Starting phenix.real_space_refine on Sat Mar 23 21:54:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp3_7546/03_2024/6cp3_7546_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp3_7546/03_2024/6cp3_7546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp3_7546/03_2024/6cp3_7546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp3_7546/03_2024/6cp3_7546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp3_7546/03_2024/6cp3_7546_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp3_7546/03_2024/6cp3_7546_updated.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 13 5.49 5 S 92 5.16 5 C 24846 2.51 5 N 6556 2.21 5 O 7375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y GLU 16": "OE1" <-> "OE2" Residue "Y TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38882 Number of models: 1 Model: "" Number of chains: 32 Chain: "K" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1317 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3852 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3836 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 484} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3865 Classifications: {'peptide': 508} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 486} Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3549 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "E" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 448} Chain: "F" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3566 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2086 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 990 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "I" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 392 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "7" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1363 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 710 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 8, 'TRANS': 80} Chain: "U" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 639 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "8" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 364 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "X" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1772 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 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: "F" 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: 19.95, per 1000 atoms: 0.51 Number of scatterers: 38882 At special positions: 0 Unit cell: (127.92, 152.52, 246, 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 92 16.00 P 13 15.00 O 7375 8.00 N 6556 7.00 C 24846 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: 14.80 Conformation dependent library (CDL) restraints added in 6.8 seconds 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9376 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 196 helices and 25 sheets defined 51.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.57 Creating SS restraints... Processing helix chain 'K' and resid 3 through 14 removed outlier: 4.032A pdb=" N LYS K 8 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR K 9 " --> pdb=" O LEU K 5 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE K 10 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 39 removed outlier: 5.662A pdb=" N ILE K 26 " --> pdb=" O GLY K 23 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA K 27 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA K 32 " --> pdb=" O VAL K 29 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN K 35 " --> pdb=" O ALA K 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY K 36 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER K 38 " --> pdb=" O ASN K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 73 removed outlier: 3.652A pdb=" N LYS K 44 " --> pdb=" O PRO K 41 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP K 45 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE K 48 " --> pdb=" O ASP K 45 " (cutoff:3.500A) Proline residue: K 49 - end of helix removed outlier: 4.034A pdb=" N PHE K 55 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU K 57 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA K 60 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR K 61 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU K 71 " --> pdb=" O VAL K 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 14 Processing helix chain 'L' and resid 17 through 38 removed outlier: 4.460A pdb=" N ILE L 24 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE L 26 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN L 35 " --> pdb=" O ALA L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 71 removed outlier: 4.052A pdb=" N LYS L 44 " --> pdb=" O PRO L 41 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP L 45 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR L 46 " --> pdb=" O ILE L 43 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE L 48 " --> pdb=" O ASP L 45 " (cutoff:3.500A) Proline residue: L 49 - end of helix removed outlier: 4.893A pdb=" N LEU L 57 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ALA L 60 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 14 Processing helix chain 'M' and resid 17 through 37 removed outlier: 4.605A pdb=" N ILE M 24 " --> pdb=" O GLY M 21 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE M 26 " --> pdb=" O GLY M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 73 removed outlier: 4.001A pdb=" N LYS M 44 " --> pdb=" O PRO M 41 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP M 45 " --> pdb=" O SER M 42 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE M 48 " --> pdb=" O ASP M 45 " (cutoff:3.500A) Proline residue: M 49 - end of helix removed outlier: 4.946A pdb=" N LEU M 57 " --> pdb=" O GLY M 54 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ALA M 60 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 14 Processing helix chain 'N' and resid 17 through 37 removed outlier: 4.978A pdb=" N GLY N 21 " --> pdb=" O GLY N 18 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA N 22 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE N 26 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL N 37 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 73 Proline residue: N 49 - end of helix removed outlier: 5.170A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 13 Processing helix chain 'O' and resid 17 through 37 removed outlier: 5.103A pdb=" N GLY O 21 " --> pdb=" O GLY O 18 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE O 26 " --> pdb=" O GLY O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 71 removed outlier: 4.036A pdb=" N LYS O 44 " --> pdb=" O PRO O 41 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASP O 45 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE O 48 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Proline