Starting phenix.real_space_refine on Wed Feb 14 04:22:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea4_27972/02_2024/8ea4_27972_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea4_27972/02_2024/8ea4_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_27972/02_2024/8ea4_27972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea4_27972/02_2024/8ea4_27972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea4_27972/02_2024/8ea4_27972_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea4_27972/02_2024/8ea4_27972_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 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. 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 23.49, per 1000 atoms: 0.40 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: 21.23 Conformation dependent library (CDL) restraints added in 6.3 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: 19.75 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: 20.29 Time building geometry restraints manager: 22.94 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: 34410 35.55 - 71.10: 2075 71.10 - 106.65: 157 106.65 - 142.20: 7 142.20 - 177.75: 9 Dihedral angle restraints: 36658 sinusoidal: 19619 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 36655 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 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: 7.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 32.010 Check model and map are aligned: 0.680 Set scattering table: 0.440 Process input model: 135.150 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 191.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 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 : 18.837 177.746 25640 Min Nonbonded Distance : 1.131 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 0.21 % Allowed : 1.39 % Favored : 98.40 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.216 0.023 TRP H 20 HIS 0.019 0.002 HIS X 258 PHE 0.088 0.010 PHE O 45 TYR 0.146 0.018 TYR I 112 ARG 0.020 0.001 ARG Z 235 *********************** 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 : 4.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 159 ASP cc_start: 0.5668 (t70) cc_final: 0.5199 (t0) REVERT: Y 381 MET cc_start: -0.2101 (mtt) cc_final: -0.3841 (ttm) REVERT: Z 238 MET cc_start: 0.1992 (mmp) cc_final: 0.1211 (tpt) outliers start: 11 outliers final: 7 residues processed: 884 average time/residue: 1.6443 time to fit residues: 1781.0392 Evaluate side-chains 312 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 305 time to evaluate : 4.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain Y residue 463 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 269 GLN E 22 GLN E 97 HIS 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 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 60067 Z= 0.244 Angle : 0.700 13.425 83296 Z= 0.367 Chirality : 0.040 0.193 9474 Planarity : 0.005 0.067 8821 Dihedral : 20.926 176.606 13511 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.03 % Allowed : 10.14 % Favored : 87.83 % 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: 0.81 (0.11), residues: 5809 helix: 0.71 (0.09), residues: 3053 sheet: 0.62 (0.20), residues: 597 loop : 0.51 (0.14), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP y 573 HIS 0.009 0.001 HIS I 97 PHE 0.030 0.002 PHE Q 158 TYR 0.024 0.002 TYR A 112 ARG 0.011 0.001 ARG C 116 *********************** 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 453 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 349 time to evaluate : 4.716 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: C 105 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8136 (tm) REVERT: G 159 ASP cc_start: 0.5449 (t0) cc_final: 0.5069 (t0) REVERT: Y 381 MET cc_start: -0.1903 (mtt) cc_final: -0.3956 (ttm) outliers start: 104 outliers final: 34 residues processed: 428 average time/residue: 1.4377 time to fit residues: 778.9088 Evaluate side-chains 270 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 235 time to evaluate : 4.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain O residue 291 MET Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain W residue 506 LEU Chi-restraints excluded: chain X residue 231 ASP Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain Z residue 306 PHE Chi-restraints excluded: chain Z residue 464 ASN Chi-restraints excluded: chain y residue 572 VAL 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: 0.7980 chunk 155 optimal weight: 3.9990 chunk 563 optimal weight: 3.9990 chunk 608 optimal weight: 20.0000 chunk 501 optimal weight: 0.0030 chunk 558 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 451 optimal weight: 1.