Starting phenix.real_space_refine on Sun Feb 18 17:12:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iah_35301/02_2024/8iah_35301_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iah_35301/02_2024/8iah_35301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iah_35301/02_2024/8iah_35301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iah_35301/02_2024/8iah_35301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iah_35301/02_2024/8iah_35301_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iah_35301/02_2024/8iah_35301_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 445 5.16 5 C 46713 2.51 5 N 12891 2.21 5 O 14247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 44": "OD1" <-> "OD2" Residue "0 GLU 53": "OE1" <-> "OE2" Residue "1 GLU 376": "OE1" <-> "OE2" Residue "2 TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 122": "OD1" <-> "OD2" Residue "3 TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 266": "OE1" <-> "OE2" Residue "4 PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 165": "OD1" <-> "OD2" Residue "5 GLU 202": "OE1" <-> "OE2" Residue "6 ASP 55": "OD1" <-> "OD2" Residue "7 ASP 165": "OD1" <-> "OD2" Residue "8 GLU 2045": "OE1" <-> "OE2" Residue "8 GLU 2144": "OE1" <-> "OE2" Residue "8 GLU 2191": "OE1" <-> "OE2" Residue "8 ASP 2216": "OD1" <-> "OD2" Residue "8 GLU 2219": "OE1" <-> "OE2" Residue "8 TYR 2405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 2415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 40": "OD1" <-> "OD2" Residue "9 GLU 65": "OE1" <-> "OE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "I TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 184": "OD1" <-> "OD2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 157": "OD1" <-> "OD2" Residue "L TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 195": "OE1" <-> "OE2" Residue "L PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 292": "OD1" <-> "OD2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M GLU 93": "OE1" <-> "OE2" Residue "M GLU 125": "OE1" <-> "OE2" Residue "N PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 51": "OE1" <-> "OE2" Residue "O ASP 33": "OD1" <-> "OD2" Residue "O ASP 81": "OD1" <-> "OD2" Residue "O ASP 117": "OD1" <-> "OD2" Residue "O GLU 125": "OE1" <-> "OE2" Residue "P ASP 50": "OD1" <-> "OD2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P GLU 114": "OE1" <-> "OE2" Residue "P ASP 117": "OD1" <-> "OD2" Residue "P GLU 125": "OE1" <-> "OE2" Residue "P ASP 140": "OD1" <-> "OD2" Residue "Q GLU 51": "OE1" <-> "OE2" Residue "Q GLU 98": "OE1" <-> "OE2" Residue "Q GLU 125": "OE1" <-> "OE2" Residue "Q ASP 140": "OD1" <-> "OD2" Residue "R GLU 98": "OE1" <-> "OE2" Residue "R ASP 117": "OD1" <-> "OD2" Residue "R GLU 125": "OE1" <-> "OE2" Residue "R ASP 137": "OD1" <-> "OD2" Residue "S PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 421": "OE1" <-> "OE2" Residue "S GLU 487": "OE1" <-> "OE2" Residue "T GLU 114": "OE1" <-> "OE2" Residue "T GLU 125": "OE1" <-> "OE2" Residue "U ASP 48": "OD1" <-> "OD2" Residue "U TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 127": "OE1" <-> "OE2" Residue "U GLU 186": "OE1" <-> "OE2" Residue "U GLU 230": "OE1" <-> "OE2" Residue "V ASP 23": "OD1" <-> "OD2" Residue "V GLU 34": "OE1" <-> "OE2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "V GLU 141": "OE1" <-> "OE2" Residue "V GLU 198": "OE1" <-> "OE2" Residue "V GLU 204": "OE1" <-> "OE2" Residue "V PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 106": "OE1" <-> "OE2" Residue "W GLU 156": "OE1" <-> "OE2" Residue "W TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 218": "OD1" <-> "OD2" Residue "X GLU 36": "OE1" <-> "OE2" Residue "X GLU 46": "OE1" <-> "OE2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "X GLU 68": "OE1" <-> "OE2" Residue "X ARG 153": "NH1" <-> "NH2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X ASP 222": "OD1" <-> "OD2" Residue "Y TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 28": "OE1" <-> "OE2" Residue "Z ASP 73": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 74320 Number of models: 1 Model: "" Number of chains: 48 Chain: "0" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "1" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2585 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 19, 'TRANS': 314} Chain breaks: 2 Chain: "2" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2263 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 16, 'TRANS': 277} Chain breaks: 1 Chain: "3" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2870 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 3 Chain: "4" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2157 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "5" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1008 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 17, 'TRANS': 105} Chain breaks: 2 Chain: "6" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 17, 'TRANS': 107} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "7" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 976 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 103} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "8" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2799 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 10, 'TRANS': 368} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 221 Chain: "9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "A" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2907 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "D" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "E" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "G" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "H" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "I" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "J" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "K" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "L" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "M" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1065 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "N" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1004 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "O" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1073 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "P" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1057 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "R" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "S" Number of atoms: 3983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3983 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1048 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "U" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1992 Classifications: {'peptide': 246} Link IDs: {'TRANS': 245} Chain: "V" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 2011 Classifications: {'peptide': 246} Link IDs: {'TRANS': 245} Chain: "W" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2017 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 247} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1974 Classifications: {'peptide': 241} Link IDs: {'TRANS': 240} Chain: "Y" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2547 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 19, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 52 Chain: "Z" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 798 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.10, per 1000 atoms: 0.38 Number of scatterers: 74320 At special positions: 0 Unit cell: (143.85, 147.96, 434.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 445 16.00 P 24 15.00 O 14247 8.00 N 12891 7.00 C 46713 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.83 Conformation dependent library (CDL) restraints added in 9.9 seconds 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 379 helices and 64 sheets defined 52.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.47 Creating SS restraints... Processing helix chain '0' and resid 33 through 40 removed outlier: 3.713A pdb=" N GLU 0 38 " --> pdb=" O GLU 0 34 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 55 Processing helix chain '0' and resid 57 through 63 Processing helix chain '0' and resid 65 through 82 Processing helix chain '1' and resid 113 through 124 Processing helix chain '1' and resid 133 through 135 No H-bonds generated for 'chain '1' and resid 133 through 135' Processing helix chain '1' and resid 140 through 158 removed outlier: 3.570A pdb=" N LEU 1 144 " --> pdb=" O LYS 1 140 " (cutoff:3.500A) Processing helix chain '1' and resid 189 through 191 No H-bonds generated for 'chain '1' and resid 189 through 191' Processing helix chain '1' and resid 221 through 230 Processing helix chain '1' and resid 243 through 249 Processing helix chain '1' and resid 260 through 265 removed outlier: 3.823A pdb=" N LEU 1 265 " --> pdb=" O GLU 1 261 " (cutoff:3.500A) Processing helix chain '1' and resid 279 through 290 Processing helix chain '1' and resid 311 through 331 removed outlier: 3.963A pdb=" N ARG 1 330 " --> pdb=" O GLU 1 326 " (cutoff:3.500A) Processing helix chain '1' and resid 346 through 351 Processing helix chain '1' and resid 374 through 387 removed outlier: 3.979A pdb=" N LEU 1 387 " --> pdb=" O MET 1 383 " (cutoff:3.500A) Processing helix chain '1' and resid 496 through 512 removed outlier: 3.726A pdb=" N GLN 1 509 " --> pdb=" O LYS 1 505 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN 1 510 " --> pdb=" O ILE 1 506 " (cutoff:3.500A) Processing helix chain '2' and resid 113 through 124 removed outlier: 3.642A pdb=" N VAL 2 124 " --> pdb=" O SER 2 120 " (cutoff:3.500A) Processing helix chain '2' and resid 140 through 158 Processing helix chain '2' and resid 189 through 191 No H-bonds generated for 'chain '2' and resid 189 through 191' Processing helix chain '2' and resid 222 through 230 removed outlier: 3.611A pdb=" N VAL 2 227 " --> pdb=" O LEU 2 223 " (cutoff:3.500A) Processing helix chain '2' and resid 243 through 250 Processing helix chain '2' and resid 260 through 265 Processing helix chain '2' and resid 280 through 290 Processing helix chain '2' and resid 311 through 335 removed outlier: 4.242A pdb=" N ARG 2 330 " --> pdb=" O GLU 2 326 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR 2 331 " --> pdb=" O ILE 2 327 " (cutoff:3.500A) Processing helix chain '2' and resid 338 through 340 No H-bonds generated for 'chain '2' and resid 338 through 340' Processing helix chain '2' and resid 346 through 353 Processing helix chain '2' and resid 374 through 387 Processing helix chain '3' and resid 118 through 121 No H-bonds generated for 'chain '3' and resid 118 through 121' Processing helix chain '3' and resid 130 through 146 Processing helix chain '3' and resid 177 through 179 No H-bonds generated for 'chain '3' and resid 177 through 179' Processing helix chain '3' and resid 209 through 218 Processing helix chain '3' and resid 231 through 238 Processing helix chain '3' and resid 248 through 253 Processing helix chain '3' and resid 268 through 278 removed outlier: 3.544A pdb=" N GLN 3 275 " --> pdb=" O ARG 3 271 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS 3 276 " --> pdb=" O ILE 3 272 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS 3 277 " --> pdb=" O ASN 3 273 " (cutoff:3.500A) Processing helix chain '3' and resid 299 through 323 Processing helix chain '3' and resid 327 through 329 No H-bonds generated for 'chain '3' and resid 327 through 329' Processing helix chain '3' and resid 334 through 337 No H-bonds generated for 'chain '3' and resid 334 through 337' Processing helix chain '3' and resid 362 through 374 Processing helix chain '3' and resid 467 through 469 No H-bonds generated for 'chain '3' and resid 467 through 469' Processing helix chain '3' and resid 492 through 508 removed outlier: 4.117A pdb=" N LEU 3 496 " --> pdb=" O PRO 3 492 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN 3 505 " --> pdb=" O LYS 3 501 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN 3 506 " --> pdb=" O ILE 3 502 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG 3 507 " --> pdb=" O ARG 3 503 " (cutoff:3.500A) Processing helix chain '3' and resid 518 through 523 removed outlier: 3.907A pdb=" N VAL 3 523 " --> pdb=" O LEU 3 519 " (cutoff:3.500A) Processing helix chain '4' and resid 118 through 121 No H-bonds generated for 'chain '4' and resid 118 through 121' Processing helix chain '4' and resid 130 through 146 removed outlier: 3.764A pdb=" N CYS 4 135 " --> pdb=" O ARG 4 131 " (cutoff:3.500A) Processing helix chain '4' and resid 208 through 218 removed outlier: 3.503A pdb=" N LEU 4 211 " --> pdb=" O GLY 4 208 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA 4 214 " --> pdb=" O LEU 4 211 " (cutoff:3.500A) Processing helix chain '4' and resid 231 through 237 Processing helix chain '4' and resid 248 through 253 Processing helix chain '4' and resid 270 through 278 Processing helix chain '4' and resid 299 through 323 removed outlier: 3.562A pdb=" N SER 4 318 " --> pdb=" O GLU 4 314 " (cutoff:3.500A) Processing helix chain '4' and resid 334 through 337 No H-bonds generated for 'chain '4' and resid 334 through 337' Processing helix chain '4' and resid 362 through 375 removed outlier: 3.593A pdb=" N GLU 4 366 " --> pdb=" O GLU 4 362 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA 4 367 " --> pdb=" O HIS 4 363 " (cutoff:3.500A) Processing helix chain '5' and resid 41 through 44 No H-bonds generated for 'chain '5' and resid 41 through 44' Processing helix chain '5' and resid 165 through 171 Processing helix chain '5' and resid 198 through 212 Processing helix chain '6' and resid 41 through 44 No H-bonds generated for 'chain '6' and resid 41 through 44' Processing helix chain '6' and resid 52 through 54 No H-bonds generated for 'chain '6' and resid 52 through 54' Processing helix chain '6' and resid 140 through 142 No H-bonds generated for 'chain '6' and resid 140 through 142' Processing helix chain '6' and resid 163 through 172 removed outlier: 3.679A pdb=" N ILE 6 167 " --> pdb=" O ILE 6 163 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS 6 172 " --> pdb=" O ILE 6 168 " (cutoff:3.500A) Processing helix chain '6' and resid 198 through 212 Processing helix chain '7' and resid 41 through 44 No H-bonds generated for 'chain '7' and resid 41 through 44' Processing helix chain '7' and resid 52 through 54 No H-bonds generated for 'chain '7' and resid 52 through 54' Processing helix chain '7' and resid 59 through 61 No H-bonds generated for 'chain '7' and resid 59 through 61' Processing helix chain '7' and resid 162 through 172 removed outlier: 3.547A pdb=" N LYS 7 172 " --> pdb=" O ILE 7 168 " (cutoff:3.500A) Processing helix chain '7' and resid 198 through 212 Processing helix chain '8' and resid 2039 through 2062 removed outlier: 3.535A pdb=" N PHE 82043 " --> pdb=" O ALA 82039 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE 82046 " --> pdb=" O LEU 82042 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER 82051 " --> pdb=" O ALA 82047 " (cutoff:3.500A) Processing helix chain '8' and resid 2074 through 2109 removed outlier: 3.654A pdb=" N SER 82088 " --> pdb=" O GLU 82084 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER 82089 " --> pdb=" O ALA 82085 " (cutoff:3.500A) Processing helix chain '8' and resid 2122 through 2180 removed outlier: 3.901A pdb=" N GLN 82141 " --> pdb=" O LYS 82137 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET 82156 " --> pdb=" O LYS 82152 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN 82162 " --> pdb=" O GLN 82158 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN 82163 " --> pdb=" O GLU 82159 " (cutoff:3.500A) Processing helix chain '8' and resid 2183 through 2186 No H-bonds generated for 'chain '8' and resid 2183 through 2186' Processing helix chain '8' and resid 2190 through 2223 removed outlier: 4.023A pdb=" N LEU 82194 " --> pdb=" O LEU 82190 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU 82195 " --> pdb=" O GLU 82191 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN 82205 " --> pdb=" O GLN 82201 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA 82206 " --> pdb=" O LYS 82202 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU 82217 " --> pdb=" O LYS 82213 " (cutoff:3.500A) Processing helix chain '8' and resid 2233 through 2261 Processing helix chain '8' and resid 2268 through 2281 Processing helix chain '8' and resid 2291 through 2300 Processing helix chain '8' and resid 2315 through 2324 Processing helix chain '8' and resid 2334 through 2345 removed outlier: 3.687A pdb=" N PHE 82340 " --> pdb=" O ASP 82336 " (cutoff:3.500A) Processing helix chain '8' and resid 2352 through 2362 removed outlier: 3.748A pdb=" N GLN 82360 " --> pdb=" O GLU 82356 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA 82361 " --> pdb=" O ASN 82357 " (cutoff:3.500A) Processing helix chain '8' and resid 2371 through 2375 Processing helix chain '8' and resid 2380 through 2389 Processing helix chain '8' and resid 2407 through 2414 Processing helix chain '9' and resid 29 through 36 Processing helix chain '9' and resid 39 through 50 Processing helix chain '9' and resid 53 through 59 Processing helix chain '9' and resid 61 through 78 Processing helix chain 'A' and resid 43 through 46 No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.602A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 251 through 262 removed outlier: 4.191A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.864A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 292 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.994A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.585A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 365 removed outlier: 3.618A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.769A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 