residue: O 49 - end of helix removed outlier: 5.306A pdb=" N LEU O 57 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA O 60 " --> pdb=" O LEU O 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 14 Processing helix chain 'P' and resid 17 through 39 removed outlier: 5.218A pdb=" N ILE P 26 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 28 " --> pdb=" O GLY P 25 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER P 38 " --> pdb=" O ASN P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 73 removed outlier: 5.576A pdb=" N THR P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY P 62 " --> pdb=" O SER P 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 14 Processing helix chain 'Q' and resid 17 through 38 removed outlier: 4.145A pdb=" N ILE Q 26 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN Q 35 " --> pdb=" O ALA Q 32 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER Q 38 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 73 removed outlier: 5.345A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY Q 62 " --> pdb=" O SER Q 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 14 Processing helix chain 'R' and resid 17 through 38 removed outlier: 3.916A pdb=" N GLY R 21 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE R 24 " --> pdb=" O GLY R 21 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE R 26 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL R 37 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 74 removed outlier: 4.239A pdb=" N LYS R 44 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASP R 45 " --> pdb=" O SER R 42 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE R 48 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Proline residue: R 49 - end of helix removed outlier: 5.567A pdb=" N LEU R 57 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALA R 60 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR R 61 " --> pdb=" O SER R 58 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU R 72 " --> pdb=" O SER R 69 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU R 73 " --> pdb=" O PHE R 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 38 removed outlier: 3.881A pdb=" N THR S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE S 17 " --> pdb=" O GLY S 13 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY S 18 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU S 20 " --> pdb=" O THR S 16 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA S 22 " --> pdb=" O GLY S 18 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA S 27 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL S 29 " --> pdb=" O GLY S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 73 removed outlier: 3.726A pdb=" N LYS S 44 " --> pdb=" O PRO S 41 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP S 45 " --> pdb=" O SER S 42 " (cutoff:3.500A) Proline residue: S 49 - end of helix removed outlier: 4.091A pdb=" N LEU S 53 " --> pdb=" O MET S 50 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU S 59 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA S 60 " --> pdb=" O LEU S 57 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU S 66 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU S 71 " --> pdb=" O VAL S 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 14 Processing helix chain 'T' and resid 17 through 37 removed outlier: 4.472A pdb=" N GLY T 21 " --> pdb=" O GLY T 18 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE T 26 " --> pdb=" O GLY T 23 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL T 37 " --> pdb=" O ILE T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 43 No H-bonds generated for 'chain 'T' and resid 41 through 43' Processing helix chain 'T' and resid 48 through 62 removed outlier: 3.663A pdb=" N ALA T 56 " --> pdb=" O ILE T 52 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY T 62 " --> pdb=" O SER T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 73 Processing helix chain 'Y' and resid 18 through 28 Processing helix chain 'Y' and resid 34 through 48 Processing helix chain 'Y' and resid 65 through 76 Processing helix chain 'Y' and resid 87 through 95 Processing helix chain 'Y' and resid 102 through 116 Processing helix chain 'Y' and resid 131 through 142 Processing helix chain 'Y' and resid 181 through 191 Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 155 through 158 No H-bonds generated for 'chain 'A' and resid 155 through 158' Processing helix chain 'A' and resid 177 through 192 removed outlier: 4.425A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 242 through 262 Proline residue: A 249 - end of helix removed outlier: 3.725A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 310 removed outlier: 4.490A pdb=" N PHE A 301 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER A 305 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU A 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU A 309 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 357 through 360 No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.848A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 407 removed outlier: 3.908A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 4.423A pdb=" N THR A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 460 through 474 removed outlier: 4.628A pdb=" N GLY A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'B' and resid 6 through 22 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 178 through 192 removed outlier: 4.127A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.678A pdb=" N VAL B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.712A pdb=" N HIS B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 344 No H-bonds generated for 'chain 'B' and resid 341 through 344' Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 414 through 429 Processing helix chain 'B' and resid 440 through 451 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 454 through 457 removed outlier: 4.468A pdb=" N GLY B 457 " --> pdb=" O HIS B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 457' Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.927A pdb=" N GLY B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 467 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 468 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 471 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 476 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 493 through 508 removed outlier: 3.689A pdb=" N PHE B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 19 removed outlier: 3.615A pdb=" N GLU C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 177 through 192 removed outlier: 4.175A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 262 Proline residue: C 249 - end of helix removed outlier: 