88 GLN W 272 HIS ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 363 GLN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 57942 Z= 0.253 Angle : 0.561 9.899 80434 Z= 0.302 Chirality : 0.038 0.188 9153 Planarity : 0.004 0.062 8462 Dihedral : 21.076 175.170 13188 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 3.06 % Allowed : 11.01 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.11), residues: 5554 helix: 1.33 (0.10), residues: 2899 sheet: 0.44 (0.22), residues: 497 loop : 0.35 (0.14), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP Z 225 HIS 0.007 0.001 HIS W 272 PHE 0.021 0.002 PHE A 190 TYR 0.021 0.002 TYR J 240 ARG 0.011 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 427 time to evaluate : 4.349 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: C 33 ILE cc_start: 0.9206 (mp) cc_final: 0.9003 (mm) REVERT: E 210 MET cc_start: 0.6816 (mtp) cc_final: 0.6513 (ttm) REVERT: E 214 MET cc_start: 0.5692 (mpp) cc_final: 0.5202 (ptp) REVERT: F 20 TRP cc_start: 0.6116 (OUTLIER) cc_final: 0.5317 (t60) REVERT: F 64 THR cc_start: 0.9077 (p) cc_final: 0.8824 (p) REVERT: G 183 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7277 (p0) REVERT: I 196 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8874 (m-10) REVERT: K 37 GLN cc_start: 0.7309 (tp40) cc_final: 0.7020 (tp40) REVERT: K 196 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8700 (m-80) REVERT: K 214 MET cc_start: 0.7492 (mmm) cc_final: 0.7073 (mtp) REVERT: L 64 THR cc_start: 0.8896 (p) cc_final: 0.8694 (p) REVERT: L 223 ASN cc_start: 0.7360 (t0) cc_final: 0.7079 (t0) REVERT: L 269 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8125 (mt0) REVERT: O 78 ARG cc_start: 0.3099 (mpt180) cc_final: 0.2716 (mmm-85) REVERT: O 81 MET cc_start: 0.7102 (mmm) cc_final: 0.6886 (mmm) REVERT: Q 72 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.8888 (t) REVERT: S 22 THR cc_start: 0.6411 (p) cc_final: 0.6193 (m) REVERT: y 581 GLU cc_start: 0.8071 (pp20) cc_final: 0.7256 (pp20) REVERT: W 488 GLU cc_start: 0.7466 (tp30) cc_final: 0.7220 (tm-30) REVERT: X 178 TRP cc_start: 0.6561 (m100) cc_final: 0.5719 (m100) REVERT: X 183 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7943 (tt) REVERT: X 488 GLU cc_start: 0.7274 (tp30) cc_final: 0.6859 (tp30) REVERT: Y 273 CYS cc_start: 0.4403 (OUTLIER) cc_final: 0.4021 (t) REVERT: Y 381 MET cc_start: 0.0675 (ttm) cc_final: -0.0063 (ttm) REVERT: Y 445 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8102 (p0) REVERT: Z 244 PHE cc_start: 0.6320 (OUTLIER) cc_final: 0.5843 (t80) REVERT: Z 426 PHE cc_start: 0.8233 (t80) cc_final: 0.7890 (t80) outliers start: 150 outliers final: 99 residues processed: 544 average time/residue: 0.5396 time to fit residues: 492.5117 Evaluate side-chains 461 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 353 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 469 ASN Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 554 VAL Chi-restraints excluded: chain O residue 597 ILE Chi-restraints excluded: chain O residue 621 ASP Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain w residue 570 ILE Chi-restraints excluded: chain x residue 573 TRP Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 199 ASN Chi-restraints excluded: chain Y residue 210 ASP Chi-restraints excluded: chain Y residue 222 SER Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 308 CYS Chi-restraints excluded: chain Y residue 445 ASN Chi-restraints excluded: chain Y residue 464 ASN Chi-restraints excluded: chain Y residue 479 THR Chi-restraints excluded: chain Z residue 236 CYS Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 265 TYR Chi-restraints excluded: chain Z residue 295 ASN Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Chi-restraints excluded: chain Z residue 491 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 478 optimal weight: 7.9990 chunk 326 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 428 optimal weight: 7.9990 chunk 237 optimal weight: 4.9990 chunk 490 optimal weight: 1.9990 chunk 397 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 516 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 223 ASN E 269 GLN F 38 GLN F 43 HIS F 80 GLN H 38 GLN L 213 GLN O 50 GLN O 342 HIS ** O 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 309 HIS Y 463 ASN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 57942 Z= 0.285 Angle : 0.564 