Starting phenix.real_space_refine (version: dev) on Mon Dec 12 05:46:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea4_27972/12_2022/8ea4_27972_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea4_27972/12_2022/8ea4_27972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea4_27972/12_2022/8ea4_27972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea4_27972/12_2022/8ea4_27972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea4_27972/12_2022/8ea4_27972_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea4_27972/12_2022/8ea4_27972_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.022 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 116": "NH1" <-> "NH2" 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 "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 76": "NH1" <-> "NH2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 184": "OE1" <-> "OE2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H GLU 238": "OE1" <-> "OE2" Residue "I GLU 19": "OE1" <-> "OE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I GLU 212": "OE1" <-> "OE2" Residue "I ASP 264": "OD1" <-> "OD2" Residue "I GLU 270": "OE1" <-> "OE2" Residue "J TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 144": "OD1" <-> "OD2" Residue "J GLU 250": "OE1" <-> "OE2" Residue "K TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 250": "OE1" <-> "OE2" Residue "O PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 130": "OE1" <-> "OE2" Residue "O PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 6": "OD1" <-> "OD2" 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 GLU 26": "OE1" <-> "OE2" 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 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 58049 Number of models: 1 Model: "" Number of chains: 46 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: "M" 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: 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: "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: "1" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2010 Classifications: {'DNA': 98} Link IDs: {'rna3p': 97} Chain: "2" 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: "3" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 980 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "4" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 982 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} 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: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 301 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} 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': 23, 'rna3p_pur': 97, 'rna3p_pyr': 90} Link IDs: {'rna2p': 42, 'rna3p': 187} Chain breaks: 2 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: "M" 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: 23.88, per 1000 atoms: 0.41 Number of scatterers: 58049 At special positions: 0 Unit cell: (142.978, 145.112, 316.899, 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 178 16.00 P 531 15.00 Mg 15 11.99 O 12063 8.00 N 10540 7.00 C 34722 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 51904 O5' DT 5 3 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.59 Conformation dependent library (CDL) restraints added in 5.3 seconds 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11018 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 278 helices and 27 sheets defined 51.0% alpha, 9.0% beta 184 base pairs and 323 stacking pairs defined. Time for finding SS restraints: 15.38 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.545A 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: 3.760A pdb=" N PHE A 154 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 160 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.191A pdb=" N ARG A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.728A 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: 3.916A 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: 3.778A pdb=" N PHE B 154 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.947A 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: 3.576A pdb=" N GLU B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.979A 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: 4.003A pdb=" N GLU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 removed outlier: 3.515A 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: 3.581A pdb=" N ASP C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 160 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.193A 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: 3.633A pdb=" N GLU C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.528A 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: 4.051A 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: 3.812A 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 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: 3.806A pdb=" N PHE D 154 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.739A 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: 3.874A pdb=" N ASP D 163 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 3.592A pdb=" N ALA D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 4.103A 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: 3.766A pdb=" N GLU D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 274 removed outlier: 3.793A pdb=" N GLU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 29 removed outlier: 3.525A 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: 3.760A pdb=" N PHE E 154 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.513A 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: 3.959A 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: 3.803A 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: 3.834A pdb=" N ARG F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.873A 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: 3.761A 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: 3.579A pdb=" N ASP F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE F 160 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.198A pdb=" N ARG F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.623A pdb=" N GLU