3.677A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN C 262 " --> pdb=" O TRP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 300 through 308 removed outlier: 3.551A pdb=" N LEU C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.991A pdb=" N SER C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.817A pdb=" N VAL C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 404 removed outlier: 3.514A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 429 Processing helix chain 'C' and resid 441 through 451 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 460 through 474 removed outlier: 5.733A pdb=" N GLY C 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 488 Processing helix chain 'C' and resid 493 through 508 Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 139 through 144 removed outlier: 3.659A pdb=" N LEU D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 174 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 226 through 245 removed outlier: 4.989A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 269 removed outlier: 3.970A pdb=" N VAL D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 292 Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 323 No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 325 through 328 Processing helix chain 'D' and resid 337 through 342 removed outlier: 4.671A pdb=" N LEU D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 363 No H-bonds generated for 'chain 'D' and resid 360 through 363' Processing helix chain 'D' and resid 365 through 386 removed outlier: 4.554A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 398 through 414 removed outlier: 3.558A pdb=" N LEU D 414 " --> pdb=" O ILE D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 425 removed outlier: 4.181A pdb=" N VAL D 423 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D 425 " --> pdb=" O GLU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 446 removed outlier: 3.726A pdb=" N ALA D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'D' and resid 463 through 474 removed outlier: 3.764A pdb=" N ALA D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 163 through 176 Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 226 through 245 removed outlier: 3.764A pdb=" N ARG E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 271 Processing helix chain 'E' and resid 285 through 293 removed outlier: 4.557A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 327 removed outlier: 4.304A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 340 No H-bonds generated for 'chain 'E' and resid 337 through 340' Processing helix chain 'E' and resid 360 through 363 No H-bonds generated for 'chain 'E' and resid 360 through 363' Processing helix chain 'E' and resid 365 through 391 removed outlier: 4.619A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA E 389 " --> pdb=" O GLN E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 413 Processing helix chain 'E' and resid 434 through 446 removed outlier: 3.978A pdb=" N ALA E 439 " --> pdb=" O LYS E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 457 No H-bonds generated for 'chain 'E' and resid 455 through 457' Processing helix chain 'E' and resid 463 through 476 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 139 through 144 removed outlier: 3.560A pdb=" N LEU F 144 " --> pdb=" O VAL F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 5.796A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 232 through 245 removed outlier: 3.540A pdb=" N PHE F 243 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 268 removed outlier: 3.773A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL F 268 " --> pdb=" O ALA F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 294 Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 328 removed outlier: 4.483A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 removed outlier: 4.387A pdb=" N LEU F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 363 No H-bonds generated for 'chain 'F' and resid 360 through 363' Processing helix chain 'F' and resid 365 through 390 removed outlier: 5.093A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 400 through 414 removed outlier: 3.569A pdb=" N ARG F 412 " --> pdb=" O ARG F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 425 No H-bonds generated for 'chain 'F' and resid 422 through 425' Processing helix chain 'F' and resid 434 through 446 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 477 Processing helix chain 'G' and resid 3 through 54 removed outlier: 4.625A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 101 removed outlier: 3.976A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 121 removed outlier: 3.916A pdb=" N ARG G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 150 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 185 through 189 removed outlier: 4.011A pdb=" N GLU G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 185 through 189' Processing helix chain 'G' and resid 205 through 274 removed outlier: 4.731A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE G 253 " --> pdb=" O ASN G 249 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP G 269 " --> pdb=" O ASN G 265 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY G 273 " --> pdb=" O ASP G 269 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA G 274 " --> pdb=" O ILE G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 114 removed outlier: 3.728A pdb=" N LEU H 104 " --> pdb=" O ASN H 100 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU H 105 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 137 removed outlier: 3.547A pdb=" N GLU H 122 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 23 Processing helix chain 'I' and resid 32 through 37 Processing helix chain 'Z' and resid 56 through 113 removed outlier: 5.253A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.604A pdb=" N ARG Z 96 " --> pdb=" O LEU Z 92 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU Z 113 " --> pdb=" O SER Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 132 removed outlier: 4.297A pdb=" N VAL Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP Z 125 " --> pdb=" O LYS Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 135 through 185 removed outlier: 3.889A pdb=" N LYS Z 143 " --> pdb=" O GLU Z 139 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY Z 185 " --> pdb=" O GLN Z 181 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 206 removed outlier: 4.664A pdb=" N VAL Z 193 " --> pdb=" O PHE Z 189 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN Z 195 " --> pdb=" O GLU Z 191 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER Z 206 " --> pdb=" O GLU Z 202 " (cutoff:3.500A) Processing helix chain '7' and resid 5 through 20 removed outlier: 4.982A pdb=" N ARG 7 20 " --> pdb=" O ILE 7 16 