192 Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.565A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 251 through 254 removed outlier: 3.960A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.814A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.096A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 373 Proline residue: B 367 - end of helix removed outlier: 5.578A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.883A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.193A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.890A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 251 through 261 removed outlier: 4.089A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 288 through 294 removed outlier: 3.940A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP C 292 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.002A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 359 through 373 Proline residue: C 367 - end of helix removed outlier: 5.659A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.913A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 203 through 215 removed outlier: 4.136A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.880A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 347 removed outlier: 5.018A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.728A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 359 through 373 Proline residue: D 367 - end of helix removed outlier: 5.715A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.698A pdb=" N SER E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 113 through 125 removed outlier: 3.986A pdb=" N GLU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 193 Processing helix chain 'E' and resid 203 through 215 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 251 through 254 removed outlier: 3.801A pdb=" N ARG E 254 " --> pdb=" O GLY E 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 251 through 254' Processing helix chain 'E' and resid 256 through 261 removed outlier: 3.695A pdb=" N ALA E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 256 through 261' Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.043A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 Processing helix chain 'E' and resid 359 through 373 Proline residue: E 367 - end of helix removed outlier: 5.683A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 194 removed outlier: 4.005A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 215 Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 251 through 262 removed outlier: 4.134A pdb=" N PHE F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 290 through 296 removed outlier: 3.644A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 296 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 335 through 348 removed outlier: 5.303A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 354 Processing helix chain 'F' and resid 359 through 373 Proline residue: F 367 - end of helix removed outlier: 5.842A pdb=" N VAL F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS F 371 " --> pdb=" O PRO F 367 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 60 removed outlier: 3.819A pdb=" N SER G 60 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 removed outlier: 3.772A pdb=" N GLU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.552A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 195 removed outlier: 3.865A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 215 removed outlier: 3.566A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 251 through 261 removed outlier: 3.962A pdb=" N ARG G 254 " --> pdb=" O GLY G 251 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE G 255 " --> pdb=" O ASN G 252 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS G 257 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Proline residue: G 258 - end of helix removed outlier: 3.519A pdb=" N LEU G 261 " --> pdb=" O PRO G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 288 through 295 removed outlier: 4.265A pdb=" N LYS G 291 " --> pdb=" O ASP G 288 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP G 292 " --> pdb=" O ILE G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 305 Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 335 through 348 removed outlier: 5.001A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY G 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 removed outlier: 3.825A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 351 through 354' Processing helix chain 'G' and resid 359 through 373 Proline residue: G 367 - end of helix removed outlier: 5.686A pdb=" N VAL G 370 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS G 371 " --> pdb=" O PRO G 367 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 194 removed outlier: 4.186A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 215 removed outlier: 4.202A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 251 through 254 removed outlier: 3.954A pdb=" N ARG H 254 " --> pdb=" O GLY H 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 251 through 254' Processing helix chain 'H' and resid 258 through 262 Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 283 Processing helix chain 'H' and resid 290 through 294 Processing helix chain 'H' and resid 302 through 305 Processing helix chain 'H' and resid 309 through 320 removed outlier: 3.537A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 348 Processing helix chain 'H' and resid 351 through 354 removed outlier: 3.555A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 351 through 354' Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 373 removed outlier: 4.104A pdb=" N VAL H 370 " --> pdb=" O PRO H 367 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS H 371 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 removed outlier: 3.697A pdb=" N SER I 60 " --> pdb=" O GLU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 79 through 91 Processing helix chain 'I' and resid 113 through 125 Processing helix chain 'I' and resid 137 through 145 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 182 through 194 removed outlier: 3.995A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 215 removed outlier: 4.212A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 232 Processing helix chain 'I' and resid 252 through 261 removed outlier: 3.883A pdb=" N PHE I 255 " --> pdb=" O ASN I 252 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG I 256 " --> pdb=" O GLU I 253 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS I 257 " --> pdb=" O ARG I 254 " (cutoff:3.500A) Proline residue: I 258 - end of helix Processing helix chain 'I' and resid 264 through 266 No H-bonds generated for 'chain 'I' and resid 264 through 266' Processing helix chain 'I' and resid 274 through 283 Processing helix chain 'I' and resid 290 through 294 Processing helix chain 'I' and resid 302 through 305 Processing helix chain 'I' and resid 309 through 320 Processing helix chain 'I' and resid 338 through 347 Processing helix chain 'I' and resid 351 through 354 removed outlier: 4.054A pdb=" N GLN I 354 " --> pdb=" O THR I 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 351 through 354' Processing helix chain 'I' and resid 359 through 372 Proline residue: I 367 - end of helix removed outlier: 5.849A pdb=" N VAL I 370 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N HIS I 371 " --> pdb=" O PRO I 367 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 79 through 91 removed outlier: 3.736A pdb=" N LYS J 84 " --> pdb=" O ASP J 80 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE J 85 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 Processing helix chain 'J' and resid 137 through 145 Processing helix chain 'J' and resid 182 through 196 removed outlier: 4.100A pdb=" N GLU J 195 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG J 196 " --> pdb=" O ILE J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 215 removed outlier: 3.535A pdb=" N ILE J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 232 Processing helix chain 'J' and resid 251 through 254 removed outlier: 3.685A pdb=" N ARG J 254 " --> pdb=" O GLY J 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 251 through 254' Processing helix chain 'J' and resid 258 through 261 Processing helix chain 'J' and resid 264 through 266 No H-bonds generated for 'chain 'J' and resid 264 through 266' Processing helix chain 'J' and resid 274 through 283 Processing helix chain 'J' and resid 290 through 295 Processing helix chain 'J' and resid 302 through 305 Processing helix chain 'J' and resid 309 through 320 Processing helix chain 'J' and resid 335 through 346 removed outlier: 5.061A pdb=" N VAL J 339 " --> pdb=" O LYS J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 354 No H-bonds generated for 'chain 'J' and resid 352 through 354' Processing helix chain 'J' and resid 359 through 373 removed outlier: 3.755A pdb=" N GLU J 364 " --> pdb=" O GLN J 360 " (cutoff:3.500A) Proline residue: J 367 - end of helix removed outlier: 5.433A pdb=" N VAL J 370 " --> pdb=" O GLY J 366 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N HIS J 371 " --> pdb=" O PRO J 367 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 79 through 90 Processing helix chain 'K' and resid 113 through 124 removed outlier: 3.816A pdb=" N GLU K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET K 123 " --> pdb=" O MET K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 145 removed outlier: 3.796A pdb=" N SER K 141 " --> pdb=" O GLN K 137 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 192 Processing helix chain 'K' and resid 203 through 215 Processing helix chain 'K' and resid 223 through 232 Processing helix chain 'K' and resid 251 through 261 removed outlier: 3.646A pdb=" N ARG K 254 " --> pdb=" O GLY K 251 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE K 255 " --> pdb=" O ASN K 252 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS K 257 " --> pdb=" O ARG K 254 " (cutoff:3.500A) Proline residue: K 258 - end of helix Processing helix chain 'K' and resid 274 through 283 Processing helix chain 'K' and resid 290 through 296 removed outlier: 3.600A pdb=" N ALA K 295 " --> pdb=" O LYS K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 305 No H-bonds generated for 'chain 'K' and resid 303 through 305' Processing helix chain 'K' and resid 309 through 320 Processing helix chain 'K' and resid 335 through 346 removed outlier: 5.429A pdb=" N VAL K 339 " --> pdb=" O LYS K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 355 Processing helix chain 'K' and resid 359 through 373 Proline residue: K 367 - end of helix removed outlier: 5.708A pdb=" N VAL K 370 " --> pdb=" O GLY K 366 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N HIS K 371 " --> pdb=" O PRO K 367 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 79 through 91 Processing helix chain 'L' and resid 98 through 100 No H-bonds generated for 'chain 'L' and resid 98 through 100' Processing helix chain 'L' and resid 113 through 125 Processing helix chain 'L' and resid 137 through 144 removed outlier: 3.865A pdb=" N SER L 141 " --> pdb=" O GLN L 137 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU L 142 " --> pdb=" O ALA L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 removed outlier: 4.547A pdb=" N GLU L 195 " --> pdb=" O LYS L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 215 removed outlier: 4.198A pdb=" N GLU L 207 " --> pdb=" O THR L 203 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE L 208 " --> pdb=" O ALA L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 232 removed outlier: 3.502A pdb=" N ALA L 228 " --> pdb=" O GLU L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 255 removed outlier: 3.937A pdb=" N ARG L 254 " --> pdb=" O GLY L 251 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE L 255 " --> pdb=" O ASN L 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 251 through 255' Processing helix chain 'L' and resid 258 through 262 Processing helix chain 'L' and resid 264 through 267 Processing helix chain 'L' and resid 274 through 283 Processing helix chain 'L' and resid 287 through 289 No H-bonds generated for 'chain 'L' and resid 287 through 289' Processing helix chain 'L' and resid 291 through 294 No H-bonds generated for 'chain 'L' and resid 291 through 294' Processing helix chain 'L' and resid 303 through 305 No H-bonds generated for 'chain 'L' and resid 303 through 305' Processing helix chain 'L' and resid 309 through 320 removed outlier: 3.673A pdb=" N LEU L 320 " --> pdb=" O GLU L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 348 Processing helix chain 'L' and resid 351 through 355 removed outlier: 4.034A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 373 Proline residue: L 367 - end of helix removed outlier: 5.511A pdb=" N VAL L 370 " --> pdb=" O GLY L 366 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N HIS L 371 " --> pdb=" O PRO L 367 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 68 removed outlier: 4.233A pdb=" N ILE M 45 " --> pdb=" O GLU M 41 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS M 46 " --> pdb=" O ARG M 42 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 84 removed outlier: 3.738A pdb=" N LEU M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG M 83 " --> pdb=" O TYR M 79 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP M 84 " --> pdb=" O LYS M 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 78 through 84' Processing helix chain 'M' and resid 86 through 96 Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.535A pdb=" N ALA M 119 " --> pdb=" O ASN M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 140 Processing helix chain 'M' and resid 143 through 155 Processing helix chain 'N' and resid 38 through 42 Processing helix chain 'N' and resid 44 through 67 removed outlier: 3.842A pdb=" N LEU N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL N 55 " --> pdb=" O GLU N 51 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS N 67 " --> pdb=" O TRP N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 83 removed outlier: 3.671A pdb=" N LEU N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG N 83 " --> pdb=" O TYR N 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 83' Processing helix chain 'N' and resid 86 through 96 Processing helix chain 'N' and resid 109 through 125 Processing helix chain 'N' and resid 135 through 140 Processing helix chain 'N' and resid 143 through 156 Processing helix chain 'O' and resid 32 through 71 removed outlier: 4.016A pdb=" N LYS O 46 " --> pdb=" O ARG O 42 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER O 66 " --> pdb=" O LYS O 62 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS O 67 " --> pdb=" O TRP O 63 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG O 70 " --> pdb=" O SER O 66 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL O 71 " --> pdb=" O HIS O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 81 No H-bonds generated for 'chain 'O' and resid 78 through 81' Processing helix chain 'O' and resid 86 through 96 Processing helix chain 'O' and resid 109 through 125 Processing helix chain 'O' and resid 135 through 140 Processing helix chain 'O' and resid 143 through 156 Processing helix chain 'P' and resid 44 through 68 removed outlier: 3.871A pdb=" N VAL P 55 " --> pdb=" O GLU P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 81 No H-bonds generated for 'chain 'P' and resid 78 through 81' Processing helix chain 'P' and resid 86 through 96 Processing helix chain 'P' and resid 109 through 125 removed outlier: 3.644A pdb=" N ALA P 119 " --> pdb=" O ASN P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 140 Processing helix chain 'P' and resid 143 through 157 Processing helix chain 'Q' and resid 33 through 68 removed outlier: 4.127A pdb=" N LYS Q 46 " --> pdb=" O ARG Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 84 removed outlier: 3.580A pdb=" N LEU Q 82 " --> pdb=" O LEU Q 78 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG Q 83 " --> pdb=" O TYR Q 79 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP Q 84 " --> pdb=" O LYS Q 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 78 through 84' Processing helix chain 'Q' and resid 86 through 96 Processing helix chain 'Q' and resid 109 through 125 Processing helix chain 'Q' and resid 135 through 140 Processing helix chain 'Q' and resid 143 through 155 Processing helix chain 'R' and resid 44 through 68 removed outlier: 3.582A pdb=" N HIS R 67 " --> pdb=" O TRP R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 96 Processing helix chain 'R' and resid 109 through 125 removed outlier: 3.649A pdb=" N ALA R 119 " --> pdb=" O ASN R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 140 Processing helix chain 'R' and resid 143 through 156 Processing helix chain 'S' and resid 32 through 69 removed outlier: 3.797A pdb=" N ILE S 45 " --> pdb=" O GLU S 41 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS S 46 " --> pdb=" O ARG S 42 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU S 48 " --> pdb=" O ARG S 44 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA S 49 " --> pdb=" O ILE S 45 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER S 66 " --> pdb=" O LYS S 62 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS S 67 " --> pdb=" O TRP S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 81 No H-bonds generated for 'chain 'S' and resid 78 through 81' Processing helix chain 'S' and resid 86 through 96 Processing helix chain 'S' and resid 109 through 125 removed outlier: 3.668A pdb=" N ALA S 119 " --> pdb=" O ASN S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 140 Processing helix chain 'S' and resid 143 through 156 Processing helix chain 