7.771 80434 Z= 0.303 Chirality : 0.039 0.190 9153 Planarity : 0.004 0.063 8462 Dihedral : 21.156 175.149 13187 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.45 % Favored : 97.53 % Rotamer: Outliers : 2.94 % Allowed : 12.13 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.11), residues: 5554 helix: 1.38 (0.10), residues: 2887 sheet: 0.28 (0.22), residues: 517 loop : 0.30 (0.14), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 20 HIS 0.006 0.001 HIS Y 200 PHE 0.019 0.002 PHE W 306 TYR 0.020 0.002 TYR J 240 ARG 0.010 0.000 ARG y 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 377 time to evaluate : 4.568 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: F 20 TRP cc_start: 0.6173 (OUTLIER) cc_final: 0.5306 (t60) REVERT: G 183 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7386 (p0) REVERT: G 188 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6508 (tp30) REVERT: I 196 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8930 (m-10) REVERT: K 37 GLN cc_start: 0.7400 (tp40) cc_final: 0.7132 (tp40) REVERT: K 196 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8682 (m-80) REVERT: K 214 MET cc_start: 0.7603 (mmm) cc_final: 0.7211 (mtp) REVERT: L 64 THR cc_start: 0.8997 (p) cc_final: 0.8753 (p) REVERT: O 492 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.7041 (mtt90) REVERT: Q 72 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8861 (t) REVERT: S 22 THR cc_start: 0.6418 (p) cc_final: 0.6176 (m) REVERT: y 581 GLU cc_start: 0.8112 (pp20) cc_final: 0.7299 (pp20) REVERT: W 488 GLU cc_start: 0.7453 (tp30) cc_final: 0.7174 (tm-30) REVERT: X 341 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8627 (t) REVERT: Y 273 CYS cc_start: 0.4270 (OUTLIER) cc_final: 0.3934 (t) REVERT: Y 283 HIS cc_start: 0.4599 (m-70) cc_final: 0.4392 (m170) REVERT: Z 244 PHE cc_start: 0.6259 (OUTLIER) cc_final: 0.5478 (t80) outliers start: 144 outliers final: 98 residues processed: 490 average time/residue: 0.5430 time to fit residues: 450.8684 Evaluate side-chains 445 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 338 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 469 ASN Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 492 ARG Chi-restraints excluded: chain O residue 597 ILE Chi-restraints excluded: chain O residue 621 ASP Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain w residue 570 ILE Chi-restraints excluded: chain x residue 573 TRP Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 199 ASN Chi-restraints excluded: chain Y residue 210 ASP Chi-restraints excluded: chain Y residue 222 SER Chi-restraints excluded: chain Y residue 237 ILE Chi-restraints excluded: chain Y residue 273 CYS Chi-restraints excluded: chain Y residue 464 ASN Chi-restraints excluded: chain Y residue 510 VAL Chi-restraints excluded: chain Z residue 236 CYS Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 265 TYR Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Chi-restraints excluded: chain Z residue 491 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 193 optimal weight: 20.0000 chunk 517 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 337 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 575 optimal weight: 3.9990 chunk 477 optimal weight: 0.6980 chunk 266 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 190 optimal weight: 3.9990 chunk 302 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 81 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS H 38 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 363 GLN Y 463 ASN Y 504 GLN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 57942 Z= 0.160 Angle : 0.513 13.218 80434 Z= 0.275 Chirality : 0.036 0.188 9153 Planarity : 0.003 0.055 8462 Dihedral : 21.063 176.881 13187 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.09 % Favored : 97.89 % Rotamer: Outliers : 2.08 % Allowed : 13.26 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.11), residues: 5554 helix: 1.60 (0.10), residues: 2884 sheet: 0.32 (0.22), residues: 516 loop : 0.35 (0.14), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 20 HIS 0.009 0.001 HIS S 50 PHE 0.022 0.001 PHE Y 306 TYR 0.015 0.001 TYR A 73 ARG 0.009 0.000 ARG y 579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 394 time to evaluate : 4.