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 22 GLN D 213 GLN G 193 HIS ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS L 213 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 465 GLN ** Z 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 464 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 60067 Z= 0.227 Angle : 0.598 11.168 83296 Z= 0.315 Chirality : 0.038 0.186 9474 Planarity : 0.004 0.056 8821 Dihedral : 20.851 179.054 13497 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.84 % Allowed : 11.19 % Favored : 86.97 % 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: 1.27 (0.11), residues: 5809 helix: 1.25 (0.09), residues: 3054 sheet: 0.29 (0.20), residues: 656 loop : 0.64 (0.14), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP y 573 HIS 0.008 0.001 HIS I 97 PHE 0.032 0.002 PHE Z 387 TYR 0.016 0.001 TYR y 582 ARG 0.012 0.000 ARG X 493 *********************** 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 361 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 267 time to evaluate : 4.805 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: Z 238 MET cc_start: 0.1815 (OUTLIER) cc_final: 0.1122 (tpt) outliers start: 94 outliers final: 43 residues processed: 349 average time/residue: 1.3864 time to fit residues: 619.0351 Evaluate side-chains 255 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 211 time to evaluate : 4.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 506 LEU Chi-restraints excluded: chain X residue 463 ASN Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain Z residue 238 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 556 optimal weight: 10.0000 chunk 423 optimal weight: 0.0870 chunk 292 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 378 optimal weight: 7.9990 chunk 565 optimal weight: 20.0000 chunk 598 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 535 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 overall best weight: 2.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN G 213 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 GLN ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 321 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 500 HIS Q 24 HIS ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 60067 Z= 0.333 Angle : 0.643 10.377 83296 Z= 0.337 Chirality : 0.039 0.350 9474 Planarity : 0.004 0.049 8821 Dihedral : 21.004 178.644 13497 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.25 % Allowed : 11.29 % Favored : 86.46 % 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: 1.28 (0.11), residues: 5809 helix: 1.36 (0.09), residues: 3050 sheet: 0.32 (0.21), residues: 539 loop : 0.45 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP y 573 HIS 0.009 0.001 HIS I 97 PHE 0.027 0.002 PHE A 190 TYR 0.025 0.002 TYR x 582 ARG 0.014 0.001 ARG W 535 *********************** 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 339 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 224 time to evaluate : 4.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7252 (ttp80) REVERT: G 38 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6773 (tm-30) REVERT: J 150 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7704 (ttmm) REVERT: L 196 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6639 (m-10) REVERT: Y 381 MET cc_start: -0.1555 (mtt) cc_final: -0.3627 (ttm) REVERT: Z 238 MET cc_start: 0.1805 (mmt) cc_final: 0.1594 (mmt) outliers start: 115 outliers final: 42 residues processed: 322 average time/residue: 1.3128 time to fit residues: 547.3436 Evaluate side-chains 241 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 4.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain W residue 405 ASP Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain w residue 574 ASP Chi-restraints excluded: chain y residue 572 VAL Chi-restraints excluded: chain y residue 574 ASP 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: 0.5980 chunk 8 optimal weight: 0.6980 chunk 445 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 chunk 510 optimal weight: 30.0000 chunk 413 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 305 optimal weight: 0.9980 chunk 537 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 213 GLN I 38 GLN I 97 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** O 367 ASN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 463 ASN Y 295 ASN Y 299 GLN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 299 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 60067 Z= 0.165 Angle : 0.551 9.735 83296 Z= 0.291 Chirality : 0.037 0.172 9474 Planarity : 0.004 0.072 8821 Dihedral : 20.939 177.912 13495 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.41 % Allowed : 12.35 % Favored : 86.25 % 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: 1.57 (0.11), residues: 5809 helix: 1.63 (0.10), residues: 3024 sheet: 0.32 (0.21), residues: 557 loop : 0.58 (0.14), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP y 573 HIS 0.005 0.001 HIS I 97 PHE 0.037 0.001 PHE A 190 TYR 0.017 0.001 TYR w 582 ARG 0.017 0.000 ARG M 116 *********************** 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 316 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 244 time to evaluate : 4.849 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: L 196 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6557 (m-10) REVERT: O 179 PHE cc_start: 0.0167 (OUTLIER) cc_final: -0.0194 (t80) REVERT: w 579 ARG cc_start: 0.5636 (tpm170) cc_final: 0.5260 (tpm170) outliers start: 72 outliers final: 37 residues processed: 302 average time/residue: 1.4191 time to fit residues: 546.9626 Evaluate side-chains 237 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 4.