'S' and resid 175 through 189 removed outlier: 3.601A pdb=" N GLY S 189 " --> pdb=" O MET S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 214 Processing helix chain 'S' and resid 227 through 245 removed outlier: 5.521A pdb=" N ARG S 231 " --> pdb=" O SER S 228 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU S 234 " --> pdb=" O ARG S 231 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS S 236 " --> pdb=" O ASN S 233 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE S 238 " --> pdb=" O GLU S 235 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU S 242 " --> pdb=" O ASP S 239 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG S 243 " --> pdb=" O VAL S 240 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN S 244 " --> pdb=" O ALA S 241 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU S 245 " --> pdb=" O GLU S 242 " (cutoff:3.500A) Processing helix chain 'S' and resid 253 through 257 Processing helix chain 'S' and resid 263 through 325 removed outlier: 3.571A pdb=" N VAL S 293 " --> pdb=" O ARG S 289 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET S 303 " --> pdb=" O GLU S 299 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR S 323 " --> pdb=" O GLU S 319 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL S 324 " --> pdb=" O GLN S 320 " (cutoff:3.500A) Processing helix chain 'S' and resid 334 through 349 Processing helix chain 'S' and resid 351 through 376 removed outlier: 4.947A pdb=" N LYS S 359 " --> pdb=" O LYS S 355 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY S 360 " --> pdb=" O PHE S 356 " (cutoff:3.500A) Processing helix chain 'S' and resid 389 through 446 removed outlier: 4.442A pdb=" N ALA S 409 " --> pdb=" O ARG S 405 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET S 433 " --> pdb=" O ARG S 429 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG S 434 " --> pdb=" O LYS S 430 " (cutoff:3.500A) Processing helix chain 'S' and resid 453 through 491 removed outlier: 3.610A pdb=" N ALA S 472 " --> pdb=" O GLU S 468 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA S 473 " --> pdb=" O THR S 469 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR S 474 " --> pdb=" O ASP S 470 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU S 476 " --> pdb=" O ALA S 472 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG S 477 " --> pdb=" O ALA S 473 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU S 488 " --> pdb=" O LEU S 484 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU S 489 " --> pdb=" O ALA S 485 " (cutoff:3.500A) Processing helix chain 'S' and resid 496 through 530 Processing helix chain 'T' and resid 32 through 69 removed outlier: 4.367A pdb=" N LYS T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 81 No H-bonds generated for 'chain 'T' and resid 78 through 81' Processing helix chain 'T' and resid 86 through 96 Processing helix chain 'T' and resid 109 through 125 Processing helix chain 'T' and resid 135 through 140 Processing helix chain 'T' and resid 143 through 156 Processing helix chain 'U' and resid 5 through 246 removed outlier: 4.160A pdb=" N GLN U 57 " --> pdb=" O ASN U 53 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE U 94 " --> pdb=" O GLY U 90 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP U 123 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG U 124 " --> pdb=" O GLU U 120 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL U 129 " --> pdb=" O LYS U 125 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA U 130 " --> pdb=" O TYR U 126 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG U 131 " --> pdb=" O GLU U 127 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU U 159 " --> pdb=" O ARG U 155 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS U 184 " --> pdb=" O GLN U 180 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS U 190 " --> pdb=" O GLU U 186 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG U 208 " --> pdb=" O GLU U 204 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU U 222 " --> pdb=" O ASP U 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS U 223 " --> pdb=" O ASP U 219 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 247 removed outlier: 3.700A pdb=" N ARG V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN V 75 " --> pdb=" O ALA V 71 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS V 92 " --> pdb=" O GLU V 88 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL V 93 " --> pdb=" O ARG V 89 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS V 125 " --> pdb=" O GLU V 121 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG V 131 " --> pdb=" O GLU V 127 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY V 138 " --> pdb=" O VAL V 134 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU V 156 " --> pdb=" O SER V 152 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS V 169 " --> pdb=" O ASP V 165 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA V 174 " --> pdb=" O CYS V 170 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU V 175 " --> pdb=" O LEU V 171 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASP V 183 " --> pdb=" O SER V 179 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS V 184 " --> pdb=" O GLN V 180 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE V 189 " --> pdb=" O TYR V 185 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE V 191 " --> pdb=" O GLU V 187 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA V 199 " --> pdb=" O LYS V 195 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU V 200 " --> pdb=" O LEU V 196 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE V 205 " --> pdb=" O THR V 201 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA V 206 " --> pdb=" O ARG V 202 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP V 219 " --> pdb=" O LYS V 215 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU V 220 " --> pdb=" O THR V 216 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU V 229 " --> pdb=" O LYS V 225 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 244 removed outlier: 3.954A pdb=" N GLN W 57 " --> pdb=" O ASN W 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU W 58 " --> pdb=" O ARG W 54 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU W 107 " --> pdb=" O GLU W 103 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN W 180 " --> pdb=" O GLU W 176 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS W 181 " --> pdb=" O LYS W 177 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU W 182 " --> pdb=" O TYR W 178 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP W 183 " --> pdb=" O SER W 179 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS W 184 " --> pdb=" O GLN W 180 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA W 199 " --> pdb=" O LYS W 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 6 through 243 removed outlier: 4.327A pdb=" N GLN X 44 " --> pdb=" O ARG X 40 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA X 45 " --> pdb=" O ALA X 41 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU X 103 " --> pdb=" O LEU X 99 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU X 159 " --> pdb=" O ARG X 155 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLN X 160 " --> pdb=" O GLU X 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN X 166 " --> pdb=" O ARG X 162 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS X 170 " --> pdb=" O GLN X 166 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU X 171 " --> pdb=" O ASN X 167 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA X 173 " --> pdb=" O LYS X 169 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP X 183 " --> pdb=" O SER X 179 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS X 184 " --> pdb=" O GLN X 180 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR X 185 " --> pdb=" O LYS X 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 21 Processing helix chain 'Y' and resid 24 through 36 Processing helix chain 'Y' and resid 64 through 76 Processing helix chain 'Y' and resid 114 through 121 Processing helix chain 'Y' and resid 125 through 135 removed outlier: 4.137A pdb=" N ASP Y 130 " --> pdb=" O ALA Y 126 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE Y 131 " --> pdb=" O GLU Y 127 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU Y 135 " --> pdb=" O ILE Y 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 143 through 151 Processing helix chain 'Y' and resid 184 through 191 Processing helix chain 'Y' and resid 210 through 221 removed outlier: 3.706A pdb=" N LYS Y 221 " --> pdb=" O ALA Y 217 " (cutoff:3.500A) Processing helix chain 'Y' and resid 238 through 250 removed outlier: 3.956A pdb=" N LYS Y 249 " --> pdb=" O ALA Y 245 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL Y 250 " --> pdb=" O GLU Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 266 through 275 Processing helix chain 'Y' and resid 296 through 306 Processing helix chain 'Y' and resid 323 through 347 Processing helix chain 'Z' and resid 14 through 29 Processing helix chain 'Z' and resid 43 through 52 Processing helix chain 'Z' and resid 79 through 88 Processing helix chain 'Z' and resid 91 through 95 Processing sheet with id= A, first strand: chain '1' and resid 169 through 171 Processing sheet with id= B, first strand: chain '1' and resid 180 through 182 Processing sheet with id= C, first strand: chain '2' and resid 198 through 200 Processing sheet with id= D, first strand: chain '3' and resid 157 through 159 removed outlier: 3.586A pdb=" N VAL 3 292 " --> pdb=" O LEU 3 228 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA 3 257 " --> pdb=" O VAL 3 286 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 168 through 170 Processing sheet with id= F, first strand: chain '3' and resid 432 through 436 Processing sheet with id= G, first strand: chain '3' and resid 441 through 443 removed outlier: 3.601A pdb=" N THR 3 461 " --> pdb=" O VAL 3 443 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '4' and resid 157 through 159 removed outlier: 3.734A pdb=" N VAL 4 292 " --> pdb=" O LEU 4 228 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA 4 257 " --> pdb=" O VAL 4 286 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '4' and resid 168 through 170 Processing sheet with id= J, first strand: chain '8' and resid 2288 through 2290 Processing sheet with id= K, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.755A pdb=" N VAL A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ALA A 135 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= M, first strand: chain 'A' and resid 150 through 155 Processing sheet with id= N, first strand: chain 'A' and resid 239 through 241 Processing sheet with id= O, first strand: chain 'B' and resid 8 through 12 Processing sheet with id= P, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= Q, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= R, first strand: chain 'B' and resid 297 through 299 removed outlier: 7.503A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= T, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= U, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= V, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= W, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.583A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 239 through 241 Processing sheet with id= Y, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.973A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 34 through 38 removed outlier: 3.704A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.450A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N MET D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 239 through 241 Processing sheet with id= AC, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.838A pdb=" N VAL E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ALA E 135 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= AE, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.389A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 239 through 241 Processing sheet with id= AG, first strand: chain 'F' and resid 8 through 12 Processing sheet with id= AH, first strand: chain 'F' and resid 52 through 54 Processing sheet with id= AI, first strand: chain 'F' and resid 103 through 107 Processing sheet with id= AJ, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.389A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 239 through 241 Processing sheet with id= AL, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.507A pdb=" N VAL G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA G 135 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N VAL G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 35 through 38 Processing sheet with id= AN, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.397A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 239 through 241 Processing sheet with id= AP, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.856A pdb=" N VAL H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ALA H 135 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N VAL H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 34 through 38 Processing sheet with id= AR, first strand: chain 'H' and resid 297 through 300 removed outlier: 6.394A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 239 through 241 Processing sheet with id= AT, first strand: chain 'I' and resid 8 through 12 Processing sheet with id= AU, first strand: chain 'I' and resid 35 through 38 removed outlier: 3.659A pdb=" N ARG I 37 " --> pdb=" O THR I 66 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'I' and resid 103 through 107 Processing sheet with id= AW, first strand: chain 'I' and resid 297 through 300 removed outlier: 6.691A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 239 through 241 Processing sheet with id= AY, first strand: chain 'J' and resid 132 through 136 removed outlier: 6.631A pdb=" N VAL J 103 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA J 135 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU J 105 " --> pdb=" O ALA J 135 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU J 8 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR J 106 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N VAL J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY J 13 " --> pdb=" O MET J 16 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET J 16 " --> pdb=" O GLY J 13 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'J' and resid 65 through 69 removed outlier: 3.729A pdb=" N ARG J 37 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'J' and resid 297 through 300 removed outlier: 6.680A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N SER J 300 " --> pdb=" O ILE J 151 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N MET J 153 " --> pdb=" O SER J 300 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'J' and resid 239 through 241 Processing sheet with id= BC, first strand: chain 'K' and resid 132 through 136 removed outlier: 7.043A pdb=" N VAL K 103 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ALA K 135 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU K 105 " --> pdb=" O ALA K 135 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'K' and resid 35 through 38 removed outlier: 3.760A pdb=" N ARG K 37 " --> pdb=" O THR K 66 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'K' and resid 329 through 331 removed outlier: 6.627A pdb=" N THR K 297 " --> pdb=" O ILE K 330 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'K' and resid 239 through 241 Processing sheet with id= BG, first strand: chain 'L' and resid 132 through 136 removed outlier: 7.086A pdb=" N VAL L 103 " --> pdb=" O TYR L 133 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ALA L 135 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU L 105 " --> pdb=" O ALA L 135 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'L' and resid 65 through 69 removed outlier: 3.562A pdb=" N ARG L 37 " --> pdb=" O THR L 66 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'L' and resid 297 through 301 removed outlier: 7.680A pdb=" N VAL L 298 " --> pdb=" O THR L 149 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE L 151 " --> pdb=" O VAL L 298 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N SER L 300 " --> pdb=" O ILE L 151 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET L 153 " --> pdb=" O SER L 300 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'L' and resid 239 through 241 Processing sheet with id= BK, first strand: chain 'Y' and resid 199 through 201 removed outlier: 6.492A pdb=" N LYS Y 228 " --> pdb=" O VAL Y 200 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR Y 256 " --> pdb=" O PHE Y 229 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU Y 284 " --> pdb=" O LEU Y 257 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS Y 314 " --> pdb=" O LEU Y 285 " (cutoff:3.500A) No H-bonds generated for sheet with id= BK Processing sheet with id= BL, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.763A pdb=" N ILE Z 3 " --> pdb=" O GLU Z 35 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL Z 37 " --> pdb=" O ILE Z 3 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL Z 5 " --> pdb=" O VAL Z 37 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN Z 68 " --> pdb=" O PHE Z 6 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASN Z 71 " --> pdb=" O TYR Z 75 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TYR Z 75 " --> pdb=" O ASN Z 71 " (cutoff:3.500A) 3586 hydrogen bonds defined for protein. 10035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 29.18 Time building geometry restraints manager: 25.