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.7000 (tp40) cc_final: 0.6695 (tp40) REVERT: F 20 TRP cc_start: 0.5993 (OUTLIER) cc_final: 0.5224 (t60) REVERT: G 183 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7249 (p0) REVERT: I 196 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8799 (m-10) REVERT: J 170 LEU cc_start: 0.9367 (mt) cc_final: 0.9146 (mt) REVERT: J 263 ILE cc_start: 0.7649 (mt) cc_final: 0.7432 (tt) REVERT: K 196 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8689 (m-80) REVERT: K 214 MET cc_start: 0.7587 (mmm) cc_final: 0.7252 (mtp) REVERT: L 64 THR cc_start: 0.8916 (p) cc_final: 0.8688 (p) REVERT: O 78 ARG cc_start: 0.2976 (mpt180) cc_final: 0.2451 (mmm-85) REVERT: S 22 THR cc_start: 0.6291 (p) cc_final: 0.6088 (m) REVERT: S 35 GLN cc_start: 0.7956 (mm110) cc_final: 0.7357 (mm-40) REVERT: w 576 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6789 (tm-30) REVERT: y 581 GLU cc_start: 0.8034 (pp20) cc_final: 0.7260 (pp20) REVERT: W 164 LEU cc_start: 0.8698 (mm) cc_final: 0.8491 (mt) REVERT: W 345 GLU cc_start: 0.8133 (mp0) cc_final: 0.7574 (mp0) REVERT: W 488 GLU cc_start: 0.7370 (tp30) cc_final: 0.7016 (tm-30) REVERT: X 341 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8619 (t) REVERT: Z 244 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.5559 (t80) outliers start: 102 outliers final: 68 residues processed: 474 average time/residue: 0.5466 time to fit residues: 435.9365 Evaluate side-chains 420 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 346 time to evaluate : 4.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 418 LEU Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 621 ASP Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain x residue 573 TRP Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 199 ASN Chi-restraints excluded: chain Y residue 210 ASP Chi-restraints excluded: chain Y residue 222 SER Chi-restraints excluded: chain Y residue 464 ASN Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 265 TYR Chi-restraints excluded: chain Z residue 435 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 555 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 chunk 420 optimal weight: 10.0000 chunk 325 optimal weight: 0.5980 chunk 484 optimal weight: 1.9990 chunk 321 optimal weight: 3.9990 chunk 573 optimal weight: 0.5980 chunk 358 optimal weight: 0.8980 chunk 349 optimal weight: 7.9990 chunk 264 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS H 38 GLN J 213 GLN y 577 GLN W 88 GLN W 152 ASN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 206 HIS Y 283 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 57942 Z= 0.167 Angle : 0.507 12.463 80434 Z= 0.271 Chirality : 0.036 0.188 9153 Planarity : 0.003 0.047 8462 Dihedral : 21.004 176.978 13187 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.27 % Favored : 97.71 % Rotamer: Outliers : 2.29 % Allowed : 13.42 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.11), residues: 5554 helix: 1.71 (0.10), residues: 2873 sheet: 0.29 (0.22), residues: 525 loop : 0.40 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 20 HIS 0.006 0.001 HIS S 50 PHE 0.025 0.001 PHE Y 306 TYR 0.019 0.001 TYR A 73 ARG 0.012 0.000 ARG y 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 369 time to evaluate : 4.373 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 37 GLN cc_start: 0.7034 (tp40) cc_final: 0.6797 (tp40) REVERT: F 20 TRP cc_start: 0.5980 (OUTLIER) cc_final: 0.5211 (t60) REVERT: G 183 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7223 (p0) REVERT: I 196 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8794 (m-10) REVERT: J 246 GLU cc_start: 0.7122 (tp30) cc_final: 0.6716 (tp30) REVERT: K 196 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: K 214 MET cc_start: 0.7677 (mmm) cc_final: 0.7271 (mtp) REVERT: L 64 THR cc_start: 0.8900 (p) cc_final: 0.8677 (p) REVERT: S 22 THR cc_start: 0.6248 (p) cc_final: 0.6030 (m) REVERT: S 35 GLN cc_start: 0.7959 (mm110) cc_final: 0.7433 (mm-40) REVERT: w 580 GLU cc_start: 0.7369 (pt0) cc_final: 0.7096 (pt0) REVERT: y 579 ARG cc_start: 0.7884 (ttm110) cc_final: 0.7130 (mtt90) REVERT: y 581 GLU cc_start: 0.8022 (pp20) cc_final: 0.7253 (pp20) REVERT: W 345 GLU cc_start: 0.8142 (mp0) cc_final: 0.7570 (mp0) REVERT: W 488 GLU cc_start: 0.7403 (tp30) cc_final: 0.7029 (tm-30) REVERT: X 341 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8614 (t) REVERT: Y 445 ASN cc_start: 0.8204 (p0) cc_final: 0.7966 (p0) REVERT: Z 244 