F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.784A 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: 3.765A 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: 3.699A pdb=" N ARG F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 274 removed outlier: 4.206A pdb=" N GLU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 37 through 52 Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.835A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 removed outlier: 3.873A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) 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: 3.759A pdb=" N PHE G 154 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE G 160 " --> pdb=" O VAL G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 182 removed outlier: 4.197A pdb=" N ARG G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.622A pdb=" N GLU G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 184 through 189' Processing helix chain 'G' and resid 201 through 214 removed outlier: 3.766A pdb=" N GLU G 209 " --> pdb=" O LYS G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 237 removed outlier: 4.357A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 258 removed outlier: 3.697A pdb=" N ARG G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 274 removed outlier: 4.205A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 29 Processing helix chain 'H' and resid 37 through 52 removed outlier: 3.573A pdb=" N GLY H 48 " --> pdb=" O ASP H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 76 removed outlier: 3.743A 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 161 removed outlier: 3.800A pdb=" N PHE H 154 " --> pdb=" O PRO H 151 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG H 158 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE H 160 " --> pdb=" O VAL H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 182 removed outlier: 4.195A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 187 No H-bonds generated for 'chain 'H' and resid 184 through 187' Processing helix chain 'H' and resid 201 through 214 removed outlier: 3.524A pdb=" N LYS H 205 " --> pdb=" O GLU H 202 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN H 206 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU H 212 " --> pdb=" O GLU H 209 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN H 213 " --> pdb=" O MET H 210 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET H 214 " --> pdb=" O TRP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 237 removed outlier: 3.549A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 258 removed outlier: 3.803A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 4.218A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 28 Processing helix chain 'I' and resid 37 through 52 Processing helix chain 'I' and resid 66 through 76 removed outlier: 3.582A pdb=" N ARG I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 112 Processing helix chain 'I' and resid 122 through 133 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: 3.758A pdb=" N PHE I 154 " --> pdb=" O PRO I 151 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG I 158 " --> pdb=" O ALA I 155 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP I 159 " --> pdb=" O ASP I 156 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP I 163 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 4.230A pdb=" N ARG I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 removed outlier: 3.883A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 214 removed outlier: 3.664A pdb=" N GLU I 209 " --> pdb=" O LYS I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 237 removed outlier: 3.707A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 258 removed outlier: 3.562A pdb=" N ARG I 258 " --> pdb=" O ARG I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 274 removed outlier: 3.894A pdb=" N GLU I 274 " --> pdb=" O GLU I 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 29 removed outlier: 3.508A pdb=" N GLU J 24 " --> pdb=" O TRP J 20 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 52 removed outlier: 3.523A pdb=" N LYS J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 76 removed outlier: 3.858A pdb=" N ARG J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 112 removed outlier: 3.602A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 135 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: 3.547A pdb=" N PHE J 154 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA J 155 " --> pdb=" O GLU J 152 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP J 159 " --> pdb=" O ASP J 156 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP J 163 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 4.020A pdb=" N ARG J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 removed outlier: 3.553A pdb=" N GLU J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 3.965A 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 Processing helix chain 'J' and resid 227 through 237 Processing helix chain 'J' and resid 241 through 258 removed outlier: 3.787A pdb=" N GLU J 246 " --> pdb=" O GLY J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 274 removed outlier: 3.758A pdb=" N GLU J 270 " --> pdb=" O ALA J 266 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU J 274 " --> pdb=" O GLU J 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 29 removed outlier: 3.631A pdb=" N GLU K 24 " --> pdb=" O TRP K 20 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA K 26 " --> pdb=" O GLN K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 52 removed outlier: 3.692A pdb=" N GLY K 48 " --> pdb=" O ASP K 44 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS K 51 " --> pdb=" O ASP K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 75 Processing helix chain 'K' and resid 102 through 112 removed outlier: 3.611A pdb=" N PHE K 106 " --> pdb=" O PRO K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 135 removed outlier: 3.656A pdb=" N ASP K 127 " --> pdb=" O SER K 123 " (cutoff:3.500A) 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 151 through 163 removed outlier: 3.784A pdb=" N PHE K 154 " --> pdb=" O PRO K 151 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG K 158 " --> pdb=" O ALA K 155 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP K 159 " --> pdb=" O ASP K 156 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU K 162 " --> pdb=" O ASP K 159 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP K 163 " --> pdb=" O ILE K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 182 removed outlier: 3.572A pdb=" N ALA K 178 " --> pdb=" O ASP K 174 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 189 removed outlier: 3.571A pdb=" N GLU K 188 " --> pdb=" O GLU K 184 " (cutoff:3.500A) removed outlier: 3.889A 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 removed outlier: 3.500A pdb=" N LYS K 205 " --> pdb=" O GLY K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 237 removed outlier: 4.003A 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: 4.398A pdb=" N GLU K 274 " --> pdb=" O GLU K 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 29 removed outlier: 3.699A pdb=" N GLU L 24 " --> pdb=" O TRP L 20 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA L 26 " --> pdb=" O GLN L 22 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU L 28 " --> pdb=" O GLU L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 52 Processing helix chain 'L' and resid 66 through 76 removed outlier: 3.857A pdb=" N ARG L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) 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: 3.590A pdb=" N PHE L 154 " --> pdb=" O PRO L 151 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP L 159 " --> pdb=" O ASP L 156 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP L 163 " --> pdb=" O ILE L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 182 removed outlier: 4.110A pdb=" N ARG L 182 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 removed outlier: 3.553A pdb=" N GLU L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 189' Processing helix chain 'L' and resid 201 through 214 Processing helix chain 'L' and resid 227 through 237 removed outlier: 3.696A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 257 Processing helix chain 'L' and resid 265 through 274 removed outlier: 3.631A pdb=" N GLU L 274 " --> pdb=" O GLU L 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 29 removed outlier: 3.522A pdb=" N ALA M 26 " --> pdb=" O GLN M 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG M 27 " --> pdb=" O ALA M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 52 removed outlier: 4.026A pdb=" N GLY M 48 " --> pdb=" O ASP M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 76 Processing helix chain 'M' and resid 102 through 112 Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 146 through 148 No H-bonds generated for 'chain 'M' and resid 146 through 148' Processing helix chain 'M' and resid 151 through 163 removed outlier: 3.784A pdb=" N PHE M 154 " --> pdb=" O PRO M 151 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE M 160 " --> pdb=" O VAL M 157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP M 163 " --> pdb=" O ILE M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 182 removed outlier: 4.054A pdb=" N ARG M 182 " --> pdb=" O ALA M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 189 removed outlier: 3.763A pdb=" N ARG M 189 " --> pdb=" O GLN M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 214 Processing helix chain 'M' and resid 227 through 237 removed outlier: 3.721A pdb=" N ILE M 232 " --> pdb=" O GLU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 258 Processing helix chain 'M' and resid 265 through 274 removed outlier: 4.094A pdb=" N GLU M 274 " --> pdb=" O GLU M 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: 3.515A pdb=" N LEU O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 51 removed outlier: 4.699A pdb=" N GLU O 46 " --> pdb=" O PRO O 43 " (cutoff:3.500A) 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: 3.905A 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: 4.248A 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: 3.723A pdb=" N LYS O 199 " --> pdb=" O TYR O 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 231 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: 4.904A 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: 3.708A pdb=" N GLN O 495 " --> pdb=" O ARG O 492 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU O 498 " --> pdb=" O GLN O 495 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER O 499 " --> pdb=" O GLN O 496 " (cutoff:3.500A) removed outlier: 3.571A 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: 4.032A 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: 3.837A 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: 4.053A pdb=" N VAL Q 50 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU Q 54 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 74 removed outlier: 3.607A pdb=" N VAL Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 84 removed outlier: 3.651A pdb=" N GLN Q 83 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) removed outlier: 3.915A 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: 3.871A pdb=" N ALA Q 162 " --> pdb=" O ALA Q 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 15 removed outlier: 3.528A pdb=" N GLU S 14 " --> pdb=" O LYS S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 43 removed outlier: 4.085A pdb=" N GLY S 41 " --> pdb=" O ASN S 37 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS S 42 " --> pdb=" O HIS S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 50 through 73 removed outlier: 3.509A pdb=" N ARG S 54 " --> pdb=" O HIS S 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY S 55 " --> pdb=" O HIS S 51 " (cutoff:3.500A) removed outlier: 3.520A 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 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: 3.772A 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: 3.668A pdb=" N GLY W 318 " --> pdb=" O SER W 315 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL W 319 " --> pdb=" O GLU W 316 " (cutoff:3.500A) removed outlier: 4.610A 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: 3.918A 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: 6.017A pdb=" N VAL X 44 " --> pdb=" O GLU X 40 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS X 45 " --> pdb=" O GLU X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 71 removed outlier: 4.178A 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: 4.034A pdb=" N LYS X 71 " --> pdb=" O GLU X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 94 removed outlier: 8.135A pdb=" N LEU X 91 " --> pdb=" O GLU X 87 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL X 92 " --> pdb=" O GLN X 88 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY X 93 " --> pdb=" O ASP X 89 " (cutoff:3.500A) removed outlier: 4.039A 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: 4.020A 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 314 through 316 No H-bonds generated for 'chain 'X' and resid 314 through 316' 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: 3.823A 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 405 through 409 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: 3.747A 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: 5.070A 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: 3.788A 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: 3.577A pdb=" N GLU Z 509 " --> pdb=" O LEU Z 506 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP Z 514 " --> pdb=" O VAL Z 511 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL Z 517 " --> pdb=" O ASP Z 514 " (cutoff:3.500A) Processing helix chain 'w' and resid 575 through 581 Processing helix chain 'x' and resid 575 through 581 removed outlier: 3.615A pdb=" N ARG x 579 " --> pdb=" O TYR x 575 " (cutoff:3.500A) Processing helix chain 'y' and resid 575 through 581 Processing helix chain 'z' and resid 575 through 581 removed outlier: 3.627A pdb=" N ARG z 579 " --> pdb=" O TYR z 575 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.728A 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: 6.947A 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: 6.729A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE C 196 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.957A 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: 6.811A 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: 6.948A 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: 6.576A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE E 196 " --> pdb=" O ARG E 57 " (cutoff:3.500A) removed outlier: 6.918A 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: 6.570A 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: 6.571A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N PHE G 196 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 6.946A 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 196 removed outlier: 6.777A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE H 196 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL H 59 " --> pdb=" O PHE H 196 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 193 through 196 removed outlier: 6.847A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE I 196 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 6.947A 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: 6.729A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N PHE J 196 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 7.020A 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: 6.749A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE K 196 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 6.645A 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: 6.780A pdb=" N ARG L 57 " --> pdb=" O LEU L 194 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE L 196 " --> pdb=" O ARG L 57 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL L 59 " --> pdb=" O PHE L 196 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 193 through 196 removed outlier: 6.786A pdb=" N ARG M 57 " --> pdb=" O LEU M 194 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N PHE M 196 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL M 59 " --> pdb=" O PHE M 196 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'O' and resid 314 through 316 removed outlier: 4.833A pdb=" N LEU O 371 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN O 351 " --> pdb=" O CYS O 376 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP O 378 " --> pdb=" O LEU O 349 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU O 349 " --> pdb=" O ASP O 378 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'O' and resid 291 through 295 Processing sheet with id= P, first strand: chain 'O' and resid 607 through 611 removed outlier: 3.581A pdb=" N GLY O 611 " --> pdb=" O LEU O 545 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER O 542 " --> pdb=" O ILE O 447 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA O 473 " --> pdb=" O VAL O 463 " (cutoff:3.500A) removed outlier: 6.384A 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= Q, first strand: chain 'W' and resid 184 through 186 Processing sheet with id= R, 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: 4.418A pdb=" N ILE W 240 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR W 227 " --> pdb=" O ILE W 240 " (cutoff:3.500A) removed outlier: 4.356A 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: 3.580A 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: 8.191A pdb=" N CYS W 204 " --> pdb=" O HIS W 283 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR W 285 " --> pdb=" O CYS W 204 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N HIS W 206 " --> pdb=" O TYR W 285 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL W 307 " --> pdb=" O PHE W 284 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR W 286 " --> pdb=" O VAL W 307 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N HIS W 309 " --> pdb=" O THR W 286 " (cutoff:3.500A) Processing sheet with id= S, 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: 5.874A pdb=" N ARG W 460 " --> pdb=" O PHE W 468 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE W 468 " --> pdb=" O ARG W 460 " (cutoff:3.500A) removed outlier: 6.164A 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: 3.745A pdb=" N ARG W 432 " --> pdb=" O HIS W 473 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 184 through 186 Processing sheet with id= U, first strand: chain 'X' and resid 237 through 243 