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 7150 1.24 - 1.38: 22098 1.38 - 1.53: 42717 1.53 - 1.68: 2971 1.68 - 1.83: 754 Bond restraints: 75690 Sorted by residual: bond pdb=" CG PRO Z 59 " pdb=" CD PRO Z 59 " ideal model delta sigma weight residual 1.503 1.089 0.414 3.40e-02 8.65e+02 1.48e+02 bond pdb=" CA LYS Z 57 " pdb=" CB LYS Z 57 " ideal model delta sigma weight residual 1.524 1.586 -0.062 1.62e-02 3.81e+03 1.47e+01 bond pdb=" N PRO Z 59 " pdb=" CD PRO Z 59 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.24e+01 bond pdb=" N ILE W 191 " pdb=" CA ILE W 191 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.03e+00 bond pdb=" N GLU W 182 " pdb=" CA GLU W 182 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.82e+00 ... (remaining 75685 not shown) Histogram of bond angle deviations from ideal: 80.20 - 91.44: 2 91.44 - 102.69: 428 102.69 - 113.93: 44805 113.93 - 125.17: 55919 125.17 - 136.42: 1150 Bond angle restraints: 102304 Sorted by residual: angle pdb=" N PRO Z 59 " pdb=" CD PRO Z 59 " pdb=" CG PRO Z 59 " ideal model delta sigma weight residual 103.20 80.20 23.00 1.50e+00 4.44e-01 2.35e+02 angle pdb=" CA PRO Z 59 " pdb=" CB PRO Z 59 " pdb=" CG PRO Z 59 " ideal model delta sigma weight residual 104.50 87.02 17.48 1.90e+00 2.77e-01 8.46e+01 angle pdb=" CB ARG X 55 " pdb=" CG ARG X 55 " pdb=" CD ARG X 55 " ideal model delta sigma weight residual 111.30 129.27 -17.97 2.30e+00 1.89e-01 6.11e+01 angle pdb=" CA PRO Z 59 " pdb=" N PRO Z 59 " pdb=" CD PRO Z 59 " ideal model delta sigma weight residual 112.00 102.65 9.35 1.40e+00 5.10e-01 4.46e+01 angle pdb=" C MET X 164 " pdb=" CA MET X 164 " pdb=" CB MET X 164 " ideal model delta sigma weight residual 110.09 120.87 -10.78 1.67e+00 3.59e-01 4.17e+01 ... (remaining 102299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.80: 42127 18.80 - 37.59: 3644 37.59 - 56.39: 512 56.39 - 75.18: 90 75.18 - 93.98: 37 Dihedral angle restraints: 46410 sinusoidal: 19074 harmonic: 27336 Sorted by residual: dihedral pdb=" CA ARG S 405 " pdb=" C ARG S 405 " pdb=" N ARG S 406 " pdb=" CA ARG S 406 " ideal model delta harmonic sigma weight residual 180.00 143.97 36.03 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA LYS 82230 " pdb=" C LYS 82230 " pdb=" N PHE 82231 " pdb=" CA PHE 82231 " ideal model delta harmonic sigma weight residual -180.00 -151.51 -28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA MET X 164 " pdb=" C MET X 164 " pdb=" N ASP X 165 " pdb=" CA ASP X 165 " ideal model delta harmonic sigma weight residual 180.00 152.56 27.44 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 46407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 10082 0.077 - 0.154: 1272 0.154 - 0.231: 71 0.231 - 0.308: 11 0.308 - 0.385: 2 Chirality restraints: 11438 Sorted by residual: chirality pdb=" CG LEU V 224 " pdb=" CB LEU V 224 " pdb=" CD1 LEU V 224 " pdb=" CD2 LEU V 224 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA MET X 164 " pdb=" N MET X 164 " pdb=" C MET X 164 " pdb=" CB MET X 164 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB ILE F 5 " pdb=" CA ILE F 5 " pdb=" CG1 ILE F 5 " pdb=" CG2 ILE F 5 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 11435 not shown) Planarity restraints: 13212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL 82112 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO 82113 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO 82113 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO 82113 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP 7 192 " 0.025 2.00e-02 2.50e+03 2.44e-02 1.48e+01 pdb=" CG TRP 7 192 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP 7 192 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP 7 192 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP 7 192 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP 7 192 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP 7 192 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP 7 192 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP 7 192 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP 7 192 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 437 " -0.015 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP S 437 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP S 437 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP S 437 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP S 437 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP S 437 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP S 437 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 437 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 437 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP S 437 " 0.005 2.00e-02 2.50e+03 ... (remaining 13209 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2986 2.72 - 3.27: 73047 3.27 - 3.81: 119232 3.81 - 4.36: 141167 4.36 - 4.90: 241988 Nonbonded interactions: 578420 Sorted by model distance: nonbonded pdb=" OG1 THR G 202 " pdb=" OE1 GLU G 205 " model vdw 2.179 2.440 nonbonded pdb=" OE2 GLU P 53 " pdb=" OH TYR P 79 " model vdw 2.188 2.440 nonbonded pdb=" OH TYR 6 64 " pdb=" O ASP F 25 " model vdw 2.195 2.440 nonbonded pdb=" O ALA S 297 " pdb=" OG1 THR S 300 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR A 202 " pdb=" OE1 GLU A 205 " model vdw 2.207 2.440 ... (remaining 578415 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 '1' and resid 101 through 405) selection = (chain '2' and (resid 101 through 352 or resid 368 through 405)) } ncs_group { reference = (chain '5' and (resid 39 through 67 or (resid 68 through 71 and (name N or name \ CA or name C or name O or name CB )) or resid 118 through 150 or resid 160 throu \ gh 201 or (resid 202 and (name N or name CA or name C or name O or name CB )) or \ resid 203 through 204 or (resid 205 through 213 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain '6' and (resid 39 through 67 or (resid 68 through 71 and (name N or name \ CA or name C or name O or name CB )) or resid 117 or resid 119 through 213)) selection = (chain '7' and (resid 39 through 150 or resid 160 through 201 or (resid 202 and \ (name N or name CA or name C or name O or name CB )) or resid 203 through 204 or \ (resid 205 through 213 and (name N or name CA or name C or name O or name CB )) \ )) } ncs_group { reference = (chain 'A' and (resid 3 through 375 or resid 401)) selection = (chain 'B' and (resid 3 through 42 or (resid 43 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 375 or resid 401)) selection = (chain 'C' and (resid 3 through 42 or (resid 43 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 375 or resid 401)) selection = (chain 'D' and (resid 3 through 42 or (resid 43 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 375 or resid 401)) selection = (chain 'E' and (resid 3 through 42 or (resid 43 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 375 or resid 401)) selection = (chain 'F' and (resid 3 through 42 or (resid 43 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 375 or resid 401)) selection = (chain 'G' and (resid 3 through 42 or (resid 43 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 375 or resid 401)) selection = (chain 'H' and (resid 3 through 42 or (resid 43 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 375 or resid 401)) selection = (chain 'I' and (resid 3 through 42 or (resid 43 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 375 or resid 401)) selection = (chain 'J' and (resid 3 through 42 or (resid 43 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 375 or resid 401)) selection = (chain 'K' and (resid 3 through 42 or (resid 43 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 375 or resid 401)) selection = (chain 'L' and (resid 3 through 42 or (resid 43 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 375 or resid 401)) } ncs_group { reference = (chain 'M' and resid 42 through 158) selection = (chain 'N' and resid 42 through 158) selection = (chain 'O' and resid 42 through 158) selection = chain 'P' selection = (chain 'Q' and resid 42 through 158) selection = chain 'R' selection = (chain 'T' and resid 42 through 158) } ncs_group { reference = (chain 'V' and resid 4 through 244) selection = (chain 'W' and resid 4 through 244) selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 24.470 Check model and map are aligned: 0.800 Set scattering table: 0.510 Process input model: 153.830 Find NCS groups from input model: 4.840 Set up NCS constraints: 0.650 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.414 75690 Z= 0.330 Angle : 0.888 23.001 102304 Z= 0.470 Chirality : 0.049 0.385 11438 Planarity : 0.006 0.112 13212 Dihedral : 13.939 93.978 28712 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.05 (0.08), residues: 9285 helix: 0.36 (0.07), residues: 4788 sheet: 0.57 (0.17), residues: 946 loop : -0.40 (0.10), residues: 3551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP 7 192 HIS 0.016 0.001 HIS W 231 PHE 0.043 0.002 PHE W 205 TYR 0.053 0.002 TYR V 178 ARG 0.029 0.001 ARG X 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 887 time to evaluate : 6.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 31 ASN cc_start: 0.8110 (t0) cc_final: 0.7905 (t0) REVERT: 0 52 MET cc_start: 0.8437 (tmm) cc_final: 0.7990 (tmm) REVERT: 0 80 LYS cc_start: 0.8817 (tmtt) cc_final: 0.8117 (mmmt) REVERT: 2 177 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7057 (pm20) REVERT: 4 135 CYS cc_start: 0.9346 (m) cc_final: 0.9143 (p) REVERT: 4 239 MET cc_start: 0.7145 (tpt) cc_final: 0.6907 (tpp) REVERT: 4 249 ASN cc_start: 0.9222 (m-40) cc_final: 0.8622 (t0) REVERT: 4 304 TYR cc_start: 0.8658 (t80) cc_final: 0.8326 (t80) REVERT: 4 365 PHE cc_start: 0.8522 (t80) cc_final: 0.8162 (t80) REVERT: 5 190 ASP cc_start: 0.8357 (t70) cc_final: 0.7990 (t70) REVERT: 5 191 TYR cc_start: 0.7047 (m-10) cc_final: 0.6821 (m-10) REVERT: 5 208 ARG cc_start: 0.6148 (mtp180) cc_final: 0.5836 (ttp80) REVERT: 6 169 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7918 (mm-30) REVERT: 8 2081 LYS cc_start: 0.6969 (mmtt) cc_final: 0.6428 (mtmt) REVERT: 8 2087 LEU cc_start: 0.4586 (mm) cc_final: 0.4163 (tt) REVERT: 8 2156 MET cc_start: 0.1636 (ppp) cc_final: 0.0018 (mmp) REVERT: 8 2199 ARG cc_start: 0.5385 (mtm-85) cc_final: 0.4386 (ptt90) REVERT: 8 2209 ARG cc_start: 0.7106 (tpm170) cc_final: 0.6859 (mtm180) REVERT: 8 2230 LYS cc_start: 0.4500 (mmpt) cc_final: 0.4179 (tptt) REVERT: 8 2378 LEU cc_start: 0.1082 (tp) cc_final: 0.0833 (tt) REVERT: 8 2382 GLN cc_start: 0.4340 (mt0) cc_final: 0.4139 (mm-40) REVERT: 8 2390 MET cc_start: 0.1958 (tmm) cc_final: 0.1657 (ppp) REVERT: 9 40 ASP cc_start: 0.8778 (p0) cc_final: 0.8483 (p0) REVERT: 9 68 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6714 (mm-30) REVERT: 9 72 GLN cc_start: 0.9173 (tp-100) cc_final: 0.8900 (tp-100) REVERT: 9 76 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7739 (mmmt) REVERT: A 82 MET cc_start: 0.8023 (mmp) cc_final: 0.6515 (mmm) REVERT: A 305 MET cc_start: 0.7476 (mmt) cc_final: 0.7243 (mmt) REVERT: B 82 MET cc_start: 0.8638 (tpp) cc_final: 0.7664 (mmm) REVERT: F 132 MET cc_start: 0.8303 (ppp) cc_final: 0.8090 (ppp) REVERT: F 283 MET cc_start: 0.7869 (tpp) cc_final: 0.7649 (mmt) REVERT: G 355 MET cc_start: 0.8750 (mmm) cc_final: 0.8196 (mtt) REVERT: H 5 ILE cc_start: 0.8876 (mm) cc_final: 0.8614 (mm) REVERT: H 41 GLN cc_start: 0.7145 (tp40) cc_final: 0.6885 (tp-100) REVERT: I 227 MET cc_start: 0.8996 (tpp) cc_final: 0.8323 (mmp) REVERT: J 283 MET cc_start: 0.8713 (mmm) cc_final: 0.7987 (mmt) REVERT: K 44 MET cc_start: 0.7888 (tpp) cc_final: 0.7621 (tpp) REVERT: L 355 MET cc_start: 0.8173 (mmp) cc_final: 0.7900 (mmm) REVERT: N 77 ASP cc_start: 0.8089 (t0) cc_final: 0.7732 (t0) REVERT: N 81 ASP cc_start: 0.7864 (m-30) cc_final: 0.7656 (m-30) REVERT: O 117 ASP cc_start: 0.8547 (t0) cc_final: 0.7933 (t0) REVERT: O 140 ASP cc_start: 0.8058 (m-30) cc_final: 0.7600 (m-30) REVERT: P 87 MET cc_start: 0.8048 (mmm) cc_final: 0.7802 (mmp) REVERT: S 185 MET cc_start: 0.2823 (ttm) cc_final: 0.2531 (ttm) REVERT: S 302 LYS cc_start: 0.7778 (mtmm) cc_final: 0.7537 (tmtt) REVERT: S 373 MET cc_start: 0.2513 (ptt) cc_final: 0.0894 (ptm) REVERT: U 148 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6503 (pt0) REVERT: V 51 SER cc_start: 0.8070 (t) cc_final: 0.7840 (p) REVERT: V 162 ARG cc_start: 0.6930 (ppt170) cc_final: 0.6275 (tmm-80) REVERT: V 164 MET cc_start: 0.5770 (mmp) cc_final: 0.5383 (mmp) REVERT: V 184 LYS cc_start: 0.6894 (pttm) cc_final: 0.6591 (mmtm) REVERT: W 126 TYR cc_start: 0.8327 (t80) cc_final: 0.7888 (t80) REVERT: W 164 MET cc_start: 0.6038 (ppp) cc_final: 0.5800 (ppp) REVERT: X 129 VAL cc_start: 0.6444 (p) cc_final: 0.6158 (m) REVERT: X 158 ASP cc_start: 0.8063 (t0) cc_final: 0.7749 (m-30) REVERT: X 164 MET cc_start: 0.8292 (ppp) cc_final: 0.8076 (ppp) REVERT: X 233 CYS cc_start: 0.4365 (m) cc_final: 0.3913 (p) REVERT: Y 103 MET cc_start: 0.2900 (ppp) cc_final: 0.2383 (ttp) REVERT: Z 63 ASN cc_start: 0.8620 (m-40) cc_final: 0.8337 (m110) outliers start: 0 outliers final: 0 residues processed: 887 average time/residue: 0.6830 time to fit residues: 1036.3058 Evaluate side-chains 667 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 667 time to evaluate : 6.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 779 optimal weight: 3.9990 chunk 699 optimal weight: 0.0980 chunk 388 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 chunk 471 optimal weight: 0.5980 chunk 373 optimal weight: 0.9980 chunk 723 optimal weight: 0.8980 chunk 279 optimal weight: 4.9990 chunk 439 optimal weight: 0.7980 chunk 538 optimal weight: 0.2980 chunk 838 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 54 GLN ** 2 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 67 HIS 6 139 ASN ** 82055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 82098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN H 41 GLN ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 HIS S 505 ASN T 67 HIS ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 96 ASN W 246 ASN X 96 ASN Y 41 ASN ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 148 GLN ** Y 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 75690 Z= 0.159 Angle : 0.565 14.968 102304 Z= 0.284 Chirality : 0.040 0.241 11438 Planarity : 0.004 0.057 13212 Dihedral : 5.454 84.320 10324 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.64 % Rotamer: Outliers : 0.66 % Allowed : 6.53 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.09), residues: 9285 helix: 1.13 (0.07), residues: 4834 sheet: 0.64 (0.17), residues: 930 loop : -0.23 (0.11), residues: 3521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP 4 241 HIS 0.008 0.001 HIS 82131 PHE 0.020 0.001 PHE Z 82 TYR 0.041 0.001 TYR 5 70 ARG 0.007 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 745 time to evaluate : 6.663 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: 0 31 ASN cc_start: 0.8133 (t0) cc_final: 0.7886 (t0) REVERT: 0 44 ASP cc_start: 0.8910 (p0) cc_final: 0.8643 (p0) REVERT: 0 77 GLU cc_start: 0.8597 (pp20) cc_final: 0.8246 (pp20) REVERT: 0 80 LYS cc_start: 0.8786 (tmtt) cc_final: 0.7986 (mmmt) REVERT: 2 177 GLN cc_start: 0.7598 (tm-30) cc_final: 0.6953 (pm20) REVERT: 3 265 MET cc_start: 0.4252 (mmm) cc_final: 0.3984 (mmm) REVERT: 3 371 MET cc_start: 0.8623 (ppp) cc_final: 0.8232 (ppp) REVERT: 4 133 MET cc_start: 0.8040 (mtt) cc_final: 0.7688 (ptp) REVERT: 4 304 TYR cc_start: 0.8632 (t80) cc_final: 0.8198 (t80) REVERT: 4 365 PHE cc_start: 0.8614 (t80) cc_final: 0.8144 (t80) REVERT: 5 43 ASP cc_start: 0.6832 (t0) cc_final: 0.6632 (t0) REVERT: 5 190 ASP cc_start: 0.8337 (t70) cc_final: 0.7975 (t70) REVERT: 6 169 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7784 (mm-30) REVERT: 8 2077 ARG cc_start: 0.5778 (mmp80) cc_final: 0.5491 (mmp80) REVERT: 8 2081 LYS cc_start: 0.6954 (mmtt) cc_final: 0.6407 (mttt) REVERT: 8 2087 LEU cc_start: 0.4996 (mm) cc_final: 0.4602 (tt) REVERT: 8 2199 ARG cc_start: 0.5378 (mtm-85) cc_final: 0.4366 (ptt90) REVERT: 8 2200 LYS cc_start: 0.0026 (mmtp) cc_final: -0.0186 (mttt) REVERT: 9 70 LEU cc_start: 0.9090 (tt) cc_final: 0.8735 (tp) REVERT: 9 72 GLN cc_start: 0.9232 (tp-100) cc_final: 0.8899 (tp-100) REVERT: 9 76 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7580 (mmmt) REVERT: A 82 MET cc_start: 0.8209 (mmp) cc_final: 0.6975 (tpp) REVERT: B 82 MET cc_start: 0.8791 (tpp) cc_final: 0.8560 (tpp) REVERT: C 16 MET cc_start: 0.8245 (mmm) cc_final: 0.7719 (mtt) REVERT: G 47 MET cc_start: 0.6629 (ptt) cc_final: 0.6129 (ptt) REVERT: G 355 MET cc_start: 0.8779 (mmm) cc_final: 0.8077 (mtt) REVERT: H 5 ILE cc_start: 0.8875 (mm) cc_final: 0.8618 (mm) REVERT: H 41 GLN cc_start: 0.7287 (tp-100) cc_final: 0.6973 (tp-100) REVERT: I 123 MET cc_start: 0.9205 (tpp) cc_final: 0.8904 (tpt) REVERT: I 305 MET cc_start: 0.8758 (tpp) cc_final: 0.8479 (mmt) REVERT: J 283 MET cc_start: 0.8670 (mmm) cc_final: 0.8059 (mmt) REVERT: L 355 MET cc_start: 0.7954 (mmp) cc_final: 0.7709 (mmm) REVERT: M 41 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8376 (tm-30) REVERT: N 77 ASP cc_start: 0.8142 (t0) cc_final: 0.7724 (t0) REVERT: N 81 ASP cc_start: 0.7769 (m-30) cc_final: 0.7556 (m-30) REVERT: O 117 ASP cc_start: 0.8528 (t0) cc_final: 0.7931 (t0) REVERT: O 140 ASP cc_start: 0.7958 (m-30) cc_final: 0.7458 (m-30) REVERT: S 185 MET cc_start: 0.2659 (ttm) cc_final: 0.2269 (ttm) REVERT: S 224 LYS cc_start: 0.4160 (pttt) cc_final: 0.3712 (pttp) REVERT: S 302 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7482 (tmtt) REVERT: S 332 ASN cc_start: 0.1446 (t0) cc_final: 0.1177 (t0) REVERT: S 373 MET cc_start: 0.3293 (ptt) cc_final: 0.3003 (ptm) REVERT: S 509 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5690 (tp) REVERT: T 53 GLU cc_start: 0.8080 (pt0) cc_final: 0.7661 (pt0) REVERT: T 98 GLU cc_start: 0.8004 (pm20) cc_final: 0.7531 (pm20) REVERT: U 102 GLU cc_start: 0.8752 (tt0) cc_final: 0.8460 (mt-10) REVERT: U 110 ILE cc_start: 0.7731 (tt) cc_final: 0.7278 (pt) REVERT: V 51 SER cc_start: 0.8100 (t) cc_final: 0.7865 (p) REVERT: V 105 MET cc_start: 0.6035 (ptm) cc_final: 0.5561 (ptp) REVERT: V 162 ARG cc_start: 0.6565 (ppt170) cc_final: 0.5988 (tmm-80) REVERT: V 164 MET cc_start: 0.5599 (mmp) cc_final: 0.5326 (mmp) REVERT: V 184 LYS cc_start: 0.6904 (pttm) cc_final: 0.6593 (mmtt) REVERT: V 185 TYR cc_start: 0.7214 (t80) cc_final: 0.6507 (t80) REVERT: W 36 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7385 (mp0) REVERT: W 126 TYR cc_start: 0.8053 (t80) cc_final: 0.7729 (t80) REVERT: W 157 MET cc_start: 0.8714 (mmm) cc_final: 0.7822 (tpp) REVERT: X 33 ARG cc_start: 0.7510 (ttp-170) cc_final: 0.6905 (ppt170) REVERT: X 105 MET cc_start: 0.7118 (tpp) cc_final: 0.6505 (tpt) REVERT: X 233 CYS cc_start: 0.4689 (m) cc_final: 0.4407 (p) REVERT: Y 347 LEU cc_start: 0.7642 (tp) cc_final: 0.7438 (tt) REVERT: Z 7 ILE cc_start: 0.7245 (mm) cc_final: 0.6520 (mp) REVERT: Z 36 GLU cc_start: 0.7091 (tp30) cc_final: 0.6720 (tp30) REVERT: Z 41 MET cc_start: 0.8414 (tmm) cc_final: 0.8187 (tmm) REVERT: Z 47 GLN cc_start: 0.8290 (tp40) cc_final: 0.8066 (pt0) REVERT: Z 63 ASN cc_start: 0.8488 (m-40) cc_final: 0.8232 (m110) outliers start: 53 outliers final: 29 residues processed: 775 average time/residue: 0.6743 time to fit residues: 903.5466 Evaluate side-chains 694 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 664 time to evaluate : 6.