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.5571 (t80) outliers start: 112 outliers final: 79 residues processed: 461 average time/residue: 0.5422 time to fit residues: 419.0016 Evaluate side-chains 424 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 339 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 418 LEU Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain O residue 621 ASP Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain x residue 573 TRP Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 381 MET Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 199 ASN Chi-restraints excluded: chain Y residue 222 SER Chi-restraints excluded: chain Y residue 283 HIS Chi-restraints excluded: chain Y residue 453 ILE Chi-restraints excluded: chain Y residue 464 ASN Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 265 TYR Chi-restraints excluded: chain Z residue 327 LEU Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 354 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 342 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 112 optimal weight: 0.0040 chunk 111 optimal weight: 0.5980 chunk 364 optimal weight: 10.0000 chunk 390 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 450 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS H 38 GLN O 479 GLN y 577 GLN W 88 GLN W 463 ASN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 241 ASN Y 206 HIS Y 283 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 57942 Z= 0.149 Angle : 0.505 12.581 80434 Z= 0.268 Chirality : 0.036 0.189 9153 Planarity : 0.003 0.061 8462 Dihedral : 20.943 177.469 13187 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.16 % Favored : 97.82 % Rotamer: Outliers : 2.08 % Allowed : 13.77 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.11), residues: 5554 helix: 1.81 (0.10), residues: 2886 sheet: 0.38 (0.22), residues: 521 loop : 0.40 (0.14), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 20 HIS 0.018 0.001 HIS Y 283 PHE 0.028 0.001 PHE Y 306 TYR 0.015 0.001 TYR A 73 ARG 0.015 0.000 ARG G 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 366 time to evaluate : 4.591 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: D 268 LEU cc_start: 0.9247 (tt) cc_final: 0.9004 (tp) REVERT: F 20 TRP cc_start: 0.5974 (OUTLIER) cc_final: 0.5211 (t60) REVERT: G 183 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7190 (p0) REVERT: I 196 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8721 (m-10) REVERT: J 246 GLU cc_start: 0.7158 (tp30) cc_final: 0.6707 (tp30) REVERT: K 196 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8599 (m-80) REVERT: K 214 MET cc_start: 0.7688 (mmm) cc_final: 0.7326 (mtp) REVERT: L 64 THR cc_start: 0.8843 (p) cc_final: 0.8614 (p) REVERT: O 304 HIS cc_start: 0.3840 (OUTLIER) cc_final: 0.3451 (p90) REVERT: S 22 THR cc_start: 0.6360 (p) cc_final: 0.6127 (m) REVERT: S 35 GLN cc_start: 0.7950 (mm110) cc_final: 0.7434 (mm-40) REVERT: y 579 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7497 (ttm170) REVERT: y 581 GLU cc_start: 0.8006 (pp20) cc_final: 0.7250 (pp20) REVERT: W 345 GLU cc_start: 0.8225 (mp0) cc_final: 0.7645 (mp0) REVERT: W 488 GLU cc_start: 0.7395 (tp30) cc_final: 0.7012 (tm-30) REVERT: X 341 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8623 (t) REVERT: Y 445 ASN cc_start: 0.8215 (p0) cc_final: 0.8000 (p0) REVERT: Z 244 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.5608 (t80) REVERT: Z 430 MET cc_start: 0.7291 (tpt) cc_final: 0.6968 (tpt) outliers start: 102 outliers final: 79 residues processed: 443 average time/residue: 0.5223 time to fit residues: 393.8088 Evaluate side-chains 426 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 340 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 304 HIS Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 418 LEU Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 469 ASN Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain x residue 573 TRP Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 199 ASN Chi-restraints excluded: chain Y residue 222 SER Chi-restraints excluded: chain Y residue 453 ILE Chi-restraints excluded: chain Y residue 464 ASN Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 265 TYR Chi-restraints excluded: chain Z residue 327 LEU Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 521 optimal weight: 1.9990 chunk 549 optimal weight: 0.9990 chunk 501 optimal weight: 4.9990 