removed outlier: 6.526A pdb=" N VAL X 229 " --> pdb=" O MET X 238 " (cutoff:3.500A) removed outlier: 4.447A 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: 4.421A pdb=" N LEU X 242 " --> pdb=" O TRP X 225 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP X 225 " --> pdb=" O LEU X 242 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR X 228 " --> pdb=" O ASP X 205 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP X 205 " --> pdb=" O THR X 228 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS X 283 " --> pdb=" O TRP X 202 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N CYS X 204 " --> pdb=" O HIS X 283 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR X 285 " --> pdb=" O CYS X 204 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N HIS X 206 " --> pdb=" O TYR X 285 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL X 307 " --> pdb=" O PHE X 284 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR X 286 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS X 309 " --> pdb=" O THR X 286 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 411 through 413 removed outlier: 6.012A 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: 6.030A pdb=" N GLU X 462 " --> pdb=" O GLU X 466 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU X 466 " --> pdb=" O GLU X 462 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 423 through 426 Processing sheet with id= X, first strand: chain 'Y' and resid 236 through 243 removed outlier: 3.510A pdb=" N CYS Y 236 " --> pdb=" O ASP Y 231 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL Y 229 " --> pdb=" O MET Y 238 " (cutoff:3.500A) removed outlier: 4.551A 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: 6.866A 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: 8.231A pdb=" N CYS Y 204 " --> pdb=" O HIS Y 283 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR Y 285 " --> pdb=" O CYS Y 204 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N HIS Y 206 " --> pdb=" O TYR Y 285 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL Y 307 " --> pdb=" O PHE Y 284 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Y' and resid 411 through 413 removed outlier: 3.596A 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: 5.508A pdb=" N PHE Y 468 " --> pdb=" O ARG Y 460 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU Y 462 " --> pdb=" O GLU Y 466 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLU Y 466 " --> pdb=" O GLU Y 462 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N MET Y 430 " --> pdb=" O GLN Y 475 " (cutoff:3.500A) Processing sheet with id= Z, 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: 4.476A pdb=" N ILE Z 240 " --> pdb=" O THR Z 227 " (cutoff:3.500A) removed outlier: 6.681A 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: 6.756A 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: 7.642A 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: 8.572A 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= AA, 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: 6.026A pdb=" N ARG Z 460 " --> pdb=" O PHE Z 468 " (cutoff:3.500A) removed outlier: 5.722A 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) 2012 hydrogen bonds defined for protein. 5466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 445 hydrogen bonds 862 hydrogen bond angles 0 basepair planarities 184 basepair parallelities 323 stacking parallelities Total time for adding SS restraints: 19.89 Time building geometry restraints manager: 22.31 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: 8502 1.29 - 1.42: 17420 1.42 - 1.56: 32832 1.56 - 1.69: 1051 1.69 - 1.83: 262 Bond restraints: 60067 Sorted by residual: bond pdb=" C VAL B 186 " pdb=" O VAL B 186 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.10e-02 8.26e+03 5.59e+01 bond pdb=" C GLU B 184 " pdb=" O GLU B 184 " ideal model delta sigma weight residual 1.236 1.151 0.085 1.18e-02 7.18e+03 5.22e+01 bond pdb=" C GLN F 38 " pdb=" O GLN F 38 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.19e-02 7.06e+03 5.20e+01 bond pdb=" C GLN A 38 " pdb=" O GLN A 38 " ideal model delta sigma weight residual 1.237 1.152 0.085 1.19e-02 7.06e+03 5.06e+01 bond pdb=" C GLN G 38 " pdb=" O GLN G 38 " ideal model delta sigma weight residual 1.237 1.152 0.085 1.19e-02 7.06e+03 5.05e+01 ... (remaining 60062 not shown) Histogram of bond angle deviations from ideal: 96.31 - 104.19: 2309 104.19 - 112.07: 28071 112.07 - 119.96: 28261 119.96 - 127.84: 23499 127.84 - 135.72: 1156 Bond angle restraints: 83296 Sorted by residual: angle pdb=" C GLN X 425 " pdb=" CA GLN X 425 " pdb=" CB GLN X 425 " ideal model delta sigma weight residual 109.37 135.54 -26.17 1.83e+00 2.99e-01 2.05e+02 angle pdb=" C ARG Y 223 " pdb=" N PRO Y 224 " pdb=" CA PRO Y 224 " ideal model delta sigma weight residual 120.14 130.19 -10.05 1.06e+00 8.90e-01 8.98e+01 angle pdb=" C3' G 7 230 " pdb=" O3' G 7 230 " pdb=" P G 7 231 " ideal model delta sigma weight residual 120.20 107.09 13.11 1.50e+00 4.44e-01 7.64e+01 angle pdb=" N VAL L 208 " pdb=" CA VAL L 208 " pdb=" C VAL L 208 " ideal model delta sigma weight residual 110.42 102.49 7.93 9.60e-01 1.09e+00 6.82e+01 angle pdb=" N VAL L 215 " pdb=" CA VAL L 215 " pdb=" C VAL L 215 " ideal model delta sigma weight residual 111.56 118.66 -7.10 8.60e-01 1.35e+00 6.82e+01 ... (remaining 83291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 33531 35.55 - 71.10: 1481 71.10 - 106.65: 95 106.65 - 142.20: 7 142.20 - 177.75: 9 Dihedral angle restraints: 35123 sinusoidal: 18084 harmonic: 17039 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 33.91 -68.91 1 8.00e+00 1.56e-02 9.60e+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 89.14 -89.14 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 29.37 -64.37 1 8.00e+00 1.56e-02 8.51e+01 ... (remaining 35120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 9271 0.215 - 0.431: 200 0.431 - 0.646: 1 0.646 - 0.861: 1 0.861 - 1.077: 1 Chirality restraints: 9474 Sorted by residual: chirality pdb=" CA GLU L 24 " pdb=" N GLU L 24 " pdb=" C GLU L 24 " pdb=" CB GLU L 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 L 22 " pdb=" N GLN L 22 " pdb=" C GLN L 22 " pdb=" CB GLN L 22 