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 129 ASP Chi-restraints excluded: chain 1 residue 325 CYS Chi-restraints excluded: chain 3 residue 313 CYS Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 8 residue 2092 ARG Chi-restraints excluded: chain 8 residue 2118 THR Chi-restraints excluded: chain 8 residue 2122 VAL Chi-restraints excluded: chain 8 residue 2244 PHE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 153 MET Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain S residue 273 PHE Chi-restraints excluded: chain S residue 427 PHE Chi-restraints excluded: chain S residue 509 LEU Chi-restraints excluded: chain U residue 109 GLU Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 161 ILE Chi-restraints excluded: chain X residue 178 TYR Chi-restraints excluded: chain Y residue 41 ASN Chi-restraints excluded: chain Y residue 145 GLN Chi-restraints excluded: chain Z residue 22 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 465 optimal weight: 0.7980 chunk 260 optimal weight: 4.9990 chunk 697 optimal weight: 4.9990 chunk 570 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 839 optimal weight: 1.9990 chunk 907 optimal weight: 9.9990 chunk 747 optimal weight: 6.9990 chunk 832 optimal weight: 3.9990 chunk 286 optimal weight: 5.9990 chunk 673 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 104 ASN 2 179 HIS ** 2 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 289 ASN 3 289 ASN 3 334 GLN ** 4 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 177 GLN ** 82055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN B 73 HIS C 88 HIS G 137 GLN H 92 ASN I 12 ASN K 12 ASN K 78 ASN ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 ASN ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 HIS Q 143 HIS R 56 GLN ** S 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 117 HIS Y 41 ASN ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 75690 Z= 0.311 Angle : 0.615 11.305 102304 Z= 0.308 Chirality : 0.042 0.229 11438 Planarity : 0.004 0.059 13212 Dihedral : 5.351 87.262 10324 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 1.36 % Allowed : 9.57 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.09), residues: 9285 helix: 1.42 (0.07), residues: 4877 sheet: 0.57 (0.18), residues: 886 loop : -0.17 (0.11), residues: 3522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 4 241 HIS 0.007 0.001 HIS S 464 PHE 0.015 0.002 PHE S 273 TYR 0.042 0.001 TYR 5 70 ARG 0.014 0.000 ARG W 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 691 time to evaluate : 6.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 31 ASN cc_start: 0.8022 (t0) cc_final: 0.7689 (t0) REVERT: 0 77 GLU cc_start: 0.8343 (pp20) cc_final: 0.8064 (pp20) REVERT: 0 80 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8016 (mmmt) REVERT: 2 114 MET cc_start: 0.8379 (mmp) cc_final: 0.8063 (mmp) REVERT: 2 123 MET cc_start: 0.8730 (tpp) cc_final: 0.8425 (tpp) REVERT: 2 177 GLN cc_start: 0.7761 (tm-30) cc_final: 0.6862 (pm20) REVERT: 3 265 MET cc_start: 0.4084 (mmm) cc_final: 0.3838 (mmm) REVERT: 3 355 MET cc_start: 0.1568 (mmp) cc_final: 0.1346 (mmp) REVERT: 3 371 MET cc_start: 0.8837 (ppp) cc_final: 0.8511 (ppp) REVERT: 3 375 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8249 (mt) REVERT: 4 224 CYS cc_start: 0.8697 (t) cc_final: 0.8080 (p) REVERT: 4 365 PHE cc_start: 0.8659 (t80) cc_final: 0.8282 (t80) REVERT: 4 371 MET cc_start: 0.8126 (tmm) cc_final: 0.7804 (tmm) REVERT: 5 190 ASP cc_start: 0.8585 (t70) cc_final: 0.8084 (t70) REVERT: 6 60 ASP cc_start: 0.8738 (t0) cc_final: 0.8442 (t0) REVERT: 6 169 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7861 (mm-30) REVERT: 8 2084 GLU cc_start: 0.2832 (OUTLIER) cc_final: 0.1677 (tp30) REVERT: 8 2156 MET cc_start: 0.2822 (ppp) cc_final: 0.2512 (ppp) REVERT: 8 2199 ARG cc_start: 0.5342 (mtm-85) cc_final: 0.4263 (ptt90) REVERT: 8 2207 MET cc_start: -0.2477 (mtm) cc_final: -0.2735 (mpp) REVERT: 8 2414 TYR cc_start: 0.2111 (OUTLIER) cc_final: 0.1058 (t80) REVERT: 9 40 ASP cc_start: 0.8567 (p0) cc_final: 0.8304 (p0) REVERT: 9 70 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8602 (mm) REVERT: 9 76 LYS cc_start: 0.8304 (mmmm) cc_final: 0.8035 (mmmt) REVERT: A 82 MET cc_start: 0.8452 (mmp) cc_final: 0.7407 (tpp) REVERT: C 153 MET cc_start: 0.8275 (tmm) cc_final: 0.7923 (tmm) REVERT: E 82 MET cc_start: 0.8895 (mmm) cc_final: 0.8573 (mmm) REVERT: G 355 MET cc_start: 0.8919 (mmm) cc_final: 0.8175 (mtt) REVERT: H 5 ILE cc_start: 0.8853 (mm) cc_final: 0.8618 (mm) REVERT: H 283 MET cc_start: 0.9260 (mmm) cc_final: 0.8851 (tpp) REVERT: H 325 MET cc_start: 0.8057 (pmm) cc_final: 0.7609 (ptp) REVERT: I 123 MET cc_start: 0.9194 (tpp) cc_final: 0.8766 (tpt) REVERT: J 283 MET cc_start: 0.8844 (mmm) cc_final: 0.8550 (mmt) REVERT: J 313 MET cc_start: 0.8453 (ttp) cc_final: 0.8252 (ttm) REVERT: K 44 MET cc_start: 0.8386 (tpp) cc_final: 0.8177 (tpp) REVERT: L 132 MET cc_start: 0.8742 (ppp) cc_final: 0.8447 (tmm) REVERT: L 355 MET cc_start: 0.8249 (mmp) cc_final: 0.7827 (mmm) REVERT: M 41 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8285 (tm-30) REVERT: N 77 ASP cc_start: 0.8253 (t0) cc_final: 0.7700 (t0) REVERT: N 81 ASP cc_start: 0.7710 (m-30) cc_final: 0.7481 (m-30) REVERT: O 117 ASP cc_start: 0.8501 (t0) cc_final: 0.7972 (t0) REVERT: O 140 ASP cc_start: 0.8114 (m-30) cc_final: 0.7675 (m-30) REVERT: P 67 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7910 (t-170) REVERT: S 185 MET cc_start: 0.2575 (ttm) cc_final: 0.2142 (ttm) REVERT: S 224 LYS cc_start: 0.3974 (pttt) cc_final: 0.3597 (pttp) REVERT: S 373 MET cc_start: 0.4091 (ptt) cc_final: 0.3803 (ptm) REVERT: S 498 ARG cc_start: 0.5017 (ttt180) cc_final: 0.4745 (ttt90) REVERT: S 525 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7483 (pp20) REVERT: T 53 GLU cc_start: 0.8111 (pt0) cc_final: 0.7651 (pt0) REVERT: T 98 GLU cc_start: 0.7666 (pm20) cc_final: 0.7130 (pm20) REVERT: U 102 GLU cc_start: 0.8862 (tt0) cc_final: 0.8525 (mt-10) REVERT: U 110 ILE cc_start: 0.7406 (tt) cc_final: 0.6945 (pt) REVERT: V 51 SER cc_start: 0.8420 (t) cc_final: 0.8160 (p) REVERT: V 67 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: V 162 ARG cc_start: 0.6601 (ppt170) cc_final: 0.6044 (tmm-80) REVERT: V 164 MET cc_start: 0.5577 (mmp) cc_final: 0.5275 (mmp) REVERT: V 184 LYS cc_start: 0.6791 (pttm) cc_final: 0.6431 (mmtt) REVERT: V 185 TYR cc_start: 0.7322 (t80) cc_final: 0.6984 (t80) REVERT: W 126 TYR cc_start: 0.8079 (t80) cc_final: 0.7763 (t80) REVERT: W 153 ARG cc_start: 0.6746 (ptm-80) cc_final: 0.6479 (ptt90) REVERT: W 157 MET cc_start: 0.8782 (mmm) cc_final: 0.7848 (tpt) REVERT: X 33 ARG cc_start: 0.7484 (ttp-170) cc_final: 0.6975 (ptt90) REVERT: X 105 MET cc_start: 0.7063 (tpp) cc_final: 0.6471 (tpt) REVERT: X 233 CYS cc_start: 0.4720 (m) cc_final: 0.4395 (p) REVERT: Z 7 ILE cc_start: 0.7833 (mm) cc_final: 0.7202 (mp) REVERT: Z 36 GLU cc_start: 0.7219 (tp30) cc_final: 0.7014 (tp30) REVERT: Z 41 MET cc_start: 0.8329 (tmm) cc_final: 0.7969 (tmm) REVERT: Z 47 GLN cc_start: 0.8535 (tp40) cc_final: 0.8186 (pt0) REVERT: Z 63 ASN cc_start: 0.8408 (m-40) cc_final: 0.8169 (m-40) outliers start: 109 outliers final: 60 residues processed: 758 average time/residue: 0.6833 time to fit residues: 895.8110 Evaluate side-chains 702 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 635 time to evaluate : 6.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 147 CYS Chi-restraints excluded: chain 1 residue 325 CYS Chi-restraints excluded: chain 2 residue 222 THR Chi-restraints excluded: chain 3 residue 313 CYS Chi-restraints excluded: chain 3 residue 314 GLU Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 375 LEU Chi-restraints excluded: chain 3 residue 498 MET Chi-restraints excluded: chain 4 residue 253 VAL Chi-restraints excluded: chain 4 residue 372 LEU Chi-restraints excluded: chain 5 residue 124 SER Chi-restraints excluded: chain 6 residue 50 ASP Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 146 ILE Chi-restraints excluded: chain 8 residue 2084 GLU Chi-restraints excluded: chain 8 residue 2122 VAL Chi-restraints excluded: chain 8 residue 2174 THR Chi-restraints excluded: chain 8 residue 2189 THR Chi-restraints excluded: chain 8 residue 2244 PHE Chi-restraints excluded: chain 8 residue 2414 TYR Chi-restraints excluded: chain 9 residue 70 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 153 MET Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 112 CYS Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain P residue 51 GLU Chi-restraints excluded: chain P residue 67 HIS Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain S residue 273 PHE Chi-restraints excluded: chain S residue 427 PHE Chi-restraints excluded: chain S residue 525 GLU Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 161 ILE Chi-restraints excluded: chain X residue 172 SER Chi-restraints excluded: chain X residue 178 TYR Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 46 ARG Chi-restraints excluded: chain Z residue 80 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 829 optimal weight: 4.9990 chunk 631 optimal weight: 3.9990 chunk 435 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 400 optimal weight: 0.6980 chunk 563 optimal weight: 0.9980 chunk 842 optimal weight: 5.9990 chunk 892 optimal weight: 9.9990 chunk 440 optimal weight: 0.0270 chunk 798 optimal weight: 5.9990 chunk 240 optimal weight: 0.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 54 GLN 1 104 ASN 1 218 GLN ** 2 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 289 ASN ** 4 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 82055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN I 12 ASN I 173 HIS K 12 ASN ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 75690 Z= 0.198 Angle : 0.547 13.456 102304 Z= 0.272 Chirality : 0.040 0.235 11438 Planarity : 0.003 0.071 13212 Dihedral : 5.182 85.848 10324 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 1.33 % Allowed : 11.21 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.09), residues: 9285 helix: 1.66 (0.07), residues: 4866 sheet: 0.53 (0.17), residues: 938 loop : -0.14 (0.11), residues: 3481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 4 241 HIS 0.009 0.001 HIS 6 161 PHE 0.016 0.001 PHE S 273 TYR 0.033 0.001 TYR 5 70 ARG 0.014 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 679 time to evaluate : 7.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 31 ASN cc_start: 0.8266 (t0) cc_final: 0.7913 (t0) REVERT: 0 77 GLU cc_start: 0.8231 (pp20) cc_final: 0.7951 (pp20) REVERT: 0 80 LYS cc_start: 0.8825 (tmtt) cc_final: 0.7952 (mmmt) REVERT: 2 119 MET cc_start: 0.8925 (mmm) cc_final: 0.8712 (mmm) REVERT: 2 123 MET cc_start: 0.8730 (tpp) cc_final: 0.8404 (tpp) REVERT: 2 177 GLN cc_start: 0.7761 (tm-30) cc_final: 0.6853 (pm20) REVERT: 3 265 MET cc_start: 0.4052 (mmm) cc_final: 0.3774 (mmm) REVERT: 3 371 MET cc_start: 0.8866 (ppp) cc_final: 0.8586 (ppp) REVERT: 3 375 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8222 (mt) REVERT: 3 464 LYS cc_start: 0.8713 (tptt) cc_final: 0.8082 (ttpp) REVERT: 4 224 CYS cc_start: 0.8710 (t) cc_final: 0.8086 (p) REVERT: 4 304 TYR cc_start: 0.8504 (t80) cc_final: 0.8021 (t80) REVERT: 4 365 PHE cc_start: 0.8585 (t80) cc_final: 0.8278 (t80) REVERT: 4 371 MET cc_start: 0.8127 (tmm) cc_final: 0.7755 (tmm) REVERT: 4 372 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8781 (mm) REVERT: 5 43 ASP cc_start: 0.7914 (t0) cc_final: 0.7680 (t0) REVERT: 5 190 ASP cc_start: 0.8597 (t70) cc_final: 0.8030 (t70) REVERT: 6 49 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8138 (mmtm) REVERT: 6 169 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7946 (mm-30) REVERT: 7 60 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8052 (p0) REVERT: 8 2084 GLU cc_start: 0.2721 (OUTLIER) cc_final: 0.1497 (tp30) REVERT: 8 2087 LEU cc_start: 0.6008 (mt) cc_final: 0.5339 (tt) REVERT: 8 2199 ARG cc_start: 0.5364 (mtm-85) cc_final: 0.4300 (ptt90) REVERT: 8 2414 TYR cc_start: 0.2058 (OUTLIER) cc_final: 0.1031 (t80) REVERT: 9 76 LYS cc_start: 0.8236 (mmmm) cc_final: 0.7993 (mmmt) REVERT: A 283 MET cc_start: 0.9080 (mmp) cc_final: 0.8851 (mmt) REVERT: C 16 MET cc_start: 0.8313 (mmm) cc_final: 0.7608 (mtt) REVERT: C 153 MET cc_start: 0.8141 (tmm) cc_final: 0.7798 (tmm) REVERT: D 83 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: D 250 ILE cc_start: 0.9167 (tp) cc_final: 0.8823 (tp) REVERT: G 47 MET cc_start: 0.6888 (ptt) cc_final: 0.6365 (ptt) REVERT: G 355 MET cc_start: 0.8832 (mmm) cc_final: 0.8069 (mtt) REVERT: H 5 ILE cc_start: 0.8915 (mm) cc_final: 0.8688 (mm) REVERT: H 283 MET cc_start: 0.9182 (mmm) cc_final: 0.8899 (tpp) REVERT: H 325 MET cc_start: 0.7972 (pmm) cc_final: 0.7645 (ptp) REVERT: J 283 MET cc_start: 0.8806 (mmm) cc_final: 0.8534 (mmt) REVERT: J 313 MET cc_start: 0.8440 (ttp) cc_final: 0.8094 (ttm) REVERT: L 132 MET cc_start: 0.8772 (ppp) cc_final: 0.8470 (tmm) REVERT: L 355 MET cc_start: 0.8225 (mmp) cc_final: 0.7739 (mmm) REVERT: M 41 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8200 (tm-30) REVERT: M 98 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7241 (tm-30) REVERT: N 71 VAL cc_start: 0.7751 (t) cc_final: 0.7516 (t) REVERT: N 77 ASP cc_start: 0.8281 (t0) cc_final: 0.7679 (t0) REVERT: N 81 ASP cc_start: 0.7709 (m-30) cc_final: 0.7471 (m-30) REVERT: O 117 ASP cc_start: 0.8550 (t0) cc_final: 0.8018 (t0) REVERT: O 140 ASP cc_start: 0.8091 (m-30) cc_final: 0.7679 (m-30) REVERT: P 67 HIS cc_start: 0.8309 (OUTLIER) cc_final: 0.7938 (t-170) REVERT: P 87 MET cc_start: 0.8446 (mmm) cc_final: 0.8240 (mmm) REVERT: Q 121 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8395 (tp-100) REVERT: S 185 MET cc_start: 0.2632 (ttm) cc_final: 0.2215 (ttm) REVERT: S 302 LYS cc_start: 0.7921 (mtmm) cc_final: 0.7222 (tmtt) REVERT: S 320 GLN cc_start: 0.6494 (pp30) cc_final: 0.6141 (mm-40) REVERT: S 373 MET cc_start: 0.4089 (ptt) cc_final: 0.3875 (ttp) REVERT: S 498 ARG cc_start: 0.4988 (ttt180) cc_final: 0.4773 (ttt90) REVERT: S 509 LEU cc_start: 0.6236 (mm) cc_final: 0.5573 (tp) REVERT: S 525 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7498 (pp20) REVERT: T 98 GLU cc_start: 0.7717 (pm20) cc_final: 0.7174 (pm20) REVERT: T 125 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: U 102 GLU cc_start: 0.8801 (tt0) cc_final: 0.8476 (mt-10) REVERT: U 110 ILE cc_start: 0.7361 (tt) cc_final: 0.6668 (pt) REVERT: U 142 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6758 (tpm170) REVERT: V 51 SER cc_start: 0.8534 (t) cc_final: 0.8201 (p) REVERT: V 67 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7056 (mp10) REVERT: V 162 ARG cc_start: 0.6754 (ppt170) cc_final: 0.6191 (tmm-80) REVERT: V 164 MET cc_start: 0.5592 (mmp) cc_final: 0.5353 (mmp) REVERT: V 184 LYS cc_start: 0.6597 (pttm) cc_final: 0.6236 (mmtt) REVERT: V 185 TYR cc_start: 0.7400 (t80) cc_final: 0.6583 (t80) REVERT: V 248 MET cc_start: 0.6037 (mmt) cc_final: 0.4617 (mtm) REVERT: W 36 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: W 126 TYR cc_start: 0.8046 (t80) cc_final: 0.7742 (t80) REVERT: W 153 ARG cc_start: 0.6745 (ptm-80) cc_final: 0.6537 (ptt90) REVERT: W 157 MET cc_start: 0.8804 (mmm) cc_final: 0.7851 (tpt) REVERT: X 33 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.7133 (ptt90) REVERT: X 105 MET cc_start: 0.7192 (tpp) cc_final: 0.6542 (tpt) REVERT: X 233 CYS cc_start: 0.5028 (m) cc_final: 0.4657 (p) REVERT: Z 41 MET cc_start: 0.8246 (tmm) cc_final: 0.7818 (tmm) REVERT: Z 47 GLN cc_start: 0.8495 (tp40) cc_final: 0.8168 (pt0) outliers start: 106 outliers final: 59 residues processed: 749 average time/residue: 0.6773 time to fit residues: 879.3144 Evaluate side-chains 719 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 648 time to evaluate : 6.