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain O residue 179 PHE Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain w residue 570 ILE Chi-restraints excluded: chain y residue 572 VAL Chi-restraints excluded: chain y residue 574 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 201 optimal weight: 3.9990 chunk 538 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 351 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 598 optimal weight: 9.9990 chunk 497 optimal weight: 0.0270 chunk 277 optimal weight: 0.5980 chunk 49 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 314 optimal weight: 6.9990 overall best weight: 1.7244 ------------------------------------------------------------------------------- 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 38 GLN K 97 HIS ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** O 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 419 GLN X 425 GLN ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 60067 Z= 0.227 Angle : 0.574 16.162 83296 Z= 0.299 Chirality : 0.037 0.190 9474 Planarity : 0.004 0.049 8821 Dihedral : 20.973 178.684 13495 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.66 % Allowed : 13.24 % Favored : 85.09 % 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: 1.62 (0.11), residues: 5809 helix: 1.69 (0.10), residues: 3021 sheet: 0.35 (0.21), residues: 557 loop : 0.58 (0.14), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP y 573 HIS 0.005 0.001 HIS K 97 PHE 0.018 0.001 PHE A 190 TYR 0.019 0.001 TYR B 93 ARG 0.010 0.000 ARG z 579 *********************** 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 299 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 214 time to evaluate : 4.890 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: O 179 PHE cc_start: 0.0168 (OUTLIER) cc_final: -0.0179 (t80) REVERT: Y 381 MET cc_start: -0.1656 (mtt) cc_final: -0.3998 (ttm) outliers start: 85 outliers final: 46 residues processed: 287 average time/residue: 1.3474 time to fit residues: 498.9048 Evaluate side-chains 238 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 4.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain O residue 179 PHE Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 405 ASP Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain y residue 572 VAL Chi-restraints excluded: chain y residue 574 ASP 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: 0.9980 chunk 341 optimal weight: 5.9990 chunk 437 optimal weight: 8.9990 chunk 338 optimal weight: 9.9990 chunk 504 optimal weight: 20.0000 chunk 334 optimal weight: 8.9990 chunk 596 optimal weight: 9.9990 chunk 373 optimal weight: 10.0000 chunk 363 optimal weight: 5.9990 chunk 275 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 HIS ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** O 496 GLN ** O 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 137 GLN ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN ** S 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 508 GLN ** X 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 428 ASN Y 475 GLN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.160 60067 Z= 0.575 Angle : 0.855 14.807 83296 Z= 0.440 Chirality : 0.044 0.249 9474 Planarity : 0.006 0.103 8821 Dihedral : 21.647 179.695 13495 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.03 % Allowed : 13.91 % Favored : 84.06 % 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: 0.59 (0.11), residues: 5809 helix: 0.82 (0.09), residues: 3018 sheet: 0.08 (0.19), residues: 689 loop : 0.09 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Z 275 HIS 0.014 0.002 HIS K 97 PHE 0.027 0.003 PHE J 190 TYR 0.043 0.003 TYR G 240 ARG 0.011 0.001 ARG E 126 *********************** 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 297 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 193 time to evaluate : 4.