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 47 removed outlier: 3.830A pdb=" N LEU 7 43 " --> pdb=" O ALA 7 39 " (cutoff:3.500A) Processing helix chain '7' and resid 57 through 60 No H-bonds generated for 'chain '7' and resid 57 through 60' Processing helix chain '7' and resid 68 through 77 Processing helix chain '7' and resid 92 through 126 removed outlier: 3.657A pdb=" N LYS 7 115 " --> pdb=" O SER 7 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER 7 126 " --> pdb=" O ASP 7 122 " (cutoff:3.500A) Processing helix chain '7' and resid 135 through 141 Processing helix chain '7' and resid 143 through 155 Processing helix chain '6' and resid 5 through 17 Processing helix chain '6' and resid 19 through 22 No H-bonds generated for 'chain '6' and resid 19 through 22' Processing helix chain '6' and resid 46 through 50 Processing helix chain '6' and resid 75 through 91 removed outlier: 4.591A pdb=" N LEU 6 80 " --> pdb=" O GLU 6 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 29 removed outlier: 4.089A pdb=" N LYS U 22 " --> pdb=" O ALA U 18 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 55 Processing helix chain 'U' and resid 63 through 84 removed outlier: 4.645A pdb=" N GLY U 77 " --> pdb=" O ILE U 74 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR U 78 " --> pdb=" O ALA U 75 " (cutoff:3.500A) Processing helix chain '8' and resid 9 through 30 Processing helix chain '8' and resid 33 through 47 removed outlier: 3.901A pdb=" N LEU 8 38 " --> pdb=" O MET 8 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 43 Processing helix chain 'X' and resid 57 through 77 removed outlier: 4.052A pdb=" N SER X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET X 72 " --> pdb=" O THR X 68 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY X 75 " --> pdb=" O ASN X 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE X 77 " --> pdb=" O THR X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 99 removed outlier: 3.775A pdb=" N PHE X 95 " --> pdb=" O THR X 91 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE X 96 " --> pdb=" O LEU X 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 137 Processing helix chain 'X' and resid 140 through 145 removed outlier: 3.510A pdb=" N LEU X 144 " --> pdb=" O PHE X 141 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE X 145 " --> pdb=" O PHE X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 196 Proline residue: X 156 - end of helix removed outlier: 4.175A pdb=" N ILE X 161 " --> pdb=" O LEU X 158 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU X 164 " --> pdb=" O ILE X 161 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE X 167 " --> pdb=" O LEU X 164 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA X 168 " --> pdb=" O SER X 165 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG X 169 " --> pdb=" O TYR X 166 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE X 171 " --> pdb=" O ALA X 168 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER X 172 " --> pdb=" O ARG X 169 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU X 173 " --> pdb=" O ALA X 170 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY X 174 " --> pdb=" O ILE X 171 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG X 176 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLY X 178 " --> pdb=" O LEU X 175 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU X 182 " --> pdb=" O SER X 179 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N HIS X 185 " --> pdb=" O LEU X 182 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU X 186 " --> pdb=" O ALA X 183 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU X 191 " --> pdb=" O MET X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 206 Processing helix chain 'X' and resid 211 through 246 removed outlier: 3.557A pdb=" N ALA X 225 " --> pdb=" O MET X 221 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN X 230 " --> pdb=" O ILE X 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 Processing sheet with id= A, first strand: chain 'Y' and resid 122 through 124 Processing sheet with id= B, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.426A pdb=" N PHE A 44 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL A 33 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= D, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= E, first strand: chain 'A' and resid 231 through 236 removed outlier: 6.852A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU A 326 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.775A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= H, first strand: chain 'B' and resid 167 through 171 removed outlier: 5.698A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 30 through 32 removed outlier: 3.944A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU C 68 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N PHE C 44 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL C 33 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 98 through 101 Processing sheet with id= K, first strand: chain 'C' and resid 169 through 172 Processing sheet with id= L, first strand: chain 'C' and resid 231 through 236 removed outlier: 6.954A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TYR C 270 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.447A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 132 through 134 removed outlier: 4.568A pdb=" N GLU D 132 " --> pdb=" O ARG D 149 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 134 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 331 through 334 removed outlier: 7.926A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLY D 157 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL D 310 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE D 181 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE D 254 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 11 through 17 removed outlier: 6.592A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 85 through 87 removed outlier: 3.552A pdb=" N VAL E 87 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 331 through 333 removed outlier: 8.757A pdb=" N ILE E 153 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER E 306 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU E 155 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN E 308 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 11 through 17 removed outlier: 6.483A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= V, first strand: chain 'F' and resid 152 through 157 removed outlier: 7.563A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 253 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 177 through 183 removed outlier: 3.913A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP G 106 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA G 76 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL G 108 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR G 109 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER G 129 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 49 through 52 removed outlier: 6.020A pdb=" N LYS H 11 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL H 85 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N PHE H 14 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER H 23 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 37 through 41 removed outlier: 6.982A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) 1841 hydrogen bonds defined for protein. 