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 325 CYS Chi-restraints excluded: chain 1 residue 485 VAL Chi-restraints excluded: chain 1 residue 492 LEU Chi-restraints excluded: chain 3 residue 314 GLU Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 375 LEU Chi-restraints excluded: chain 3 residue 498 MET Chi-restraints excluded: chain 3 residue 510 VAL Chi-restraints excluded: chain 4 residue 141 TYR Chi-restraints excluded: chain 4 residue 372 LEU Chi-restraints excluded: chain 5 residue 146 ILE Chi-restraints excluded: chain 5 residue 166 LEU Chi-restraints excluded: chain 5 residue 191 TYR Chi-restraints excluded: chain 7 residue 56 ILE Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 61 LEU Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain 8 residue 2084 GLU Chi-restraints excluded: chain 8 residue 2118 THR Chi-restraints excluded: chain 8 residue 2122 VAL Chi-restraints excluded: chain 8 residue 2174 THR Chi-restraints excluded: chain 8 residue 2244 PHE Chi-restraints excluded: chain 8 residue 2408 VAL Chi-restraints excluded: chain 8 residue 2414 TYR Chi-restraints excluded: chain 9 residue 73 GLU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain M residue 112 CYS Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain P residue 51 GLU Chi-restraints excluded: chain P residue 67 HIS Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain S residue 273 PHE Chi-restraints excluded: chain S residue 369 ILE Chi-restraints excluded: chain S residue 427 PHE Chi-restraints excluded: chain S residue 525 GLU Chi-restraints excluded: chain T residue 125 GLU Chi-restraints excluded: chain U residue 142 ARG Chi-restraints excluded: chain U residue 178 TYR Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 GLU Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 161 ILE Chi-restraints excluded: chain X residue 178 TYR Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 80 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 743 optimal weight: 0.9980 chunk 506 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 664 optimal weight: 1.9990 chunk 368 optimal weight: 0.0170 chunk 761 optimal weight: 0.9990 chunk 616 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 455 optimal weight: 2.9990 chunk 800 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 54 GLN ** 2 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 289 ASN ** 4 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 82055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 82256 GLN 82257 GLN D 12 ASN ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 215 HIS T 34 ASN ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 117 HIS ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 75690 Z= 0.157 Angle : 0.523 12.709 102304 Z= 0.259 Chirality : 0.039 0.206 11438 Planarity : 0.003 0.052 13212 Dihedral : 4.992 82.970 10324 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 1.51 % Allowed : 12.17 % Favored : 86.32 % 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 (0.09), residues: 9285 helix: 1.81 (0.08), residues: 4874 sheet: 0.58 (0.17), residues: 934 loop : -0.09 (0.11), residues: 3477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 4 241 HIS 0.010 0.001 HIS S 213 PHE 0.018 0.001 PHE 3 307 TYR 0.019 0.001 TYR Y 146 ARG 0.010 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 679 time to evaluate : 6.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 31 ASN cc_start: 0.8265 (t0) cc_final: 0.7905 (t0) REVERT: 0 60 MET cc_start: 0.9039 (mmm) cc_final: 0.8528 (mmt) REVERT: 0 77 GLU cc_start: 0.8092 (pp20) cc_final: 0.7881 (pp20) REVERT: 0 80 LYS cc_start: 0.8818 (tmtt) cc_final: 0.7956 (mmmt) REVERT: 2 123 MET cc_start: 0.8655 (tpp) cc_final: 0.8303 (tpp) REVERT: 2 177 GLN cc_start: 0.7779 (tm-30) cc_final: 0.6877 (pm20) REVERT: 3 265 MET cc_start: 0.4022 (mmm) cc_final: 0.3749 (mmm) REVERT: 3 371 MET cc_start: 0.8985 (ppp) cc_final: 0.8783 (ppp) REVERT: 3 375 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8136 (mt) REVERT: 3 464 LYS cc_start: 0.8718 (tptt) cc_final: 0.8142 (ttpp) REVERT: 4 224 CYS cc_start: 0.8704 (t) cc_final: 0.8062 (p) REVERT: 4 304 TYR cc_start: 0.8482 (t80) cc_final: 0.8024 (t80) REVERT: 4 365 PHE cc_start: 0.8429 (t80) cc_final: 0.8145 (t80) REVERT: 4 371 MET cc_start: 0.8193 (tmm) cc_final: 0.7942 (tmm) REVERT: 5 43 ASP cc_start: 0.7882 (t0) cc_final: 0.7573 (t0) REVERT: 5 190 ASP cc_start: 0.8599 (t70) cc_final: 0.8098 (t70) REVERT: 6 49 LYS cc_start: 0.8427 (mmtt) cc_final: 0.8136 (mmtm) REVERT: 8 2084 GLU cc_start: 0.2667 (OUTLIER) cc_final: 0.1560 (tp30) REVERT: 8 2087 LEU cc_start: 0.6143 (mt) cc_final: 0.5415 (tt) REVERT: 8 2199 ARG cc_start: 0.5383 (mtm-85) cc_final: 0.4318 (ptt90) REVERT: 8 2414 TYR cc_start: 0.2031 (OUTLIER) cc_final: 0.1012 (t80) REVERT: 9 30 GLU cc_start: 0.6747 (mp0) cc_final: 0.6540 (mp0) REVERT: 9 76 LYS cc_start: 0.8279 (mmmm) cc_final: 0.8020 (mmmt) REVERT: A 132 MET cc_start: 0.8417 (tmm) cc_final: 0.7983 (tmm) REVERT: A 283 MET cc_start: 0.9062 (mmp) cc_final: 0.8855 (mmt) REVERT: C 16 MET cc_start: 0.8299 (mmm) cc_final: 0.7679 (mtt) REVERT: C 47 MET cc_start: 0.7377 (mmm) cc_final: 0.6644 (mmm) REVERT: C 153 MET cc_start: 0.8126 (tmm) cc_final: 0.7786 (tmm) REVERT: D 83 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: D 250 ILE cc_start: 0.9171 (tp) cc_final: 0.8865 (tp) REVERT: G 355 MET cc_start: 0.8769 (mmm) cc_final: 0.7990 (mtt) REVERT: H 5 ILE cc_start: 0.8924 (mm) cc_final: 0.8704 (mm) REVERT: J 313 MET cc_start: 0.8458 (ttp) cc_final: 0.8070 (ttm) REVERT: K 44 MET cc_start: 0.8386 (tpp) cc_final: 0.8048 (tpp) REVERT: L 132 MET cc_start: 0.8845 (ppp) cc_final: 0.8538 (tmm) REVERT: L 355 MET cc_start: 0.8187 (mmp) cc_final: 0.7727 (mmm) REVERT: M 41 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8157 (tm-30) REVERT: M 99 MET cc_start: 0.7772 (tpp) cc_final: 0.7570 (tpp) REVERT: N 61 THR cc_start: 0.9248 (m) cc_final: 0.8860 (p) REVERT: N 71 VAL cc_start: 0.7702 (t) cc_final: 0.7398 (t) REVERT: N 77 ASP cc_start: 0.8205 (t0) cc_final: 0.7535 (t0) REVERT: N 81 ASP cc_start: 0.7700 (m-30) cc_final: 0.7445 (m-30) REVERT: O 117 ASP cc_start: 0.8519 (t0) cc_final: 0.7933 (t0) REVERT: O 140 ASP cc_start: 0.8055 (m-30) cc_final: 0.7639 (m-30) REVERT: P 67 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.7833 (t-170) REVERT: P 155 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8792 (tt) REVERT: Q 121 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8433 (mm-40) REVERT: S 302 LYS cc_start: 0.7802 (mtmm) cc_final: 0.7080 (tmtt) REVERT: S 320 GLN cc_start: 0.6432 (pp30) cc_final: 0.6085 (mm-40) REVERT: S 373 MET cc_start: 0.3999 (ptt) cc_final: 0.3787 (ttp) REVERT: S 498 ARG cc_start: 0.5090 (ttt180) cc_final: 0.4770 (ttt90) REVERT: S 525 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7530 (pp20) REVERT: T 98 GLU cc_start: 0.7794 (pm20) cc_final: 0.7249 (pm20) REVERT: T 125 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: U 102 GLU cc_start: 0.8811 (tt0) cc_final: 0.8531 (mt-10) REVERT: U 105 MET cc_start: 0.7453 (mmm) cc_final: 0.7219 (tpt) REVERT: U 110 ILE cc_start: 0.7099 (tt) cc_final: 0.6649 (pt) REVERT: U 142 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6654 (tpm170) REVERT: V 51 SER cc_start: 0.8370 (t) cc_final: 0.8164 (p) REVERT: V 67 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: V 164 MET cc_start: 0.5567 (mmp) cc_final: 0.5349 (mmp) REVERT: V 184 LYS cc_start: 0.6567 (pttm) cc_final: 0.6220 (mmtt) REVERT: V 248 MET cc_start: 0.6001 (mmt) cc_final: 0.4700 (mtm) REVERT: W 36 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: W 126 TYR cc_start: 0.8096 (t80) cc_final: 0.7848 (t80) REVERT: W 153 ARG cc_start: 0.7026 (ptm-80) cc_final: 0.6769 (ptt90) REVERT: W 157 MET cc_start: 0.8863 (mmm) cc_final: 0.8353 (mmm) REVERT: W 222 ASP cc_start: 0.7876 (t0) cc_final: 0.7465 (m-30) REVERT: X 33 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.7069 (ptt90) REVERT: X 233 CYS cc_start: 0.5044 (m) cc_final: 0.4752 (p) REVERT: Z 41 MET cc_start: 0.8233 (tmm) cc_final: 0.7767 (tmm) REVERT: Z 47 GLN cc_start: 0.8556 (tp40) cc_final: 0.8176 (pt0) outliers start: 121 outliers final: 71 residues processed: 762 average time/residue: 0.7085 time to fit residues: 943.3465 Evaluate side-chains 728 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 646 time to evaluate : 6.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 325 CYS Chi-restraints excluded: chain 1 residue 485 VAL Chi-restraints excluded: chain 1 residue 492 LEU Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 375 LEU Chi-restraints excluded: chain 3 residue 498 MET Chi-restraints excluded: chain 3 residue 510 VAL Chi-restraints excluded: chain 4 residue 141 TYR Chi-restraints excluded: chain 5 residue 124 SER Chi-restraints excluded: chain 5 residue 146 ILE Chi-restraints excluded: chain 5 residue 166 LEU Chi-restraints excluded: chain 5 residue 170 SER Chi-restraints excluded: chain 5 residue 191 TYR Chi-restraints excluded: chain 6 residue 50 ASP Chi-restraints excluded: chain 6 residue 67 HIS Chi-restraints excluded: chain 7 residue 39 LEU Chi-restraints excluded: chain 7 residue 56 ILE Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain 8 residue 2071 VAL Chi-restraints excluded: chain 8 residue 2084 GLU Chi-restraints excluded: chain 8 residue 2092 ARG Chi-restraints excluded: chain 8 residue 2118 THR Chi-restraints excluded: chain 8 residue 2122 VAL Chi-restraints excluded: chain 8 residue 2174 THR Chi-restraints excluded: chain 8 residue 2244 PHE Chi-restraints excluded: chain 8 residue 2408 VAL Chi-restraints excluded: chain 8 residue 2414 TYR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 374 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain M residue 112 CYS Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain P residue 51 GLU Chi-restraints excluded: chain P residue 67 HIS Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 273 PHE Chi-restraints excluded: chain S residue 369 ILE Chi-restraints excluded: chain S residue 525 GLU Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain T residue 125 GLU Chi-restraints excluded: chain U residue 142 ARG Chi-restraints excluded: chain U residue 178 TYR Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 GLU Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 161 ILE Chi-restraints excluded: chain X residue 178 TYR Chi-restraints excluded: chain X residue 220 LEU Chi-restraints excluded: chain Y residue 41 ASN Chi-restraints excluded: chain Y residue 347 LEU Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 80 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 300 optimal weight: 5.9990 chunk 803 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 523 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 893 optimal weight: 10.0000 chunk 741 optimal weight: 7.9990 chunk 413 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 295 optimal weight: 3.9990 chunk 468 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 104 ASN ** 1 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 218 GLN ** 2 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 287 GLN 3 262 ASN 4 389 GLN ** 82055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 82150 GLN B 41 GLN B 161 HIS D 115 ASN H 41 GLN I 12 ASN J 161 HIS ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 HIS ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 143 HIS U 246 ASN ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 75690 Z= 0.486 Angle : 0.737 11.674 102304 Z= 0.369 Chirality : 0.046 0.239 11438 Planarity : 0.005 0.069 13212 Dihedral : 5.530 98.775 10324 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 1.85 % Allowed : 13.05 % Favored : 85.10 % 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: 0.87 (0.09), residues: 9285 helix: 1.45 (0.07), residues: 4850 sheet: -0.01 (0.20), residues: 700 loop : -0.40 (0.10), residues: 3735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 79 HIS 0.010 0.002 HIS H 275 PHE 0.019 0.002 PHE 3 307 TYR 0.035 0.002 TYR U 185 ARG 0.007 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 657 time to evaluate : 7.251 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: 0 31 ASN cc_start: 0.8304 (t0) cc_final: 0.7999 (t0) REVERT: 0 60 MET cc_start: 0.9170 (mmm) cc_final: 0.8613 (mmt) REVERT: 0 77 GLU cc_start: 0.8262 (pp20) cc_final: 0.8008 (pp20) REVERT: 2 114 MET cc_start: 0.8430 (mmp) cc_final: 0.7976 (mmp) REVERT: 2 123 MET cc_start: 0.8744 (tpp) cc_final: 0.8439 (tpp) REVERT: 2 177 GLN cc_start: 0.7897 (tm-30) cc_final: 0.6882 (pm20) REVERT: 3 315 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7434 (tp) REVERT: 3 371 MET cc_start: 0.8915 (ppp) cc_final: 0.8664 (ppp) REVERT: 3 375 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8187 (mt) REVERT: 4 224 CYS cc_start: 0.8740 (t) cc_final: 0.7985 (p) REVERT: 4 371 MET cc_start: 0.8169 (tmm) cc_final: 0.7906 (tmm) REVERT: 5 43 ASP cc_start: 0.8193 (t0) cc_final: 0.7889 (t0) REVERT: 5 70 TYR cc_start: 0.7263 (t80) cc_final: 0.6877 (t80) REVERT: 5 190 ASP cc_start: 0.8687 (t70) cc_final: 0.8190 (t70) REVERT: 6 60 ASP cc_start: 0.8225 (m-30) cc_final: 0.7987 (m-30) REVERT: 8 2084 GLU cc_start: 0.2401 (OUTLIER) cc_final: 0.1530 (tp30) REVERT: 8 2087 LEU cc_start: 0.6207 (mt) cc_final: 0.5512 (tt) REVERT: 8 2199 ARG cc_start: 0.5478 (mtm-85) cc_final: 0.4363 (ptt90) REVERT: 8 2414 TYR cc_start: 0.2152 (OUTLIER) cc_final: 0.1074 (t80) REVERT: 9 30 GLU cc_start: 0.6465 (mp0) cc_final: 0.6242 (mp0) REVERT: 9 76 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8398 (mmmt) REVERT: A 176 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7873 (mm) REVERT: B 82 MET cc_start: 0.8988 (tpp) cc_final: 0.8755 (tpp) REVERT: C 153 MET cc_start: 0.8293 (tmm) cc_final: 0.7902 (tmm) REVERT: E 82 MET cc_start: 0.8931 (mmm) cc_final: 0.8668 (mmm) REVERT: G 47 MET cc_start: 0.7381 (ptt) cc_final: 0.6974 (ptt) REVERT: G 355 MET cc_start: 0.8927 (mmm) cc_final: 0.8150 (mtt) REVERT: H 5 ILE cc_start: 0.8875 (mm) cc_final: 0.8651 (mm) REVERT: J 244 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8800 (t0) REVERT: K 44 MET cc_start: 0.8530 (tpp) cc_final: 0.7997 (mtp) REVERT: K 72 GLU cc_start: 0.7891 (tp30) cc_final: 0.7683 (tp30) REVERT: K 107 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: M 41 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8339 (tm-30) REVERT: N 71 VAL cc_start: 0.7734 (t) cc_final: 0.7390 (t) REVERT: N 77 ASP cc_start: 0.8421 (t0) cc_final: 0.7752 (t0) REVERT: N 81 ASP cc_start: 0.7747 (m-30) cc_final: 0.7532 (m-30) REVERT: O 117 ASP cc_start: 0.8574 (t0) cc_final: 0.8023 (t0) REVERT: P 67 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.8129 (t-170) REVERT: P 108 MET cc_start: 0.8538 (mmt) cc_final: 0.7900 (mmt) REVERT: S 243 ARG cc_start: 0.2117 (tpt170) cc_final: 0.1890 (mtp85) REVERT: S 320 GLN cc_start: 0.6354 (pp30) cc_final: 0.6103 (mm-40) REVERT: S 495 ASP cc_start: 0.7500 (t0) cc_final: 0.7045 (t0) REVERT: S 498 ARG cc_start: 0.5082 (ttt180) cc_final: 0.4642 (ttt90) REVERT: S 525 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: T 98 GLU cc_start: 0.7912 (pm20) cc_final: 0.7494 (pm20) REVERT: T 125 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: U 110 ILE cc_start: 0.7201 (tt) cc_final: 0.6705 (pt) REVERT: V 51 SER cc_start: 0.8399 (t) cc_final: 0.8182 (p) REVERT: V 67 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6986 (mp10) REVERT: V 164 MET cc_start: 0.5471 (mmp) cc_final: 0.5180 (mmp) REVERT: V 184 LYS cc_start: 0.6272 (pttm) cc_final: 0.5837 (mmtt) REVERT: V 248 MET cc_start: 0.4950 (mmt) cc_final: 0.3671 (mtm) REVERT: W 126 TYR cc_start: 0.8243 (t80) cc_final: 0.7904 (t80) REVERT: W 153 ARG cc_start: 0.6951 (ptm-80) cc_final: 0.6728 (ptt90) REVERT: W 157 MET cc_start: 0.8706 (mmm) cc_final: 0.7832 (tpt) REVERT: X 33 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7313 (ptt90) REVERT: X 91 MET cc_start: 0.6343 (tpt) cc_final: 0.6130 (tpt) REVERT: X 105 MET cc_start: 0.7279 (tpp) cc_final: 0.6615 (tpt) REVERT: Z 19 LYS cc_start: 0.8395 (mmtp) cc_final: 0.8090 (mmtp) REVERT: Z 33 GLU cc_start: 0.7740 (pp20) cc_final: 0.7253 (pp20) REVERT: Z 41 MET cc_start: 0.8314 (tmm) cc_final: 0.7816 (tmm) REVERT: Z 98 LYS cc_start: 0.8251 (tppt) cc_final: 0.7056 (pttt) outliers start: 148 outliers final: 92 residues processed: 769 average time/residue: 0.6567 time to fit residues: 879.6725 Evaluate side-chains 726 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 623 time to evaluate : 6.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 121 LEU Chi-restraints excluded: chain 1 residue 241 HIS Chi-restraints excluded: chain 1 residue 325 CYS Chi-restraints excluded: chain 2 residue 222 THR Chi-restraints excluded: chain 3 residue 313 CYS Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 375 LEU Chi-restraints excluded: chain 3 residue 498 MET Chi-restraints excluded: chain 3 residue 510 VAL Chi-restraints excluded: chain 4 residue 137 ILE Chi-restraints excluded: chain 4 residue 141 TYR Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 5 residue 124 SER Chi-restraints excluded: chain 5 residue 166 LEU Chi-restraints excluded: chain 5 residue 170 SER Chi-restraints excluded: chain 6 residue 50 ASP Chi-restraints excluded: chain 6 residue 168 ILE Chi-restraints excluded: chain 6 residue 200 VAL Chi-restraints excluded: chain 7 residue 39 LEU Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 146 ILE Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain 8 residue 2084 GLU Chi-restraints excluded: chain 8 residue 2118 THR Chi-restraints excluded: chain 8 residue 2122 VAL Chi-restraints excluded: chain 8 residue 2174 THR Chi-restraints excluded: chain 8 residue 2244 PHE Chi-restraints excluded: chain 8 residue 2414 TYR Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain P residue 51 GLU Chi-restraints excluded: chain P residue 67 HIS Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 273 PHE Chi-restraints excluded: chain S residue 427 PHE Chi-restraints excluded: chain S residue 525 GLU Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain T residue 125 GLU Chi-restraints excluded: chain U residue 178 TYR Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 161 ILE Chi-restraints excluded: chain W residue 168 LEU Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 161 ILE Chi-restraints excluded: chain X residue 178 TYR Chi-restraints excluded: chain Y residue 41 ASN Chi-restraints excluded: chain Y residue 347 LEU Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 80 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 861 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 508 optimal weight: 1.9990 chunk 652 optimal weight: 0.7980 chunk 505 optimal weight: 1.9990 chunk 751 optimal weight: 5.9990 chunk 498 optimal weight: 0.7980 chunk 889 optimal weight: 8.9990 chunk 556 optimal weight: 0.6980 chunk 542 optimal weight: 5.9990 chunk 410 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 104 ASN ** 2 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 262 ASN ** 82055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN K 252 ASN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN V 117 HIS ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 75690 Z= 0.164 Angle : 0.554 12.971 102304 Z= 0.275 Chirality : 0.040 0.219 11438 Planarity : 0.003 0.053 13212 Dihedral : 5.137 87.811 10324 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Rotamer: Outliers : 1.43 % Allowed : 14.18 % Favored : 84.39 % 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: 1.31 (0.09), residues: 9285 helix: 1.81 (0.07), residues: 4865 sheet: 0.31 (0.18), residues: 809 loop : -0.24 (0.11), residues: 3611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 340 HIS 0.008 0.001 HIS S 213 PHE 0.019 0.001 PHE 3 307 TYR 0.023 0.001 TYR Y 146 ARG 0.006 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 672 time to evaluate : 6.