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 119 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.7026 (tmtt) REVERT: J 196 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7898 (m-10) REVERT: L 196 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.6832 (m-10) REVERT: O 179 PHE cc_start: -0.0129 (OUTLIER) cc_final: -0.0621 (t80) REVERT: Y 381 MET cc_start: -0.1897 (mtt) cc_final: -0.3781 (ttm) outliers start: 104 outliers final: 56 residues processed: 286 average time/residue: 1.2928 time to fit residues: 482.7212 Evaluate side-chains 225 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 165 time to evaluate : 4.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain O residue 179 PHE Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 405 ASP Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Y residue 272 HIS Chi-restraints excluded: chain Y residue 296 HIS Chi-restraints excluded: chain Y residue 435 TYR Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain w residue 570 ILE Chi-restraints excluded: chain w residue 574 ASP Chi-restraints excluded: chain y residue 572 VAL Chi-restraints excluded: chain y residue 574 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 369 optimal weight: 10.0000 chunk 238 optimal weight: 0.9980 chunk 356 optimal weight: 10.0000 chunk 179 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 379 optimal weight: 6.9990 chunk 406 optimal weight: 1.9990 chunk 294 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 468 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN M 80 GLN ** 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** O 484 ASN O 522 HIS ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 375 GLN X 123 ASN ** X 419 GLN ** 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 Z 299 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 60067 Z= 0.181 Angle : 0.614 14.311 83296 Z= 0.322 Chirality : 0.038 0.204 9474 Planarity : 0.004 0.049 8821 Dihedral : 21.452 178.145 13495 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.31 % Allowed : 14.79 % Favored : 83.90 % 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: 1.28 (0.11), residues: 5809 helix: 1.46 (0.09), residues: 3009 sheet: 0.17 (0.21), residues: 549 loop : 0.33 (0.14), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP y 573 HIS 0.009 0.001 HIS D 193 PHE 0.050 0.001 PHE Z 332 TYR 0.015 0.001 TYR F 115 ARG 0.014 0.000 ARG W 535 *********************** 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 264 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 197 time to evaluate : 5.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 150 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7684 (mtmm) REVERT: O 179 PHE cc_start: -0.0245 (OUTLIER) cc_final: -0.0595 (t80) REVERT: Y 381 MET cc_start: -0.1653 (mtt) cc_final: -0.3860 (ttm) REVERT: Z 381 MET cc_start: -0.0685 (mtp) cc_final: -0.1395 (mtt) REVERT: w 580 GLU cc_start: 0.5516 (pp20) cc_final: 0.4800 (pp20) outliers start: 67 outliers final: 38 residues processed: 253 average time/residue: 1.3289 time to fit residues: 436.0796 Evaluate side-chains 214 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 174 time to evaluate : 4.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain O residue 179 PHE Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 163 LYS Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Y residue 296 HIS Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain w residue 570 ILE Chi-restraints excluded: chain y residue 572 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 542 optimal weight: 8.9990 chunk 571 optimal weight: 3.9990 chunk 521 optimal weight: 9.9990 chunk 555 optimal weight: 30.0000 chunk 334 optimal weight: 0.3980 chunk 242 optimal weight: 0.0870 chunk 436 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 502 optimal weight: 8.9990 chunk 525 optimal weight: 8.9990 chunk 554 optimal weight: 20.0000 overall best weight: 3.6964 ------------------------------------------------------------------------------- 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** C 22 GLN D 193 HIS ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 ASN ** 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 83 GLN ** Q 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 167 GLN ** X 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 60067 Z= 0.411 Angle : 0.726 14.615 83296 Z= 0.374 Chirality : 0.041 0.285 9474 Planarity : 0.005 0.054 8821 Dihedral : 21.593 178.025 13495 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.45 % Allowed : 15.00 % Favored : 83.55 % 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: 1.29 (0.09), residues: 3008 sheet: 0.15 (0.19), residues: 679 loop : 0.15 (0.14), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP y 573 HIS 0.014 0.002 HIS I 97 PHE 0.036 0.002 PHE Z 332 TYR 0.027 0.002 TYR G 240 ARG 0.009 0.001 ARG W 535 *********************** 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 250 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 176 time to evaluate : 4.