4470 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: 14.13 Time building geometry restraints manager: 16.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11511 1.33 - 1.46: 7159 1.46 - 1.58: 20652 1.58 - 1.70: 21 1.70 - 1.82: 168 Bond restraints: 39511 Sorted by residual: bond pdb=" CA LYS Y 145 " pdb=" C LYS Y 145 " ideal model delta sigma weight residual 1.524 1.428 0.096 1.26e-02 6.30e+03 5.76e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.31e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.92e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.78e+01 ... (remaining 39506 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.76: 680 104.76 - 112.65: 21298 112.65 - 120.55: 18284 120.55 - 128.44: 13080 128.44 - 136.34: 206 Bond angle restraints: 53548 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 115.75 24.12 1.00e+00 1.00e+00 5.82e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 115.94 23.93 1.00e+00 1.00e+00 5.73e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.30 22.57 1.00e+00 1.00e+00 5.09e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 115.23 21.60 1.00e+00 1.00e+00 4.67e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.57 20.26 1.00e+00 1.00e+00 4.10e+02 ... (remaining 53543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 22636 17.46 - 34.92: 960 34.92 - 52.37: 222 52.37 - 69.83: 30 69.83 - 87.29: 22 Dihedral angle restraints: 23870 sinusoidal: 9266 harmonic: 14604 Sorted by residual: dihedral pdb=" CA ALA E 278 " pdb=" C ALA E 278 " pdb=" N VAL E 279 " pdb=" CA VAL E 279 " ideal model delta harmonic sigma weight residual 180.00 -125.20 -54.80 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA ALA D 278 " pdb=" C ALA D 278 " pdb=" N VAL D 279 " pdb=" CA VAL D 279 " ideal model delta harmonic sigma weight residual 180.00 -132.18 -47.82 0 5.00e+00 4.00e-02 9.15e+01 dihedral pdb=" CA GLY 6 26 " pdb=" C GLY 6 26 " pdb=" N ASN 6 27 " pdb=" CA ASN 6 27 " ideal model delta harmonic sigma weight residual 180.00 -136.52 -43.48 0 5.00e+00 4.00e-02 7.56e+01 ... (remaining 23867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5733 0.099 - 0.198: 587 0.198 - 0.297: 28 0.297 - 0.396: 2 0.396 - 0.496: 2 Chirality restraints: 6352 Sorted by residual: chirality pdb=" CB ILE U 5 " pdb=" CA ILE U 5 " pdb=" CG1 ILE U 5 " pdb=" CG2 ILE U 5 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" CA GLU Y 16 " pdb=" N GLU Y 16 " pdb=" C GLU Y 16 " pdb=" CB GLU Y 16 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CB ILE P 43 " pdb=" CA ILE P 43 " pdb=" CG1 ILE P 43 " pdb=" CG2 ILE P 43 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 6349 not shown) Planarity restraints: 6846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 321 " -0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO D 322 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA 6 17 " -0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO 6 18 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO 6 18 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO 6 18 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO U 6 " -0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO U 7 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO U 7 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO U 7 " -0.047 5.00e-02 4.00e+02 ... (remaining 6843 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4224 2.74 - 3.28: 39590 3.28 - 3.82: 65973 3.82 - 4.36: 77713 4.36 - 4.90: 127995 Nonbonded interactions: 315495 Sorted by model distance: nonbonded pdb=" O GLY Y 172 " pdb=" OD1 ASP Y 173 " model vdw 2.196 3.040 nonbonded pdb=" O ALA M 12 " pdb=" OG1 THR M 16 " model vdw 2.224 2.440 nonbonded pdb=" O ARG C 130 " pdb=" OG SER C 254 " model vdw 2.242 2.440 nonbonded pdb=" O VAL E 87 " pdb=" OG SER E 111 " model vdw 2.247 2.440 nonbonded pdb=" OG SER C 378 " pdb=" O VAL D 423 " model vdw 2.267 2.440 ... (remaining 315490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 22 or (resid 23 and (name N or name CA or name C \ or name O or name CB )) or resid 24 through 28 or (resid 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 45 or (resid 46 and (n \ ame N or name CA or name C or name O or name CB )) or resid 47 through 509 or re \ sid 600)) selection = (chain 'B' and (resid 4 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 509 or resid 600)) selection = (chain 'C' and (resid 4 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 and (name N or name \ CA or name C or name O or name CB )) or resid 24 through 28 or (resid 29 and (n \ ame N or name CA or name C or name O or name CB )) or resid 30 through 45 or (re \ sid 46 and (name N or name CA or name C or name O or name CB )) or resid 47 thro \ ugh 509 or resid 600)) } ncs_group { reference = (chain 'D' and resid 7 through 475) selection = (chain 'E' and resid 7 through 475) selection = (chain 'F' and resid 7 through 475) } ncs_group { reference = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 74)) selection = chain 'L' selection = (chain 'M' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 74)) selection = chain 'N' selection = (chain 'O' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 74)) selection = (chain 'P' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 74)) selection = chain 'Q' selection = (chain 'R' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 74)) selection = chain 'S' selection = (chain 'T' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 74)) } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 9.260 Check model and map are aligned: 0.550 Set scattering table: 0.330 Process input model: 97.140 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.009 0.126 39511 Z= 0.586 Angle : 1.182 24.119 53548 Z= 0.673 Chirality : 0.061 0.496 6352 Planarity : 0.008 0.089 6846 Dihedral : 11.296 87.288 14494 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.29 % Favored : 92.41 % Rotamer: Outliers : 1.07 % Allowed : 4.56 % Favored : 94.37 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.88 (0.10), residues: 5062 helix: -2.52 (0.08), residues: 2510 sheet: -2.15 (0.19), residues: 584 loop : -2.53 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP B 258 HIS 0.018 0.003 HIS 6 92 PHE 0.023 0.003 PHE X 224 TYR 0.033 0.003 TYR C 339 ARG 0.015 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1500 time to evaluate : 4.