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA LEU W 477 " pdb=" N LEU W 477 " pdb=" C LEU W 477 " pdb=" CB LEU W 477 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 9471 not shown) Planarity restraints: 8821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 7 174 " 0.359 2.00e-02 2.50e+03 1.44e-01 6.26e+02 pdb=" N9 G 7 174 " -0.063 2.00e-02 2.50e+03 pdb=" C8 G 7 174 " -0.084 2.00e-02 2.50e+03 pdb=" N7 G 7 174 " -0.117 2.00e-02 2.50e+03 pdb=" C5 G 7 174 " -0.089 2.00e-02 2.50e+03 pdb=" C6 G 7 174 " 0.045 2.00e-02 2.50e+03 pdb=" O6 G 7 174 " 0.194 2.00e-02 2.50e+03 pdb=" N1 G 7 174 " 0.099 2.00e-02 2.50e+03 pdb=" C2 G 7 174 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G 7 174 " -0.081 2.00e-02 2.50e+03 pdb=" N3 G 7 174 " -0.116 2.00e-02 2.50e+03 pdb=" C4 G 7 174 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA 1 62 " 0.323 2.00e-02 2.50e+03 1.41e-01 5.46e+02 pdb=" N9 DA 1 62 " -0.033 2.00e-02 2.50e+03 pdb=" C8 DA 1 62 " -0.087 2.00e-02 2.50e+03 pdb=" N7 DA 1 62 " -0.108 2.00e-02 2.50e+03 pdb=" C5 DA 1 62 " -0.087 2.00e-02 2.50e+03 pdb=" C6 DA 1 62 " 0.036 2.00e-02 2.50e+03 pdb=" N6 DA 1 62 " 0.197 2.00e-02 2.50e+03 pdb=" N1 DA 1 62 " 0.083 2.00e-02 2.50e+03 pdb=" C2 DA 1 62 " -0.056 2.00e-02 2.50e+03 pdb=" N3 DA 1 62 " -0.138 2.00e-02 2.50e+03 pdb=" C4 DA 1 62 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT 3 -1 " 0.139 2.00e-02 2.50e+03 1.15e-01 3.29e+02 pdb=" N1 DT 3 -1 " 0.058 2.00e-02 2.50e+03 pdb=" C2 DT 3 -1 " -0.012 2.00e-02 2.50e+03 pdb=" O2 DT 3 -1 " -0.250 2.00e-02 2.50e+03 pdb=" N3 DT 3 -1 " 0.115 2.00e-02 2.50e+03 pdb=" C4 DT 3 -1 " 0.077 2.00e-02 2.50e+03 pdb=" O4 DT 3 -1 " 0.068 2.00e-02 2.50e+03 pdb=" C5 DT 3 -1 " -0.019 2.00e-02 2.50e+03 pdb=" C7 DT 3 -1 " -0.147 2.00e-02 2.50e+03 pdb=" C6 DT 3 -1 " -0.028 2.00e-02 2.50e+03 ... (remaining 8818 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 61 1.88 - 2.64: 1072 2.64 - 3.39: 75293 3.39 - 4.15: 149754 4.15 - 4.90: 247068 Nonbonded interactions: 473248 Sorted by model distance: nonbonded pdb=" NH1 ARG O 300 " pdb=" N2 G 7 86 " model vdw 1.131 3.200 nonbonded pdb=" CZ ARG L 191 " pdb=" NH2 ARG M 243 " model vdw 1.265 3.350 nonbonded pdb=" NE2 HIS O 503 " pdb=" OP1 U 7 242 " model vdw 1.373 2.520 nonbonded pdb=" OE1 GLN X 330 " pdb=" OH TYR X 368 " model vdw 1.421 2.440 nonbonded pdb=" OG1 THR G 67 " pdb="MG MG G 301 " model vdw 1.432 2.170 ... (remaining 473243 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)) selection = (chain '5' and (resid 1 through 11 or resid 13 through 18 or resid 20 through 25 \ or resid 27)) } 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' selection = chain 'M' } 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 531 5.49 5 Mg 15 5.21 5 S 178 5.16 5 C 34722 2.51 5 N 10540 2.21 5 O 12063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.160 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: 0.050 Extract box with map and model: 34.130 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.370 Process input model: 124.770 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:9.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 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 0.087 60067 Z= 0.848 Angle : 1.628 26.173 83296 Z= 1.135 Chirality : 0.084 1.077 9474 Planarity : 0.020 0.494 8821 Dihedral : 16.782 177.746 24105 Min Nonbonded Distance : 1.131 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.22 % 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: -1.13 (0.10), residues: 5809 helix: -1.21 (0.08), residues: 3036 sheet: 0.30 (0.20), residues: 584 loop : -0.01 (0.13), residues: 2189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 879 time to evaluate : 4.826 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 outliers start: 11 outliers final: 7 residues processed: 884 average time/residue: 1.5505 time to fit residues: 1689.6510 Evaluate side-chains 312 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 305 time to evaluate : 4.890 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 2 average time/residue: 0.5725 time to fit residues: 8.1118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 522 optimal weight: 0.6980 chunk 469 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 316 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 485 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 361 optimal weight: 7.9990 chunk 562 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN C 22 GLN D 37 GLN D 269 GLN E 22 GLN E 97 HIS E 213 GLN F 213 GLN F 269 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS M 37 GLN ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 269 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 370 HIS ** O 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 HIS W 463 ASN ** Z 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 464 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 60067 Z= 0.239 Angle : 0.701 13.450 83296 Z= 0.368 Chirality : 0.040 0.202 9474 Planarity : 0.005 0.089 8821 Dihedral : 17.907 177.771 11960 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.11), residues: 5809 helix: 0.70 (0.09), residues: 3051 sheet: 0.64 (0.20), residues: 588 loop : 0.46 (0.14), residues: 2170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 345 time to evaluate : 4.846 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 outliers start: 103 outliers final: 34 residues processed: 423 average time/residue: 1.3850 time to fit residues: 748.1358 Evaluate side-chains 265 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 231 time to evaluate : 4.828 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 30 residues processed: 5 average time/residue: 0.8441 time to fit residues: 12.1880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 312 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 467 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 563 optimal weight: 0.9980 chunk 608 optimal weight: 10.0000 chunk 501 optimal weight: 8.9990 chunk 558 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 451 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 185 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS K 269 GLN ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 321 