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 31 ASN cc_start: 0.8205 (t0) cc_final: 0.7834 (t0) REVERT: 0 60 MET cc_start: 0.9045 (mmm) cc_final: 0.8512 (mmt) REVERT: 0 69 GLU cc_start: 0.8935 (pp20) cc_final: 0.8328 (tp30) REVERT: 0 77 GLU cc_start: 0.8094 (pp20) cc_final: 0.7819 (pp20) REVERT: 0 80 LYS cc_start: 0.8962 (tmtt) cc_final: 0.8042 (mmmt) REVERT: 2 123 MET cc_start: 0.8580 (tpp) cc_final: 0.8184 (tpp) REVERT: 2 177 GLN cc_start: 0.7826 (tm-30) cc_final: 0.6856 (pm20) REVERT: 3 315 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7475 (tp) REVERT: 3 371 MET cc_start: 0.8958 (ppp) cc_final: 0.8741 (ppp) REVERT: 3 375 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8238 (mt) REVERT: 4 112 MET cc_start: 0.7916 (tmm) cc_final: 0.7707 (tpp) REVERT: 4 224 CYS cc_start: 0.8607 (t) cc_final: 0.7838 (p) REVERT: 4 371 MET cc_start: 0.8123 (tmm) cc_final: 0.7908 (tmm) REVERT: 5 43 ASP cc_start: 0.8282 (t0) cc_final: 0.7993 (t0) REVERT: 5 70 TYR cc_start: 0.7279 (t80) cc_final: 0.7010 (t80) REVERT: 5 190 ASP cc_start: 0.8562 (t70) cc_final: 0.8103 (t70) REVERT: 7 67 HIS cc_start: 0.4083 (OUTLIER) cc_final: 0.3879 (m-70) REVERT: 8 2084 GLU cc_start: 0.2415 (OUTLIER) cc_final: 0.1679 (tp30) REVERT: 8 2087 LEU cc_start: 0.6195 (mt) cc_final: 0.5587 (tt) REVERT: 8 2199 ARG cc_start: 0.5401 (mtm-85) cc_final: 0.4344 (ptt90) REVERT: 8 2238 GLN cc_start: 0.4675 (OUTLIER) cc_final: 0.4437 (mm-40) REVERT: 8 2414 TYR cc_start: 0.2056 (OUTLIER) cc_final: 0.1015 (t80) REVERT: 9 76 LYS cc_start: 0.8525 (mmmm) cc_final: 0.8281 (mmmt) REVERT: A 82 MET cc_start: 0.7621 (tpp) cc_final: 0.6814 (mmm) REVERT: A 305 MET cc_start: 0.7733 (mmt) cc_final: 0.7417 (mmt) REVERT: C 16 MET cc_start: 0.8438 (mmm) cc_final: 0.7899 (mtt) REVERT: C 47 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6872 (mmm) REVERT: C 153 MET cc_start: 0.8223 (tmm) cc_final: 0.7893 (tmm) REVERT: G 47 MET cc_start: 0.6772 (ptt) cc_final: 0.6401 (ptt) REVERT: G 355 MET cc_start: 0.8805 (mmm) cc_final: 0.7984 (mtt) REVERT: H 5 ILE cc_start: 0.8905 (mm) cc_final: 0.8691 (mm) REVERT: J 313 MET cc_start: 0.8614 (ttp) cc_final: 0.8190 (ttm) REVERT: K 44 MET cc_start: 0.8534 (tpp) cc_final: 0.8134 (tpp) REVERT: K 107 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: L 132 MET cc_start: 0.8764 (ppp) cc_final: 0.8426 (tmm) REVERT: M 41 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8112 (tm-30) REVERT: M 98 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7507 (tm-30) REVERT: M 99 MET cc_start: 0.7718 (tpp) cc_final: 0.7510 (tpp) REVERT: M 137 ASP cc_start: 0.9173 (t0) cc_final: 0.8931 (t0) REVERT: N 71 VAL cc_start: 0.7903 (t) cc_final: 0.7590 (t) REVERT: N 77 ASP cc_start: 0.8246 (t0) cc_final: 0.7558 (t0) REVERT: N 81 ASP cc_start: 0.7665 (m-30) cc_final: 0.7399 (m-30) REVERT: N 125 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7194 (tm-30) REVERT: N 126 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8289 (mm-40) REVERT: O 117 ASP cc_start: 0.8579 (t0) cc_final: 0.7980 (t0) REVERT: O 140 ASP cc_start: 0.8129 (m-30) cc_final: 0.7631 (m-30) REVERT: Q 121 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8435 (mm-40) REVERT: S 302 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7177 (tmtt) REVERT: S 320 GLN cc_start: 0.6439 (pp30) cc_final: 0.6114 (mm-40) REVERT: S 482 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7366 (mm-30) REVERT: S 495 ASP cc_start: 0.7274 (t0) cc_final: 0.6930 (t0) REVERT: S 498 ARG cc_start: 0.5019 (ttt180) cc_final: 0.4494 (ttt90) REVERT: S 525 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: T 98 GLU cc_start: 0.7795 (pm20) cc_final: 0.7417 (pm20) REVERT: U 110 ILE cc_start: 0.7118 (tt) cc_final: 0.6669 (pt) REVERT: V 67 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6966 (mp10) REVERT: V 164 MET cc_start: 0.5619 (mmp) cc_final: 0.5360 (mmp) REVERT: V 184 LYS cc_start: 0.6427 (pttm) cc_final: 0.5955 (mmtm) REVERT: V 248 MET cc_start: 0.5067 (mmt) cc_final: 0.3955 (mtm) REVERT: W 36 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: W 126 TYR cc_start: 0.8138 (t80) cc_final: 0.7844 (t80) REVERT: W 153 ARG cc_start: 0.7084 (ptm-80) cc_final: 0.6768 (ptt90) REVERT: W 157 MET cc_start: 0.8713 (mmm) cc_final: 0.7720 (tpt) REVERT: W 222 ASP cc_start: 0.7739 (t0) cc_final: 0.7298 (m-30) REVERT: X 33 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7274 (ptt90) REVERT: X 91 MET cc_start: 0.6321 (tpt) cc_final: 0.5690 (tpt) REVERT: X 105 MET cc_start: 0.7098 (tpp) cc_final: 0.6738 (tpt) REVERT: Z 33 GLU cc_start: 0.8108 (pp20) cc_final: 0.7617 (pp20) REVERT: Z 34 PHE cc_start: 0.8001 (p90) cc_final: 0.7785 (p90) REVERT: Z 41 MET cc_start: 0.8293 (tmm) cc_final: 0.7775 (tmm) REVERT: Z 98 LYS cc_start: 0.8284 (tppt) cc_final: 0.7041 (pttt) outliers start: 114 outliers final: 71 residues processed: 748 average time/residue: 0.6775 time to fit residues: 880.2471 Evaluate side-chains 722 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 640 time to evaluate : 6.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 121 LEU Chi-restraints excluded: chain 1 residue 492 LEU Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 375 LEU Chi-restraints excluded: chain 3 residue 498 MET Chi-restraints excluded: chain 3 residue 510 VAL Chi-restraints excluded: chain 4 residue 141 TYR Chi-restraints excluded: chain 4 residue 375 LEU Chi-restraints excluded: chain 5 residue 124 SER Chi-restraints excluded: chain 5 residue 166 LEU Chi-restraints excluded: chain 5 residue 177 GLN Chi-restraints excluded: chain 5 residue 191 TYR Chi-restraints excluded: chain 6 residue 50 ASP Chi-restraints excluded: chain 6 residue 200 VAL Chi-restraints excluded: chain 7 residue 67 HIS Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain 8 residue 2071 VAL Chi-restraints excluded: chain 8 residue 2084 GLU Chi-restraints excluded: chain 8 residue 2092 ARG Chi-restraints excluded: chain 8 residue 2122 VAL Chi-restraints excluded: chain 8 residue 2189 THR Chi-restraints excluded: chain 8 residue 2238 GLN Chi-restraints excluded: chain 8 residue 2244 PHE Chi-restraints excluded: chain 8 residue 2414 TYR Chi-restraints excluded: chain 9 residue 34 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain M residue 112 CYS Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain P residue 51 GLU Chi-restraints excluded: chain Q residue 67 HIS Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 273 PHE Chi-restraints excluded: chain S residue 366 LEU Chi-restraints excluded: chain S residue 525 GLU Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain U residue 178 TYR Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 GLU Chi-restraints excluded: chain W residue 161 ILE Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 161 ILE Chi-restraints excluded: chain X residue 178 TYR Chi-restraints excluded: chain X residue 220 LEU Chi-restraints excluded: chain Y residue 347 LEU Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 80 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 550 optimal weight: 3.9990 chunk 355 optimal weight: 0.8980 chunk 531 optimal weight: 0.0040 chunk 267 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 172 optimal weight: 30.0000 chunk 565 optimal weight: 6.9990 chunk 606 optimal weight: 0.9980 chunk 439 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 699 optimal weight: 0.4980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 104 ASN ** 2 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 82055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 57 GLN ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 75690 Z= 0.167 Angle : 0.552 12.784 102304 Z= 0.272 Chirality : 0.040 0.229 11438 Planarity : 0.003 0.052 13212 Dihedral : 4.946 85.825 10324 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 1.29 % Allowed : 14.57 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.09), residues: 9285 helix: 1.92 (0.07), residues: 4872 sheet: 0.38 (0.18), residues: 802 loop : -0.18 (0.11), residues: 3611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 4 241 HIS 0.008 0.001 HIS S 213 PHE 0.017 0.001 PHE U 205 TYR 0.048 0.001 TYR U 185 ARG 0.005 0.000 ARG 0 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 664 time to evaluate : 6.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 31 ASN cc_start: 0.8236 (t0) cc_final: 0.7868 (t0) REVERT: 0 60 MET cc_start: 0.9020 (mmm) cc_final: 0.8452 (mmt) REVERT: 0 69 GLU cc_start: 0.8919 (pp20) cc_final: 0.8313 (tp30) REVERT: 0 77 GLU cc_start: 0.7968 (pp20) cc_final: 0.7705 (pp20) REVERT: 0 80 LYS cc_start: 0.8955 (tmtt) cc_final: 0.8067 (mmmt) REVERT: 1 251 MET cc_start: 0.6751 (tmm) cc_final: 0.5997 (mmt) REVERT: 2 177 GLN cc_start: 0.7821 (tm-30) cc_final: 0.6843 (pm20) REVERT: 3 315 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7272 (tp) REVERT: 3 371 MET cc_start: 0.8967 (ppp) cc_final: 0.8743 (ppp) REVERT: 3 375 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8200 (mt) REVERT: 4 365 PHE cc_start: 0.8507 (t80) cc_final: 0.8123 (t80) REVERT: 4 369 MET cc_start: 0.7114 (mmp) cc_final: 0.6831 (mtp) REVERT: 5 43 ASP cc_start: 0.8152 (t0) cc_final: 0.7843 (t0) REVERT: 5 70 TYR cc_start: 0.7327 (t80) cc_final: 0.7046 (t80) REVERT: 5 190 ASP cc_start: 0.8596 (t70) cc_final: 0.8052 (t70) REVERT: 7 60 ASP cc_start: 0.8089 (p0) cc_final: 0.7883 (p0) REVERT: 8 2084 GLU cc_start: 0.2949 (OUTLIER) cc_final: 0.2147 (tp30) REVERT: 8 2087 LEU cc_start: 0.5935 (mt) cc_final: 0.5280 (tt) REVERT: 8 2199 ARG cc_start: 0.5441 (mtm-85) cc_final: 0.4418 (ptt90) REVERT: 8 2238 GLN cc_start: 0.4789 (OUTLIER) cc_final: 0.4451 (mm-40) REVERT: 8 2414 TYR cc_start: 0.2003 (OUTLIER) cc_final: 0.0945 (t80) REVERT: 9 76 LYS cc_start: 0.8533 (mmmm) cc_final: 0.8286 (mmmt) REVERT: C 16 MET cc_start: 0.8337 (mmm) cc_final: 0.7789 (mtt) REVERT: C 47 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6875 (mmm) REVERT: C 153 MET cc_start: 0.8169 (tmm) cc_final: 0.7850 (tmm) REVERT: D 83 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: G 47 MET cc_start: 0.6763 (ptt) cc_final: 0.6390 (ptt) REVERT: G 269 MET cc_start: 0.8720 (mtm) cc_final: 0.8518 (mtm) REVERT: G 355 MET cc_start: 0.8803 (mmm) cc_final: 0.8032 (mtt) REVERT: H 5 ILE cc_start: 0.8876 (mm) cc_final: 0.8657 (mm) REVERT: J 244 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8620 (t0) REVERT: J 313 MET cc_start: 0.8588 (ttp) cc_final: 0.8152 (ttm) REVERT: K 44 MET cc_start: 0.8511 (tpp) cc_final: 0.8142 (tpp) REVERT: K 107 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: L 81 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8625 (t70) REVERT: L 132 MET cc_start: 0.8746 (ppp) cc_final: 0.8389 (tmm) REVERT: M 41 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7814 (tm-30) REVERT: M 98 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7455 (tm-30) REVERT: M 99 MET cc_start: 0.7787 (tpp) cc_final: 0.7576 (tpp) REVERT: M 137 ASP cc_start: 0.9131 (t0) cc_final: 0.8922 (t0) REVERT: N 71 VAL cc_start: 0.7833 (t) cc_final: 0.7491 (t) REVERT: N 77 ASP cc_start: 0.8332 (t0) cc_final: 0.7642 (t0) REVERT: N 81 ASP cc_start: 0.7646 (m-30) cc_final: 0.7382 (m-30) REVERT: O 108 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7830 (mtm) REVERT: O 117 ASP cc_start: 0.8586 (t0) cc_final: 0.7986 (t0) REVERT: O 140 ASP cc_start: 0.8067 (m-30) cc_final: 0.7636 (m-30) REVERT: Q 121 GLN cc_start: 0.8661 (tp-100) cc_final: 0.8411 (mm-40) REVERT: S 320 GLN cc_start: 0.6432 (pp30) cc_final: 0.6115 (mm-40) REVERT: S 495 ASP cc_start: 0.7243 (t0) cc_final: 0.6958 (t0) REVERT: S 498 ARG cc_start: 0.5184 (ttt180) cc_final: 0.4884 (ttt90) REVERT: S 525 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: T 98 GLU cc_start: 0.7869 (pm20) cc_final: 0.7322 (pm20) REVERT: U 110 ILE cc_start: 0.7091 (tt) cc_final: 0.6645 (pt) REVERT: V 67 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6958 (mp10) REVERT: V 164 MET cc_start: 0.5580 (mmp) cc_final: 0.5350 (mmp) REVERT: V 184 LYS cc_start: 0.6378 (pttm) cc_final: 0.5936 (mmtm) REVERT: V 185 TYR cc_start: 0.7258 (t80) cc_final: 0.6936 (t80) REVERT: V 227 THR cc_start: 0.3310 (m) cc_final: 0.3071 (p) REVERT: V 237 MET cc_start: 0.7401 (tpp) cc_final: 0.6983 (mmp) REVERT: V 248 MET cc_start: 0.4956 (mmt) cc_final: 0.3703 (mtm) REVERT: W 36 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: W 126 TYR cc_start: 0.8009 (t80) cc_final: 0.7739 (t80) REVERT: W 153 ARG cc_start: 0.7081 (ptm-80) cc_final: 0.6775 (ptt90) REVERT: W 157 MET cc_start: 0.8717 (mmm) cc_final: 0.7721 (tpt) REVERT: W 164 MET cc_start: 0.5563 (ppp) cc_final: 0.5153 (ppp) REVERT: W 222 ASP cc_start: 0.7702 (t0) cc_final: 0.7383 (m-30) REVERT: X 33 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7390 (ptt90) REVERT: X 57 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7749 (tp40) REVERT: X 91 MET cc_start: 0.6296 (tpt) cc_final: 0.5643 (tpt) REVERT: X 105 MET cc_start: 0.7089 (tpp) cc_final: 0.6730 (tpt) REVERT: Z 33 GLU cc_start: 0.8111 (pp20) cc_final: 0.7634 (pp20) REVERT: Z 41 MET cc_start: 0.8245 (tmm) cc_final: 0.7702 (tmm) REVERT: Z 98 LYS cc_start: 0.8277 (tppt) cc_final: 0.7051 (pttt) outliers start: 103 outliers final: 75 residues processed: 734 average time/residue: 0.6761 time to fit residues: 868.2326 Evaluate side-chains 735 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 646 time to evaluate : 6.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 121 LEU Chi-restraints excluded: chain 1 residue 241 HIS Chi-restraints excluded: chain 1 residue 492 LEU Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 375 LEU Chi-restraints excluded: chain 3 residue 498 MET Chi-restraints excluded: chain 3 residue 510 VAL Chi-restraints excluded: chain 4 residue 141 TYR Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 375 LEU Chi-restraints excluded: chain 5 residue 124 SER Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 166 LEU Chi-restraints excluded: chain 6 residue 50 ASP Chi-restraints excluded: chain 6 residue 200 VAL Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain 8 residue 2071 VAL Chi-restraints excluded: chain 8 residue 2084 GLU Chi-restraints excluded: chain 8 residue 2092 ARG Chi-restraints excluded: chain 8 residue 2122 VAL Chi-restraints excluded: chain 8 residue 2238 GLN Chi-restraints excluded: chain 8 residue 2244 PHE Chi-restraints excluded: chain 8 residue 2414 TYR Chi-restraints excluded: chain 9 residue 34 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 51 GLU Chi-restraints excluded: chain Q residue 67 HIS Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 185 MET Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 273 PHE Chi-restraints excluded: chain S residue 366 LEU Chi-restraints excluded: chain S residue 525 GLU Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain U residue 178 TYR Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 GLU Chi-restraints excluded: chain W residue 161 ILE Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 161 ILE Chi-restraints excluded: chain X residue 178 TYR Chi-restraints excluded: chain X residue 220 LEU Chi-restraints excluded: chain Y residue 41 ASN Chi-restraints excluded: chain Y residue 347 LEU Chi-restraints excluded: chain Z residue 80 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 809 optimal weight: 8.9990 chunk 852 optimal weight: 1.9990 chunk 777 optimal weight: 6.9990 chunk 829 optimal weight: 9.9990 chunk 498 optimal weight: 2.9990 chunk 361 optimal weight: 0.2980 chunk 650 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 749 optimal weight: 4.9990 chunk 784 optimal weight: 0.4980 chunk 826 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 104 ASN ** 2 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 82055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 GLN ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 75690 Z= 0.184 Angle : 0.556 12.620 102304 Z= 0.273 Chirality : 0.040 0.209 11438 Planarity : 0.003 0.052 13212 Dihedral : 4.867 84.373 10324 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 1.40 % Allowed : 14.70 % 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: 1.50 (0.09), residues: 9285 helix: 1.97 (0.07), residues: 4881 sheet: 0.38 (0.18), residues: 809 loop : -0.16 (0.11), residues: 3595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 4 241 HIS 0.007 0.001 HIS S 213 PHE 0.025 0.001 PHE 3 307 TYR 0.035 0.001 TYR U 185 ARG 0.005 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 654 time to evaluate : 6.