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 63 LEU cc_start: 0.7987 (mt) cc_final: 0.7686 (tt) REVERT: L 5 LEU cc_start: 0.6078 (pt) cc_final: 0.5814 (pt) REVERT: L 63 LEU cc_start: 0.8049 (mt) cc_final: 0.7593 (mt) REVERT: M 48 PHE cc_start: 0.7076 (t80) cc_final: 0.6362 (t80) REVERT: N 15 SER cc_start: 0.6730 (p) cc_final: 0.6522 (t) REVERT: N 50 MET cc_start: 0.7173 (ttm) cc_final: 0.6770 (ttp) REVERT: O 70 PHE cc_start: 0.7400 (m-80) cc_final: 0.7103 (m-80) REVERT: P 41 PRO cc_start: 0.8217 (Cg_exo) cc_final: 0.7828 (Cg_endo) REVERT: P 71 LEU cc_start: 0.7151 (pp) cc_final: 0.6692 (tp) REVERT: P 72 LEU cc_start: 0.6292 (tp) cc_final: 0.5953 (mm) REVERT: Q 55 PHE cc_start: 0.6018 (t80) cc_final: 0.5299 (t80) REVERT: R 46 THR cc_start: 0.7071 (m) cc_final: 0.6666 (m) REVERT: R 47 VAL cc_start: 0.8399 (m) cc_final: 0.8134 (t) REVERT: R 70 PHE cc_start: 0.6577 (t80) cc_final: 0.6331 (t80) REVERT: T 35 ASN cc_start: 0.8299 (m-40) cc_final: 0.7996 (m110) REVERT: Y 138 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7934 (mt-10) REVERT: A 30 THR cc_start: 0.7140 (p) cc_final: 0.6921 (p) REVERT: A 67 ASN cc_start: 0.8151 (m-40) cc_final: 0.7854 (p0) REVERT: A 170 ILE cc_start: 0.9243 (tt) cc_final: 0.9027 (mt) REVERT: A 274 SER cc_start: 0.8341 (m) cc_final: 0.7562 (p) REVERT: A 284 SER cc_start: 0.8389 (m) cc_final: 0.8105 (t) REVERT: A 471 LEU cc_start: 0.8544 (mt) cc_final: 0.7931 (mt) REVERT: B 84 VAL cc_start: 0.8434 (t) cc_final: 0.8221 (t) REVERT: B 138 ILE cc_start: 0.8853 (pt) cc_final: 0.8125 (mt) REVERT: B 153 LYS cc_start: 0.7580 (mtpt) cc_final: 0.7293 (mtpp) REVERT: B 271 ASP cc_start: 0.7381 (t70) cc_final: 0.7081 (t70) REVERT: B 335 ASP cc_start: 0.7756 (t70) cc_final: 0.7548 (p0) REVERT: C 9 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: C 11 SER cc_start: 0.6758 (m) cc_final: 0.4649 (m) REVERT: C 150 THR cc_start: 0.8852 (p) cc_final: 0.8636 (p) REVERT: C 299 ASP cc_start: 0.7740 (p0) cc_final: 0.7520 (p0) REVERT: C 369 VAL cc_start: 0.8230 (t) cc_final: 0.7919 (p) REVERT: D 39 ILE cc_start: 0.9185 (tp) cc_final: 0.8951 (tt) REVERT: D 178 HIS cc_start: 0.5381 (t-90) cc_final: 0.5005 (t70) REVERT: D 222 MET cc_start: 0.7603 (ptp) cc_final: 0.7115 (ptp) REVERT: D 256 ASP cc_start: 0.7930 (t70) cc_final: 0.7726 (t0) REVERT: E 133 ILE cc_start: 0.7518 (mm) cc_final: 0.7220 (mm) REVERT: E 263 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7811 (mm-40) REVERT: F 282 GLN cc_start: 0.8990 (pm20) cc_final: 0.7993 (pm20) REVERT: F 319 ASP cc_start: 0.8233 (t70) cc_final: 0.7823 (t0) REVERT: F 348 VAL cc_start: 0.8878 (t) cc_final: 0.8650 (m) REVERT: F 352 ASP cc_start: 0.6269 (t70) cc_final: 0.5834 (t0) REVERT: F 449 TYR cc_start: 0.7359 (m-80) cc_final: 0.7138 (m-80) REVERT: F 473 LEU cc_start: 0.8179 (mt) cc_final: 0.7962 (mt) REVERT: G 251 TYR cc_start: 0.8405 (m-80) cc_final: 0.8052 (m-80) REVERT: G 255 TYR cc_start: 0.8924 (t80) cc_final: 0.8638 (t80) REVERT: H 51 GLN cc_start: 0.7039 (pt0) cc_final: 0.6512 (pt0) REVERT: Z 133 LEU cc_start: 0.7450 (mt) cc_final: 0.7242 (tt) REVERT: Z 179 ARG cc_start: 0.5753 (mpp80) cc_final: 0.4368 (mmp80) REVERT: 7 43 LEU cc_start: 0.8290 (pp) cc_final: 0.7885 (mt) REVERT: 6 60 THR cc_start: 0.6963 (p) cc_final: 0.6375 (t) REVERT: 6 87 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6691 (mm-30) REVERT: U 48 LEU cc_start: 0.6901 (mp) cc_final: 0.6673 (mp) REVERT: 8 36 LEU cc_start: 0.8574 (tt) cc_final: 0.8341 (tt) REVERT: 8 37 ARG cc_start: 0.7312 (mtp180) cc_final: 0.7047 (tpp80) REVERT: X 51 ASN cc_start: 0.5624 (m-40) cc_final: 0.4958 (m-40) REVERT: X 96 ILE cc_start: 0.8848 (mt) cc_final: 0.8647 (mm) REVERT: X 131 ILE cc_start: 0.7868 (mm) cc_final: 0.7651 (mm) REVERT: X 173 LEU cc_start: 0.7066 (tp) cc_final: 0.6483 (tp) REVERT: X 215 MET cc_start: 0.6417 (ttp) cc_final: 0.5922 (tpt) REVERT: X 232 TYR cc_start: 0.7822 (t80) cc_final: 0.7494 (t80) REVERT: X 237 LEU cc_start: 0.8884 (mp) cc_final: 0.8493 (mt) REVERT: J 4 ARG cc_start: 0.6709 (ttt180) cc_final: 0.6452 (ttm170) outliers start: 44 outliers final: 7 residues processed: 1521 average time/residue: 0.5481 time to fit residues: 1315.7264 Evaluate side-chains 824 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 816 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 38 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 422 optimal weight: 10.0000 chunk 378 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 129 optimal weight: 0.2980 chunk 255 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 391 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 238 optimal weight: 0.0370 chunk 291 optimal weight: 3.9990 chunk 454 optimal weight: 9.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 2 GLN Y 188 ASN A 145 HIS A 217 GLN A 220 GLN A 262 ASN A 332 GLN A 432 GLN B 192 ASN B 262 ASN B 398 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN C 381 GLN C 478 HIS D 27 GLN D 52 GLN D 385 GLN E 35 ASN E 127 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 ASN Z 171 GLN ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 88 GLN ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 38 ASN 6 57 ASN ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 HIS U 60 ASN U 85 HIS 8 29 GLN ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39511 Z= 0.210 Angle : 0.726 14.128 53548 Z= 0.363 Chirality : 0.044 0.199 6352 Planarity : 0.005 0.072 6846 Dihedral : 7.617 89.855 5575 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.70 % Favored : 95.12 % Rotamer: Outliers : 3.02 % Allowed : 13.78 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.11), residues: 5062 helix: -1.10 (0.09), residues: 2597 sheet: -1.63 (0.21), residues: 566 loop : -1.93 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 234 HIS 0.011 0.001 HIS 6 92 PHE 0.028 0.002 PHE H 69 TYR 0.027 0.002 TYR X 241 ARG 0.008 0.001 ARG 7 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 923 time to evaluate : 4.