chunk 534 optimal weight: 9.9990 chunk 321 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 419 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 482 optimal weight: 9.9990 chunk 505 optimal weight: 2.9990 chunk 532 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS I 269 GLN ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 303 GLN Y 206 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 57942 Z= 0.230 Angle : 0.535 9.181 80434 Z= 0.285 Chirality : 0.037 0.186 9153 Planarity : 0.004 0.058 8462 Dihedral : 21.013 176.180 13187 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.54 % Favored : 97.44 % Rotamer: Outliers : 2.17 % Allowed : 13.85 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.11), residues: 5554 helix: 1.75 (0.10), residues: 2888 sheet: 0.29 (0.22), residues: 518 loop : 0.34 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 20 HIS 0.007 0.001 HIS Y 206 PHE 0.025 0.001 PHE Y 306 TYR 0.014 0.001 TYR W 61 ARG 0.012 0.000 ARG G 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 346 time to evaluate : 4.355 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: F 20 TRP cc_start: 0.6036 (OUTLIER) cc_final: 0.5280 (t60) REVERT: G 183 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7293 (p0) REVERT: I 37 GLN cc_start: 0.7986 (tp40) cc_final: 0.7701 (tp40) REVERT: I 196 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8819 (m-10) REVERT: J 246 GLU cc_start: 0.7404 (tp30) cc_final: 0.6862 (tp30) REVERT: K 196 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8673 (m-80) REVERT: L 64 THR cc_start: 0.8991 (p) cc_final: 0.8767 (p) REVERT: O 304 HIS cc_start: 0.3862 (OUTLIER) cc_final: 0.3318 (p90) REVERT: S 22 THR cc_start: 0.6432 (p) cc_final: 0.6169 (m) REVERT: S 35 GLN cc_start: 0.7937 (mm110) cc_final: 0.7494 (mm-40) REVERT: y 581 GLU cc_start: 0.8070 (pp20) cc_final: 0.7294 (pp20) REVERT: W 345 GLU cc_start: 0.8243 (mp0) cc_final: 0.7658 (mp0) REVERT: W 488 GLU cc_start: 0.7435 (tp30) cc_final: 0.7067 (tm-30) REVERT: X 341 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8658 (t) REVERT: Y 445 ASN cc_start: 0.8159 (p0) cc_final: 0.7955 (p0) REVERT: Z 244 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.5788 (t80) REVERT: Z 430 MET cc_start: 0.7195 (tpt) cc_final: 0.6847 (tpt) outliers start: 106 outliers final: 83 residues processed: 430 average time/residue: 0.5218 time to fit residues: 381.8974 Evaluate side-chains 421 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 331 time to evaluate : 4.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 304 HIS Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 418 LEU Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 469 ASN Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain x residue 573 TRP Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 381 MET Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 199 ASN Chi-restraints excluded: chain Y residue 222 SER Chi-restraints excluded: chain Y residue 453 ILE Chi-restraints excluded: chain Y residue 464 ASN Chi-restraints excluded: chain Y residue 510 VAL Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 265 TYR Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 350 optimal weight: 0.9990 chunk 565 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 392 optimal weight: 8.9990 chunk 592 optimal weight: 3.9990 chunk 545 optimal weight: 0.5980 chunk 472 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 364 optimal weight: 8.9990 chunk 289 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 ASN y 577 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 206 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 463 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 57942 Z= 0.175 Angle : 0.519 13.803 80434 Z= 0.276 Chirality : 0.036 0.208 9153 Planarity : 0.003 0.050 8462 Dihedral : 20.975 177.080 13187 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.20 % Favored : 97.79 % Rotamer: Outliers : 1.98 % Allowed : 14.16 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.11), residues: 5554 helix: 1.81 (0.10), residues: 2886 sheet: 0.35 (0.22), residues: 514 loop : 0.34 (0.14), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 20 HIS 0.007 0.001 HIS Y 206 PHE 0.025 0.001 PHE Y 306 TYR 0.014 0.001 TYR A 73 ARG 0.012 0.000 ARG y 579 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 362 time to evaluate : 4.367 