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 603 GLN Q 24 HIS ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 465 GLN Y 299 GLN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.084 60067 Z= 0.353 Angle : 0.677 10.839 83296 Z= 0.353 Chirality : 0.039 0.187 9474 Planarity : 0.005 0.060 8821 Dihedral : 18.100 179.277 11960 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 2.36 % 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: 1.08 (0.11), residues: 5809 helix: 1.15 (0.09), residues: 3040 sheet: 0.24 (0.22), residues: 533 loop : 0.44 (0.14), residues: 2236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 252 time to evaluate : 5.264 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 outliers start: 121 outliers final: 45 residues processed: 357 average time/residue: 1.3234 time to fit residues: 610.5061 Evaluate side-chains 241 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 196 time to evaluate : 4.840 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 41 residues processed: 5 average time/residue: 0.6457 time to fit residues: 11.2625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 556 optimal weight: 0.0170 chunk 423 optimal weight: 0.8980 chunk 292 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 268 optimal weight: 0.6980 chunk 378 optimal weight: 6.9990 chunk 565 optimal weight: 10.0000 chunk 598 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 535 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 463 ASN Y 295 ASN Y 299 GLN ** Z 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 60067 Z= 0.162 Angle : 0.567 10.435 83296 Z= 0.297 Chirality : 0.037 0.206 9474 Planarity : 0.004 0.100 8821 Dihedral : 18.062 178.954 11960 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 1.80 % 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: 1.45 (0.11), residues: 5809 helix: 1.45 (0.09), residues: 3049 sheet: 0.43 (0.19), residues: 655 loop : 0.61 (0.15), residues: 2105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 244 time to evaluate : 5.104 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 outliers start: 92 outliers final: 47 residues processed: 320 average time/residue: 1.2972 time to fit residues: 539.0389 Evaluate side-chains 247 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 200 time to evaluate : 4.861 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 41 residues processed: 8 average time/residue: 0.8830 time to fit residues: 16.2206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 498 optimal weight: 10.0000 chunk 339 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 445 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 510 optimal weight: 30.0000 chunk 413 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 chunk 537 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 HIS K 97 HIS L 213 GLN ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 367 ASN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 425 GLN ** X 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 60067 Z= 0.167 Angle : 0.556 11.522 83296 Z= 0.288 Chirality : 0.036 0.183 9474 Planarity : 0.003 0.047 8821 Dihedral : 18.058 179.391 11960 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.74 % 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: 1.59 (0.11), residues: 5809 helix: 1.59 (0.10), residues: 3025 sheet: 0.47 (0.19), residues: 660 loop : 0.64 (0.14), residues: 2124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 231 time to evaluate : 4.991 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 outliers start: 89 outliers final: 50 residues processed: 305 average time/residue: 1.3022 time to fit residues: 516.3733 Evaluate side-chains 241 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 191 time to evaluate : 4.863 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 48 residues processed: 3 average time/residue: 0.5470 time to fit residues: 8.9695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 201 optimal weight: 4.9990 chunk 538 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 351 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 598 optimal weight: 10.0000 chunk 497 optimal weight: 7.9990 chunk 277 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 314 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS M 38 GLN ** M 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 GLN O 102 GLN O 269 GLN ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 500 HIS ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN ** S 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 60067 Z= 0.348 Angle : 0.663 16.120 83296 Z= 0.342 Chirality : 0.039 0.175 9474 Planarity : 0.005 0.062 8821 Dihedral : 18.403 179.992 11960 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 2.17 % 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: 1.33 (0.11), residues: 5809 helix: 1.46 (0.09), residues: 3040 sheet: 0.27 (0.21), residues: 538 loop : 0.40 (0.14), residues: 2231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 196 time to evaluate : 4.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 60 residues processed: 293 average time/residue: 1.2485 time to fit residues: 481.4288 Evaluate side-chains 235 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 175 time to evaluate : 4.870 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 56 residues processed: 5 average time/residue: 0.5474 time to fit residues: 10.8568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 577 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 341 optimal weight: 0.8980 chunk 437 optimal weight: 3.9990 chunk 338 optimal weight: 6.9990 chunk 504 optimal weight: 20.0000 chunk 334 optimal weight: 7.9990 chunk 596 optimal weight: 9.9990 chunk 373 optimal weight: 10.0000 chunk 363 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN I 38 GLN ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** L 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 GLN O 269 GLN ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 484 ASN O 496 GLN O 522 HIS Q 34 HIS ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 137 GLN W 508 GLN X 123 ASN X 167 GLN X 344 GLN ** X 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 475 