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 196 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.6675 (m-10) REVERT: O 179 PHE cc_start: 0.0133 (OUTLIER) cc_final: -0.0245 (t80) REVERT: Y 381 MET cc_start: -0.1489 (mtt) cc_final: -0.3427 (ttm) outliers start: 74 outliers final: 49 residues processed: 240 average time/residue: 1.2985 time to fit residues: 407.6572 Evaluate side-chains 218 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 4.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain O residue 179 PHE Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 405 ASP Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 365 LEU Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Y residue 296 HIS Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain w residue 570 ILE Chi-restraints excluded: chain y residue 572 VAL Chi-restraints excluded: chain y residue 574 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 365 optimal weight: 5.9990 chunk 587 optimal weight: 3.9990 chunk 358 optimal weight: 0.6980 chunk 278 optimal weight: 0.9980 chunk 408 optimal weight: 0.6980 chunk 616 optimal weight: 10.0000 chunk 567 optimal weight: 20.0000 chunk 491 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 379 optimal weight: 7.9990 chunk 301 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** G 213 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** O 430 ASN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 60067 Z= 0.235 Angle : 0.648 12.880 83296 Z= 0.336 Chirality : 0.039 0.237 9474 Planarity : 0.004 0.076 8821 Dihedral : 21.516 177.746 13495 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.09 % Allowed : 15.35 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.11), residues: 5809 helix: 1.47 (0.09), residues: 3011 sheet: 0.10 (0.21), residues: 556 loop : 0.25 (0.14), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP y 573 HIS 0.018 0.001 HIS D 193 PHE 0.031 0.001 PHE Z 332 TYR 0.025 0.001 TYR A 112 ARG 0.020 0.000 ARG z 579 ********************** 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 231 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 175 time to evaluate : 4.881 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: L 196 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6509 (m-10) REVERT: O 179 PHE cc_start: -0.0308 (OUTLIER) cc_final: -0.0587 (t80) REVERT: X 129 MET cc_start: 0.7192 (tpt) cc_final: 0.6707 (tpt) REVERT: Y 381 MET cc_start: -0.1550 (mtt) cc_final: -0.3527 (ttm) REVERT: Z 430 MET cc_start: 0.5453 (tpp) cc_final: 0.5139 (tmm) REVERT: w 580 GLU cc_start: 0.5721 (pp20) cc_final: 0.4940 (pp20) outliers start: 56 outliers final: 44 residues processed: 225 average time/residue: 1.3596 time to fit residues: 397.2374 Evaluate side-chains 216 residues out of total 5121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 4.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 269 GLN Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain O residue 179 PHE Chi-restraints excluded: chain O residue 453 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 457 LEU Chi-restraints excluded: chain X residue 267 SER Chi-restraints excluded: chain X residue 365 LEU Chi-restraints excluded: chain X residue 385 THR Chi-restraints excluded: chain X residue 479 THR Chi-restraints excluded: chain Z residue 272 HIS Chi-restraints excluded: chain y residue 572 VAL Chi-restraints excluded: chain y residue 574 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 390 optimal weight: 0.0470 chunk 523 optimal weight: 0.0970 chunk 150 optimal weight: 4.9990 chunk 452 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 491 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 505 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 ASN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** X 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 464 ASN ** Y 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.062261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.042229 restraints weight = 331181.573| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 4.40 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.6431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 60067 Z= 0.167 Angle : 0.629 15.474 83296 Z= 0.323 Chirality : 0.038 0.229 9474 Planarity : 0.004 0.061 8821 Dihedral : 21.313 179.925 13495 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.88 % Allowed : 15.53 % Favored : 83.59 % 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: 1.44 (0.11), residues: 5809 helix: 1.65 (0.10), residues: 3009 sheet: 0.22 (0.21), residues: 553 loop : 0.33 (0.14), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP y 573 HIS 0.008 0.001 HIS I 97 PHE 0.028 0.001 PHE Z 332 TYR 0.019 0.001 TYR M 75 ARG 0.016 0.000 ARG W 535 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12285.01 seconds wall clock time: 217 minutes 41.04 seconds (13061.04 seconds total)