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 ILE cc_start: 0.8444 (mm) cc_final: 0.8113 (tp) REVERT: N 50 MET cc_start: 0.6427 (ttm) cc_final: 0.5708 (ttp) REVERT: N 57 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.4812 (mt) REVERT: P 41 PRO cc_start: 0.7824 (Cg_exo) cc_final: 0.7324 (Cg_endo) REVERT: P 71 LEU cc_start: 0.7542 (pp) cc_final: 0.6766 (tp) REVERT: P 72 LEU cc_start: 0.6235 (tp) cc_final: 0.5922 (mm) REVERT: R 52 ILE cc_start: 0.9044 (tp) cc_final: 0.8808 (tp) REVERT: R 61 THR cc_start: 0.8193 (p) cc_final: 0.7894 (t) REVERT: R 70 PHE cc_start: 0.6865 (t80) cc_final: 0.6477 (t80) REVERT: S 5 LEU cc_start: 0.7892 (pt) cc_final: 0.7558 (pt) REVERT: S 30 PHE cc_start: 0.7724 (m-80) cc_final: 0.7522 (m-80) REVERT: T 8 LYS cc_start: 0.8050 (ptmt) cc_final: 0.7626 (ptmt) REVERT: T 67 MET cc_start: 0.7793 (ppp) cc_final: 0.7540 (ppp) REVERT: A 272 ASP cc_start: 0.7940 (p0) cc_final: 0.7380 (p0) REVERT: A 274 SER cc_start: 0.8294 (m) cc_final: 0.7732 (p) REVERT: A 284 SER cc_start: 0.8837 (m) cc_final: 0.8294 (t) REVERT: B 139 LEU cc_start: 0.8963 (tp) cc_final: 0.8754 (mm) REVERT: B 239 SER cc_start: 0.8620 (p) cc_final: 0.7805 (t) REVERT: B 335 ASP cc_start: 0.8039 (t70) cc_final: 0.7537 (p0) REVERT: B 462 ARG cc_start: 0.6326 (ttt-90) cc_final: 0.6030 (ttt90) REVERT: C 9 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: C 150 THR cc_start: 0.9018 (p) cc_final: 0.8749 (p) REVERT: C 299 ASP cc_start: 0.7767 (p0) cc_final: 0.7548 (p0) REVERT: C 309 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7683 (mm-30) REVERT: C 369 VAL cc_start: 0.8399 (t) cc_final: 0.8099 (p) REVERT: D 294 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7000 (mm-30) REVERT: D 334 VAL cc_start: 0.8829 (t) cc_final: 0.8627 (p) REVERT: E 316 ASP cc_start: 0.7329 (t0) cc_final: 0.7016 (m-30) REVERT: F 64 MET cc_start: 0.8262 (mmm) cc_final: 0.7944 (mmp) REVERT: F 282 GLN cc_start: 0.9054 (pm20) cc_final: 0.8044 (pm20) REVERT: F 284 THR cc_start: 0.8236 (p) cc_final: 0.8028 (t) REVERT: F 319 ASP cc_start: 0.8092 (t70) cc_final: 0.7856 (t0) REVERT: G 23 MET cc_start: 0.8354 (tpp) cc_final: 0.8132 (tpp) REVERT: G 59 ASN cc_start: 0.7647 (p0) cc_final: 0.6039 (t0) REVERT: G 255 TYR cc_start: 0.8844 (t80) cc_final: 0.8539 (t80) REVERT: H 11 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8129 (mmmt) REVERT: Z 179 ARG cc_start: 0.5763 (mpp80) cc_final: 0.4629 (mmp80) REVERT: 7 170 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7337 (tp) REVERT: 6 87 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6242 (mm-30) REVERT: U 64 LYS cc_start: 0.7728 (mtmt) cc_final: 0.7035 (mmtt) REVERT: 8 17 PHE cc_start: 0.6171 (t80) cc_final: 0.5733 (t80) REVERT: 8 34 MET cc_start: 0.7979 (ppp) cc_final: 0.7559 (ppp) REVERT: 8 36 LEU cc_start: 0.8527 (tt) cc_final: 0.8311 (tt) REVERT: X 63 GLU cc_start: 0.7108 (tp30) cc_final: 0.6590 (tp30) REVERT: X 173 LEU cc_start: 0.6812 (tp) cc_final: 0.6391 (tp) REVERT: X 176 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7662 (ttm110) REVERT: X 237 LEU cc_start: 0.8958 (mp) cc_final: 0.8743 (mt) REVERT: J 13 TYR cc_start: 0.4030 (m-10) cc_final: 0.3650 (m-10) outliers start: 124 outliers final: 63 residues processed: 993 average time/residue: 0.4897 time to fit residues: 798.6330 Evaluate side-chains 796 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 730 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 141 GLN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 50 ARG Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 252 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 377 optimal weight: 8.9990 chunk 309 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 454 optimal weight: 9.9990 chunk 491 optimal weight: 0.8980 chunk 405 optimal weight: 10.0000 chunk 451 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 364 optimal weight: 4.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN M 2 GLN ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 304 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 GLN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 GLN D 52 GLN D 118 HIS E 263 GLN F 24 HIS F 52 GLN F 53 HIS ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 GLN H 51 GLN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN Z 93 ASN ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS U 85 HIS ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 39511 Z= 0.451 Angle : 0.811 10.595 53548 Z= 0.409 Chirality : 0.047 0.185 6352 Planarity : 0.005 0.072 6846 Dihedral : 7.336 82.211 5572 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.83 % Favored : 93.97 % Rotamer: Outliers : 5.15 % Allowed : 15.63 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.85 (0.11), residues: 5062 helix: -0.69 (0.10), residues: 2635 sheet: -1.42 (0.21), residues: 567 loop : -1.77 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 234 HIS 0.010 0.002 HIS B 304 PHE 0.034 0.003 PHE H 96 TYR 0.029 0.002 TYR X 44 ARG 0.007 0.001 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 735 time to evaluate : 4.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7746 (mt) cc_final: 0.7453 (mm) REVERT: K 71 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7698 (mm) REVERT: L 43 ILE cc_start: 0.8508 (mm) cc_final: 0.8286 (tp) REVERT: N 15 SER cc_start: 0.6766 (p) cc_final: 0.6303 (t) REVERT: R 5 LEU cc_start: 0.8145 (tp) cc_final: 0.7929 (tp) REVERT: R 52 ILE cc_start: 0.9083 (tp) cc_final: 0.8782 (tp) REVERT: R 70 PHE cc_start: 0.6674 (t80) cc_final: 0.6337 (t80) REVERT: Y 138 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7843 (mt-10) REVERT: A 15 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7202 (mm-30) REVERT: A 30 THR cc_start: 0.7507 (p) cc_final: 0.7143 (p) REVERT: A 272 ASP cc_start: 0.7986 (p0) cc_final: 0.7309 (p0) REVERT: A 274 SER cc_start: 0.8766 (m) cc_final: 0.8164 (p) REVERT: B 335 ASP cc_start: 0.8614 (t70) cc_final: 0.8298 (t0) REVERT: B 398 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.8001 (tm130) REVERT: C 17 ARG cc_start: 0.7451 (mtp180) cc_final: 0.7210 (ttm-80) REVERT: C 299 ASP cc_start: 0.8141 (p0) cc_final: 0.7891 (p0) REVERT: C 369 VAL cc_start: 0.8798 (t) cc_final: 0.8541 (p) REVERT: E 64 MET cc_start: 0.8855 (mmm) cc_final: 0.8423 (mmt) REVERT: E 353 SER cc_start: 0.8397 (m) cc_final: 0.7865 (p) REVERT: E 459 MET cc_start: 0.8079 (tpp) cc_final: 0.7759 (tpp) REVERT: G 117 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: H 11 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8203 (mmmt) REVERT: H 69 PHE cc_start: 0.8070 (t80) cc_final: 0.7789 (t80) REVERT: I 28 GLU cc_start: 0.6117 (pm20) cc_final: 0.5767 (pm20) REVERT: Z 179 ARG cc_start: 0.5973 (mpp80) cc_final: 0.4688 (mmp80) REVERT: 6 21 LEU cc_start: 0.2704 (OUTLIER) cc_final: 0.2276 (tp) REVERT: 6 87 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6334 (mm-30) REVERT: U 64 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7243 (mmtt) REVERT: 8 17 PHE cc_start: 0.6048 (t80) cc_final: 0.5646 (t80) REVERT: 8 29 GLN cc_start: 0.7555 (tt0) cc_final: 0.7275 (tt0) REVERT: 8 34 MET cc_start: 0.8002 (ppp) cc_final: 0.7581 (ppp) REVERT: X 46 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6782 (pp) REVERT: X 63 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6783 (tp30) REVERT: X 76 GLN cc_start: 0.7121 (tm-30) cc_final: 0.6553 (tm-30) outliers start: 211 outliers final: 138 residues processed: 862 average time/residue: 0.4832 time to fit residues: 686.7992 Evaluate side-chains 796 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 652 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 