GLN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.084 60067 Z= 0.388 Angle : 0.675 12.576 83296 Z= 0.351 Chirality : 0.040 0.189 9474 Planarity : 0.005 0.078 8821 Dihedral : 18.816 177.604 11960 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.11), residues: 5809 helix: 1.33 (0.09), residues: 3027 sheet: 0.11 (0.21), residues: 542 loop : 0.28 (0.14), residues: 2240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 192 time to evaluate : 4.913 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 outliers start: 108 outliers final: 63 residues processed: 289 average time/residue: 1.2514 time to fit residues: 477.8234 Evaluate side-chains 236 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 173 time to evaluate : 4.875 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 60 residues processed: 5 average time/residue: 0.6779 time to fit residues: 11.4428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 369 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 356 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 379 optimal weight: 1.9990 chunk 406 optimal weight: 7.9990 chunk 294 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 468 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 375 GLN ** X 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 60067 Z= 0.200 Angle : 0.603 16.096 83296 Z= 0.312 Chirality : 0.038 0.192 9474 Planarity : 0.004 0.049 8821 Dihedral : 18.757 178.932 11960 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.62 % 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: 1.47 (0.11), residues: 5809 helix: 1.58 (0.09), residues: 3021 sheet: 0.40 (0.20), residues: 661 loop : 0.45 (0.14), residues: 2127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 195 time to evaluate : 5.101 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 outliers start: 83 outliers final: 63 residues processed: 273 average time/residue: 1.3422 time to fit residues: 478.4869 Evaluate side-chains 241 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 178 time to evaluate : 4.908 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 60 residues processed: 3 average time/residue: 0.4761 time to fit residues: 8.7944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 542 optimal weight: 9.9990 chunk 571 optimal weight: 10.0000 chunk 521 optimal weight: 3.9990 chunk 555 optimal weight: 0.7980 chunk 334 optimal weight: 9.9990 chunk 242 optimal weight: 4.9990 chunk 436 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 502 optimal weight: 9.9990 chunk 525 optimal weight: 0.0970 chunk 554 optimal weight: 20.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 60067 Z= 0.306 Angle : 0.655 15.131 83296 Z= 0.336 Chirality : 0.039 0.217 9474 Planarity : 0.004 0.050 8821 Dihedral : 18.807 178.344 11960 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.11), residues: 5809 helix: 1.54 (0.09), residues: 3020 sheet: 0.32 (0.20), residues: 661 loop : 0.39 (0.14), residues: 2128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 180 time to evaluate : 4.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 63 residues processed: 250 average time/residue: 1.2935 time to fit residues: 427.0078 Evaluate side-chains 234 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 171 time to evaluate : 4.913 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 60 residues processed: 3 average time/residue: 0.4826 time to fit residues: 8.9108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 365 optimal weight: 10.0000 chunk 587 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 408 optimal weight: 5.9990 chunk 616 optimal weight: 10.0000 chunk 567 optimal weight: 1.9990 chunk 491 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 379 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN G 223 ASN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 GLN ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN K 97 HIS ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 269 GLN ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 430 ASN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 299 GLN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 295 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.098 60067 Z= 0.395 Angle : 0.732 15.072 83296 Z= 0.376 Chirality : 0.041 0.212 9474 Planarity : 0.005 0.071 8821 Dihedral : 19.106 178.906 11960 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.11), residues: 5809 helix: 1.25 (0.09), residues: 3035 sheet: 0.13 (0.18), residues: 742 loop : 0.24 (0.15), residues: 2032 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11618 Ramachandran restraints generated. 5809 Oldfield, 0 Emsley, 5809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 174 time to evaluate : 5.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 64 residues processed: 240 average time/residue: 1.2511 time to fit residues: 398.7239 Evaluate side-chains 230 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 166 time to evaluate : 4.869 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 61 residues processed: 4 average time/residue: 0.8867 time to fit residues: 11.2788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 390 optimal weight: 0.3980 chunk 523 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 452 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 491 optimal weight: 20.0000 chunk 205 optimal weight: 0.7980 chunk 505 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 ASN O 269 GLN ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.061709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.041555 restraints weight = 329687.784| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 4.36 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 60067 Z= 0.174 Angle : 0.639 13.686 83296 Z= 0.327 Chirality : 0.038 0.221 9474 Planarity : 0.004 0.069 8821 Dihedral : 18.930 179.711 11960 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.11), residues: 5809 helix: 1.58 (0.10), residues: 3007 sheet: 0.37 (0.20), residues: 683 loop : 0.41 (0.15), residues: 2119 =============================================================================== Job complete usr+sys time: 11512.92 seconds wall clock time: 204 minutes 26.21 seconds (12266.21 seconds total)