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: F 20 TRP cc_start: 0.5878 (OUTLIER) cc_final: 0.5232 (t60) REVERT: G 183 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7242 (p0) REVERT: I 37 GLN cc_start: 0.7874 (tp40) cc_final: 0.7571 (tp40) REVERT: I 196 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8756 (m-10) REVERT: J 246 GLU cc_start: 0.7382 (tp30) cc_final: 0.7041 (tp30) REVERT: K 196 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8663 (m-80) REVERT: L 64 THR cc_start: 0.8956 (p) cc_final: 0.8731 (p) REVERT: O 304 HIS cc_start: 0.3858 (OUTLIER) cc_final: 0.3357 (p90) REVERT: S 22 THR cc_start: 0.6364 (p) cc_final: 0.6093 (m) REVERT: S 35 GLN cc_start: 0.7927 (mm110) cc_final: 0.7508 (mm-40) REVERT: x 576 GLU cc_start: 0.7128 (pp20) cc_final: 0.6777 (pp20) REVERT: y 581 GLU cc_start: 0.8035 (pp20) cc_final: 0.7269 (pp20) REVERT: W 345 GLU cc_start: 0.8203 (mp0) cc_final: 0.7603 (mp0) REVERT: W 488 GLU cc_start: 0.7401 (tp30) cc_final: 0.7027 (tm-30) REVERT: X 341 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8650 (t) REVERT: Y 445 ASN cc_start: 0.8164 (p0) cc_final: 0.7948 (p0) REVERT: Z 244 PHE cc_start: 0.6330 (OUTLIER) cc_final: 0.5752 (t80) REVERT: Z 430 MET cc_start: 0.7088 (tpt) cc_final: 0.6750 (tpt) REVERT: Z 516 LEU cc_start: 0.8129 (pp) cc_final: 0.7840 (mp) outliers start: 97 outliers final: 82 residues processed: 439 average time/residue: 0.5238 time to fit residues: 391.4669 Evaluate side-chains 429 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 340 time to evaluate : 4.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 235 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 196 PHE Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 263 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 304 HIS Chi-restraints excluded: chain O residue 413 ASP Chi-restraints excluded: chain O residue 414 THR Chi-restraints excluded: chain O residue 418 LEU Chi-restraints excluded: chain O residue 463 VAL Chi-restraints excluded: chain O residue 469 ASN Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain S residue 14 GLU Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain x residue 573 TRP Chi-restraints excluded: chain z residue 572 VAL Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 381 MET Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 485 ASP Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain X residue 408 ILE Chi-restraints excluded: chain Y residue 199 ASN Chi-restraints excluded: chain Y residue 222 SER Chi-restraints excluded: chain Y residue 453 ILE Chi-restraints excluded: chain Y residue 464 ASN Chi-restraints excluded: chain Z residue 244 PHE Chi-restraints excluded: chain Z residue 265 TYR Chi-restraints excluded: chain Z residue 435 TYR Chi-restraints excluded: chain Z residue 449 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 374 optimal weight: 10.0000 chunk 502 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 435 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 472 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 485 optimal weight: 0.7980 chunk 59 optimal weight: 0.0870 chunk 87 optimal weight: 0.0270 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN S 20 ASN y 577 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 200 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.114174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.077548 restraints weight = 138990.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078744 restraints weight = 73816.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.078962 restraints weight = 48120.011| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 57942 Z= 0.145 Angle : 0.509 12.467 80434 Z= 0.270 Chirality : 0.036 0.190 9153 Planarity : 0.003 0.055 8462 Dihedral : 20.896 177.820 13187 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.30 % Favored : 97.68 % Rotamer: Outliers : 1.74 % Allowed : 14.59 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.11), residues: 5554 helix: 1.83 (0.10), residues: 2906 sheet: 0.40 (0.22), residues: 516 loop : 0.33 (0.14), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 20 HIS 0.008 0.001 HIS Y 200 PHE 0.025 0.001 PHE Y 306 TYR 0.014 0.001 TYR A 73 ARG 0.012 0.000 ARG y 579 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9951.18 seconds wall clock time: 177 minutes 35.40 seconds (10655.40 seconds total)