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 31 ASN cc_start: 0.8236 (t0) cc_final: 0.7865 (t0) REVERT: 0 60 MET cc_start: 0.8985 (mmm) cc_final: 0.8448 (mmt) REVERT: 0 69 GLU cc_start: 0.8930 (pp20) cc_final: 0.8322 (tp30) REVERT: 0 77 GLU cc_start: 0.7996 (pp20) cc_final: 0.7751 (pp20) REVERT: 0 80 LYS cc_start: 0.8936 (tmtt) cc_final: 0.8058 (mmmt) REVERT: 1 251 MET cc_start: 0.6628 (tmm) cc_final: 0.5765 (mmt) REVERT: 2 177 GLN cc_start: 0.7778 (tm-30) cc_final: 0.6841 (pm20) REVERT: 3 315 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7269 (tp) REVERT: 3 371 MET cc_start: 0.8977 (ppp) cc_final: 0.8755 (ppp) REVERT: 3 375 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8115 (mt) REVERT: 3 475 MET cc_start: 0.5504 (mtt) cc_final: 0.5205 (mtt) REVERT: 4 256 MET cc_start: 0.5815 (mtm) cc_final: 0.5564 (mtm) REVERT: 5 43 ASP cc_start: 0.8145 (t0) cc_final: 0.7837 (t0) REVERT: 5 70 TYR cc_start: 0.7300 (t80) cc_final: 0.7005 (t80) REVERT: 5 190 ASP cc_start: 0.8592 (t70) cc_final: 0.8044 (t70) REVERT: 7 67 HIS cc_start: 0.4286 (OUTLIER) cc_final: 0.3958 (m-70) REVERT: 8 2084 GLU cc_start: 0.3020 (OUTLIER) cc_final: 0.2224 (tp30) REVERT: 8 2087 LEU cc_start: 0.5956 (mt) cc_final: 0.5279 (tt) REVERT: 8 2199 ARG cc_start: 0.5421 (mtm-85) cc_final: 0.4422 (ptt90) REVERT: 8 2238 GLN cc_start: 0.4777 (OUTLIER) cc_final: 0.4347 (mm-40) REVERT: 8 2414 TYR cc_start: 0.2021 (OUTLIER) cc_final: 0.0960 (t80) REVERT: 9 76 LYS cc_start: 0.8549 (mmmm) cc_final: 0.8311 (mmmt) REVERT: A 82 MET cc_start: 0.7704 (tpp) cc_final: 0.6740 (mmm) REVERT: C 16 MET cc_start: 0.8330 (mmm) cc_final: 0.7806 (mtt) REVERT: C 47 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6790 (mmm) REVERT: C 153 MET cc_start: 0.8167 (tmm) cc_final: 0.7845 (tmm) REVERT: D 83 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: F 283 MET cc_start: 0.7886 (tpp) cc_final: 0.7522 (mmt) REVERT: G 47 MET cc_start: 0.6623 (ptt) cc_final: 0.6248 (ptt) REVERT: G 355 MET cc_start: 0.8818 (mmm) cc_final: 0.8046 (mtt) REVERT: H 5 ILE cc_start: 0.8876 (mm) cc_final: 0.8664 (mm) REVERT: H 283 MET cc_start: 0.8585 (tpp) cc_final: 0.8113 (mpp) REVERT: J 244 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8609 (t0) REVERT: J 313 MET cc_start: 0.8595 (ttp) cc_final: 0.8157 (ttm) REVERT: K 44 MET cc_start: 0.8512 (tpp) cc_final: 0.8181 (tpp) REVERT: K 107 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: L 81 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8628 (t70) REVERT: L 132 MET cc_start: 0.8793 (ppp) cc_final: 0.8400 (tmm) REVERT: L 355 MET cc_start: 0.8418 (mmt) cc_final: 0.7897 (mmm) REVERT: M 41 GLU cc_start: 0.8490 (tm-30) cc_final: 0.7811 (tm-30) REVERT: M 98 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7408 (tm-30) REVERT: M 99 MET cc_start: 0.7851 (tpp) cc_final: 0.7466 (tpp) REVERT: N 71 VAL cc_start: 0.7814 (t) cc_final: 0.7477 (t) REVERT: N 77 ASP cc_start: 0.8339 (t0) cc_final: 0.7640 (t0) REVERT: N 81 ASP cc_start: 0.7654 (m-30) cc_final: 0.7391 (m-30) REVERT: O 117 ASP cc_start: 0.8551 (t0) cc_final: 0.7935 (t0) REVERT: O 140 ASP cc_start: 0.8078 (m-30) cc_final: 0.7755 (m-30) REVERT: P 155 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8709 (tt) REVERT: Q 121 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8402 (mm-40) REVERT: S 302 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7192 (mmtp) REVERT: S 320 GLN cc_start: 0.6432 (pp30) cc_final: 0.6119 (mm-40) REVERT: S 495 ASP cc_start: 0.7137 (t0) cc_final: 0.6760 (t0) REVERT: S 498 ARG cc_start: 0.5126 (ttt180) cc_final: 0.4736 (ttt90) REVERT: S 525 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: T 98 GLU cc_start: 0.7794 (pm20) cc_final: 0.7414 (pm20) REVERT: U 110 ILE cc_start: 0.7017 (tt) cc_final: 0.6573 (pt) REVERT: V 67 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6994 (mp10) REVERT: V 105 MET cc_start: 0.5573 (ptp) cc_final: 0.5321 (ptp) REVERT: V 164 MET cc_start: 0.5577 (mmp) cc_final: 0.5371 (mmp) REVERT: V 184 LYS cc_start: 0.6595 (pttm) cc_final: 0.6173 (mmtm) REVERT: V 185 TYR cc_start: 0.7344 (t80) cc_final: 0.6928 (t80) REVERT: V 227 THR cc_start: 0.3305 (m) cc_final: 0.3061 (p) REVERT: V 237 MET cc_start: 0.7244 (tpp) cc_final: 0.6900 (mmp) REVERT: V 248 MET cc_start: 0.4959 (mmt) cc_final: 0.3972 (tpt) REVERT: W 36 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: W 126 TYR cc_start: 0.8001 (t80) cc_final: 0.7747 (t80) REVERT: W 153 ARG cc_start: 0.7110 (ptm-80) cc_final: 0.6782 (ptt90) REVERT: W 157 MET cc_start: 0.8801 (mmm) cc_final: 0.7770 (tpt) REVERT: W 222 ASP cc_start: 0.7690 (t0) cc_final: 0.7390 (m-30) REVERT: X 33 ARG cc_start: 0.7681 (ttp-170) cc_final: 0.7418 (ptt90) REVERT: X 57 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7822 (tp40) REVERT: X 91 MET cc_start: 0.6298 (tpt) cc_final: 0.5600 (tpt) REVERT: X 105 MET cc_start: 0.7106 (tpp) cc_final: 0.6745 (tpt) REVERT: X 127 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.5302 (tm-30) REVERT: Z 19 LYS cc_start: 0.8331 (mmtp) cc_final: 0.8109 (mmtp) REVERT: Z 33 GLU cc_start: 0.8167 (pp20) cc_final: 0.7638 (pp20) REVERT: Z 41 MET cc_start: 0.8252 (tmm) cc_final: 0.7848 (tmm) REVERT: Z 98 LYS cc_start: 0.8343 (tppt) cc_final: 0.7101 (pttt) outliers start: 112 outliers final: 87 residues processed: 735 average time/residue: 0.6752 time to fit residues: 870.9063 Evaluate side-chains 744 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 641 time to evaluate : 6.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 121 LEU Chi-restraints excluded: chain 1 residue 165 ILE Chi-restraints excluded: chain 1 residue 241 HIS Chi-restraints excluded: chain 1 residue 492 LEU Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 375 LEU Chi-restraints excluded: chain 3 residue 498 MET Chi-restraints excluded: chain 3 residue 510 VAL Chi-restraints excluded: chain 4 residue 141 TYR Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 375 LEU Chi-restraints excluded: chain 5 residue 124 SER Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 166 LEU Chi-restraints excluded: chain 6 residue 50 ASP Chi-restraints excluded: chain 6 residue 200 VAL Chi-restraints excluded: chain 7 residue 39 LEU Chi-restraints excluded: chain 7 residue 67 HIS Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain 8 residue 2071 VAL Chi-restraints excluded: chain 8 residue 2084 GLU Chi-restraints excluded: chain 8 residue 2122 VAL Chi-restraints excluded: chain 8 residue 2238 GLN Chi-restraints excluded: chain 8 residue 2244 PHE Chi-restraints excluded: chain 8 residue 2408 VAL Chi-restraints excluded: chain 8 residue 2414 TYR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain P residue 51 GLU Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain Q residue 67 HIS Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 185 MET Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 273 PHE Chi-restraints excluded: chain S residue 366 LEU Chi-restraints excluded: chain S residue 525 GLU Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain U residue 178 TYR Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 GLU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 161 ILE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 140 LEU Chi-restraints excluded: chain X residue 161 ILE Chi-restraints excluded: chain X residue 178 TYR Chi-restraints excluded: chain X residue 220 LEU Chi-restraints excluded: chain Y residue 41 ASN Chi-restraints excluded: chain Y residue 347 LEU Chi-restraints excluded: chain Z residue 80 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 544 optimal weight: 0.8980 chunk 876 optimal weight: 1.9990 chunk 535 optimal weight: 0.9980 chunk 415 optimal weight: 1.9990 chunk 609 optimal weight: 2.9990 chunk 919 optimal weight: 0.9990 chunk 846 optimal weight: 10.0000 chunk 732 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 565 optimal weight: 0.2980 chunk 448 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 82055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 GLN ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 75690 Z= 0.161 Angle : 0.549 12.688 102304 Z= 0.269 Chirality : 0.040 0.207 11438 Planarity : 0.003 0.052 13212 Dihedral : 4.781 81.840 10324 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 1.40 % Allowed : 14.66 % Favored : 83.94 % 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: 1.56 (0.09), residues: 9285 helix: 2.01 (0.07), residues: 4889 sheet: 0.43 (0.19), residues: 809 loop : -0.13 (0.11), residues: 3587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 241 HIS 0.007 0.001 HIS S 213 PHE 0.028 0.001 PHE 3 307 TYR 0.032 0.001 TYR U 185 ARG 0.005 0.000 ARG D 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18570 Ramachandran restraints generated. 9285 Oldfield, 0 Emsley, 9285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 669 time to evaluate : 6.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 31 ASN cc_start: 0.8232 (t0) cc_final: 0.7862 (t0) REVERT: 0 60 MET cc_start: 0.8932 (mmm) cc_final: 0.8351 (mmt) REVERT: 0 69 GLU cc_start: 0.8934 (pp20) cc_final: 0.8288 (tp30) REVERT: 0 77 GLU cc_start: 0.7956 (pp20) cc_final: 0.7736 (pp20) REVERT: 0 80 LYS cc_start: 0.8918 (tmtt) cc_final: 0.8054 (mmmt) REVERT: 1 251 MET cc_start: 0.6565 (tmm) cc_final: 0.5772 (mmt) REVERT: 2 177 GLN cc_start: 0.7770 (tm-30) cc_final: 0.6850 (pm20) REVERT: 3 315 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7091 (tp) REVERT: 3 375 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8158 (mt) REVERT: 3 475 MET cc_start: 0.5572 (mtt) cc_final: 0.5309 (mtt) REVERT: 4 256 MET cc_start: 0.5799 (mtm) cc_final: 0.5549 (mtm) REVERT: 5 43 ASP cc_start: 0.8127 (t0) cc_final: 0.7808 (t0) REVERT: 5 70 TYR cc_start: 0.7294 (t80) cc_final: 0.7001 (t80) REVERT: 5 190 ASP cc_start: 0.8569 (t70) cc_final: 0.8015 (t70) REVERT: 7 67 HIS cc_start: 0.4408 (OUTLIER) cc_final: 0.4065 (m-70) REVERT: 8 2084 GLU cc_start: 0.3125 (OUTLIER) cc_final: 0.2382 (tp30) REVERT: 8 2087 LEU cc_start: 0.6186 (mt) cc_final: 0.5537 (tt) REVERT: 8 2156 MET cc_start: 0.2176 (ppp) cc_final: 0.0121 (mmt) REVERT: 8 2199 ARG cc_start: 0.5369 (mtm-85) cc_final: 0.4362 (ptt90) REVERT: 8 2238 GLN cc_start: 0.4780 (OUTLIER) cc_final: 0.4348 (mm-40) REVERT: 8 2414 TYR cc_start: 0.1975 (OUTLIER) cc_final: 0.0937 (t80) REVERT: 9 76 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8344 (mmmt) REVERT: A 82 MET cc_start: 0.7802 (tpp) cc_final: 0.6863 (mmm) REVERT: C 16 MET cc_start: 0.8342 (mmm) cc_final: 0.7865 (mtt) REVERT: C 47 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6802 (mmm) REVERT: D 83 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: F 283 MET cc_start: 0.7844 (tpp) cc_final: 0.7543 (mmt) REVERT: G 47 MET cc_start: 0.6584 (ptt) cc_final: 0.6214 (ptt) REVERT: G 355 MET cc_start: 0.8798 (mmm) cc_final: 0.8037 (mtt) REVERT: H 5 ILE cc_start: 0.8881 (mm) cc_final: 0.8674 (mm) REVERT: J 244 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8560 (t0) REVERT: J 313 MET cc_start: 0.8562 (ttp) cc_final: 0.8130 (ttm) REVERT: K 44 MET cc_start: 0.8498 (tpp) cc_final: 0.8128 (tpp) REVERT: K 107 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: L 81 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8615 (t70) REVERT: L 132 MET cc_start: 0.8799 (ppp) cc_final: 0.8391 (tmm) REVERT: M 41 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7798 (tm-30) REVERT: M 98 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7403 (tm-30) REVERT: M 99 MET cc_start: 0.7896 (tpp) cc_final: 0.7495 (tpp) REVERT: N 71 VAL cc_start: 0.7809 (t) cc_final: 0.7466 (t) REVERT: N 77 ASP cc_start: 0.8335 (t0) cc_final: 0.7643 (t0) REVERT: N 81 ASP cc_start: 0.7693 (m-30) cc_final: 0.7389 (m-30) REVERT: O 98 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7960 (mp0) REVERT: O 117 ASP cc_start: 0.8528 (t0) cc_final: 0.7932 (t0) REVERT: O 140 ASP cc_start: 0.7984 (m-30) cc_final: 0.7692 (m-30) REVERT: P 155 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8706 (tt) REVERT: Q 121 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8409 (mm-40) REVERT: S 302 LYS cc_start: 0.7755 (mtmm) cc_final: 0.6894 (tmtt) REVERT: S 320 GLN cc_start: 0.6282 (pp30) cc_final: 0.5958 (mm-40) REVERT: S 495 ASP cc_start: 0.7140 (t0) cc_final: 0.6880 (t0) REVERT: S 498 ARG cc_start: 0.5044 (ttt180) cc_final: 0.4713 (ttt90) REVERT: S 525 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: T 98 GLU cc_start: 0.7900 (pm20) cc_final: 0.7349 (pm20) REVERT: U 110 ILE cc_start: 0.6808 (tt) cc_final: 0.6304 (pt) REVERT: V 67 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: V 164 MET cc_start: 0.5562 (mmp) cc_final: 0.5300 (mmp) REVERT: V 184 LYS cc_start: 0.6590 (pttm) cc_final: 0.6217 (mmtm) REVERT: V 185 TYR cc_start: 0.7463 (t80) cc_final: 0.7199 (t80) REVERT: V 227 THR cc_start: 0.3230 (m) cc_final: 0.2970 (p) REVERT: V 237 MET cc_start: 0.7414 (tpp) cc_final: 0.6942 (mmp) REVERT: V 248 MET cc_start: 0.4982 (mmt) cc_final: 0.3989 (tpt) REVERT: W 36 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: W 126 TYR cc_start: 0.8020 (t80) cc_final: 0.7797 (t80) REVERT: W 153 ARG cc_start: 0.7022 (ptm-80) cc_final: 0.6766 (ptt90) REVERT: W 157 MET cc_start: 0.8803 (mmm) cc_final: 0.7767 (tpt) REVERT: W 222 ASP cc_start: 0.7675 (t0) cc_final: 0.7402 (m-30) REVERT: X 33 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7501 (ptt90) REVERT: X 57 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7817 (tp40) REVERT: X 91 MET cc_start: 0.6322 (tpt) cc_final: 0.5615 (tpt) REVERT: X 105 MET cc_start: 0.7106 (tpp) cc_final: 0.6748 (tpt) REVERT: X 127 GLU cc_start: 0.5884 (OUTLIER) cc_final: 0.5339 (tm-30) REVERT: X 237 MET cc_start: 0.3589 (mmm) cc_final: 0.2520 (mmm) REVERT: Z 33 GLU cc_start: 0.8183 (pp20) cc_final: 0.7628 (pp20) REVERT: Z 41 MET cc_start: 0.8242 (tmm) cc_final: 0.7829 (tmm) REVERT: Z 98 LYS cc_start: 0.8311 (tppt) cc_final: 0.7304 (pttt) outliers start: 112 outliers final: 88 residues processed: 750 average time/residue: 0.6767 time to fit residues: 889.7046 Evaluate side-chains 748 residues out of total 8131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 644 time to evaluate : 6.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 121 LEU Chi-restraints excluded: chain 1 residue 165 ILE Chi-restraints excluded: chain 1 residue 241 HIS Chi-restraints excluded: chain 1 residue 492 LEU Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 375 LEU Chi-restraints excluded: chain 3 residue 498 MET Chi-restraints excluded: chain 3 residue 510 VAL Chi-restraints excluded: chain 4 residue 141 TYR Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 375 LEU Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 5 residue 124 SER Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 166 LEU Chi-restraints excluded: chain 6 residue 50 ASP Chi-restraints excluded: chain 6 residue 200 VAL Chi-restraints excluded: chain 7 residue 39 LEU Chi-restraints excluded: chain 7 residue 67 HIS Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain 8 residue 2071 VAL Chi-restraints excluded: chain 8 residue 2084 GLU Chi-restraints excluded: chain 8 residue 2122 VAL Chi-restraints excluded: chain 8 residue 2189 THR Chi-restraints excluded: chain 8 residue 2238 GLN Chi-restraints excluded: chain 8 residue 2244 PHE Chi-restraints excluded: chain 8 residue 2408 VAL Chi-restraints excluded: chain 8 residue 2414 TYR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 370 VAL Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain P residue 51 GLU Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain Q residue 67 HIS Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 273 PHE Chi-restraints excluded: chain S residue 366 LEU Chi-restraints excluded: chain S residue 525 GLU Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain U residue 178 TYR Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 GLU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 161 ILE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 140 LEU Chi-restraints excluded: chain X residue 161 ILE Chi-restraints excluded: chain X residue 178 TYR Chi-restraints excluded: chain X residue 220 LEU Chi-restraints excluded: chain Y residue 41 ASN Chi-restraints excluded: chain Y residue 347 LEU Chi-restraints excluded: chain Z residue 80 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 581 optimal weight: 0.9990 chunk 780 optimal weight: 0.0070 chunk 224 optimal weight: 0.0470 chunk 675 optimal weight: 1.9990 chunk 108 optimal weight: 0.0770 chunk 203 optimal weight: 8.9990 chunk 733 optimal weight: 2.9990 chunk 306 optimal weight: 0.0570 chunk 753 optimal weight: 0.0470 chunk 92 optimal weight: 10.0000 chunk 135 optimal weight: 0.0270 overall best weight: 0.0370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 104 ASN ** 2 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 82055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 50 GLN ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.114654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077802 restraints weight = 195661.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.080824 restraints weight = 106029.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.080729 restraints weight = 58732.251| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 75690 Z= 0.140 Angle : 0.547 12.935 102304 Z= 0.268 Chirality : 0.039 0.224 11438 Planarity : 0.003 0.053 13212 Dihedral : 4.574 79.282 10324 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer: Outliers : 0.98 % Allowed : 15.16 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.09), residues: 9285 helix: 2.09 (0.07), residues: 4857 sheet: 0.54 (0.19), residues: 804 loop : 0.02 (0.11), residues: 3624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP 6 192 HIS 0.009 0.001 HIS S 213 PHE 0.020 0.001 PHE G 375 TYR 0.027 0.001 TYR U 185 ARG 0.010 0.000 ARG S 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14889.74 seconds wall clock time: 264 minutes 39.04 seconds (15879.04 seconds total)