48 PHE Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 43 ILE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 87 ASN Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 115 ASN Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 6 residue 21 LEU Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 207 VAL Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 219 ILE Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 449 optimal weight: 8.9990 chunk 341 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 217 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 456 optimal weight: 20.0000 chunk 483 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 432 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS B 192 ASN B 398 GLN C 67 ASN C 145 HIS ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 385 GLN E 57 ASN E 118 HIS ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 GLN F 52 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39511 Z= 0.260 Angle : 0.689 13.752 53548 Z= 0.343 Chirality : 0.044 0.178 6352 Planarity : 0.005 0.071 6846 Dihedral : 6.940 79.754 5569 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.94 % Favored : 94.90 % Rotamer: Outliers : 4.39 % Allowed : 17.63 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.12), residues: 5062 helix: -0.34 (0.10), residues: 2647 sheet: -1.30 (0.21), residues: 561 loop : -1.57 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 234 HIS 0.011 0.001 HIS Z 99 PHE 0.033 0.002 PHE E 418 TYR 0.039 0.002 TYR Q 9 ARG 0.006 0.001 ARG 7 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 737 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 71 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7884 (mm) REVERT: N 15 SER cc_start: 0.6407 (p) cc_final: 0.6182 (t) REVERT: Q 50 MET cc_start: 0.7654 (mpp) cc_final: 0.7363 (ptp) REVERT: Q 59 GLU cc_start: 0.7971 (pt0) cc_final: 0.7723 (pt0) REVERT: R 52 ILE cc_start: 0.9082 (tp) cc_final: 0.8812 (tp) REVERT: R 53 LEU cc_start: 0.8053 (tt) cc_final: 0.7642 (mt) REVERT: R 70 PHE cc_start: 0.6970 (t80) cc_final: 0.6638 (t80) REVERT: S 57 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7636 (mp) REVERT: Y 77 THR cc_start: 0.6469 (OUTLIER) cc_final: 0.6176 (m) REVERT: Y 167 LEU cc_start: 0.8273 (mp) cc_final: 0.7955 (mt) REVERT: A 30 THR cc_start: 0.7427 (p) cc_final: 0.7053 (p) REVERT: A 272 ASP cc_start: 0.7797 (p0) cc_final: 0.7032 (p0) REVERT: A 274 SER cc_start: 0.8692 (m) cc_final: 0.8134 (p) REVERT: B 228 MET cc_start: 0.7200 (mmm) cc_final: 0.6939 (mmt) REVERT: B 281 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8207 (ttt180) REVERT: B 335 ASP cc_start: 0.8563 (t70) cc_final: 0.7864 (p0) REVERT: B 395 PHE cc_start: 0.7146 (t80) cc_final: 0.6738 (t80) REVERT: C 9 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: C 150 THR cc_start: 0.9071 (p) cc_final: 0.8785 (p) REVERT: C 299 ASP cc_start: 0.7879 (p0) cc_final: 0.7621 (p0) REVERT: D 72 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7326 (mtp85) REVERT: E 57 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7887 (t0) REVERT: E 64 MET cc_start: 0.8809 (mmm) cc_final: 0.8447 (mmt) REVERT: E 353 SER cc_start: 0.8390 (m) cc_final: 0.7857 (p) REVERT: E 459 MET cc_start: 0.8131 (tpp) cc_final: 0.7858 (tpp) REVERT: F 64 MET cc_start: 0.8585 (mmm) cc_final: 0.8094 (mmp) REVERT: G 117 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: H 11 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8470 (mmmt) REVERT: 7 41 ARG cc_start: 0.7469 (ppt170) cc_final: 0.7120 (ppt170) REVERT: 6 87 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6322 (mm-30) REVERT: U 64 LYS cc_start: 0.7855 (mtmt) cc_final: 0.7609 (mmtt) REVERT: 8 17 PHE cc_start: 0.5976 (t80) cc_final: 0.5535 (t80) REVERT: 8 34 MET cc_start: 0.7988 (ppp) cc_final: 0.7508 (ppp) REVERT: X 76 GLN cc_start: 0.6975 (tm-30) cc_final: 0.6502 (tm-30) outliers start: 180 outliers final: 118 residues processed: 851 average time/residue: 0.4755 time to fit residues: 671.5651 Evaluate side-chains 780 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 654 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 68 HIS Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 175 LEU Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 207 VAL Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 242 LEU Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 402 optimal weight: 0.7980 chunk 274 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 359 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 412 optimal weight: 0.9980 chunk 334 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 433 optimal weight: 5.9990 chunk 121 optimal weight: 0.0370 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN A 145 HIS B 174 GLN B 398 GLN C 145 HIS ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 GLN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN G 49 GLN G 217 GLN H 51 GLN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 39511 Z= 0.212 Angle : 0.675 12.629 53548 Z= 0.331 Chirality : 0.043 0.200 6352 Planarity : 0.004 0.072 6846 Dihedral : 6.653 79.701 5567 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.92 % Favored : 94.92 % Rotamer: Outliers : 4.10 % Allowed : 19.29 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.12), residues: 5062 helix: -0.03 (0.10), residues: 2589 sheet: -1.11 (0.22), residues: 544 loop : -1.48 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP X 126 HIS 0.012 0.001 HIS U 68 PHE 0.050 0.002 PHE P 64 TYR 0.023 0.002 TYR S 9 ARG 0.011 0.001 ARG 8 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 732 time to evaluate : 4.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 71 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8227 (mm) REVERT: L 53 LEU cc_start: 0.7147 (mm) cc_final: 0.6946 (tt) REVERT: N 72 LEU cc_start: 0.6972 (tp) cc_final: 0.6660 (tp) REVERT: P 46 THR cc_start: 0.5702 (m) cc_final: 0.5481 (m) REVERT: Q 40 ASN cc_start: 0.7957 (t0) cc_final: 0.7700 (t0) REVERT: Q 50 MET cc_start: 0.7546 (mpp) cc_final: 0.7328 (ptp) REVERT: Q 59 GLU cc_start: 0.8032 (pt0) cc_final: 0.7694 (pt0) REVERT: R 52 ILE cc_start: 0.9212 (tp) cc_final: 0.8876 (tp) REVERT: R 53 LEU cc_start: 0.7846 (tt) cc_final: 0.7569 (mt) REVERT: R 70 PHE cc_start: 0.6923 (t80) cc_final: 0.6579 (t80) REVERT: S 43 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6931 (tp) REVERT: Y 25 GLN cc_start: 0.7737 (mm110) cc_final: 0.7206 (mm110) REVERT: Y 77 THR cc_start: 0.6343 (OUTLIER) cc_final: 0.6080 (m) REVERT: A 30 THR cc_start: 0.7410 (p) cc_final: 0.7016 (p) REVERT: A 272 ASP cc_start: 0.7692 (p0) cc_final: 0.6899 (p0) REVERT: A 274 SER cc_start: 0.8601 (m) cc_final: 0.8029 (p) REVERT: B 281 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8160 (ttt180) REVERT: B 335 ASP cc_start: 0.8448 (t70) cc_final: 0.7916 (p0) REVERT: C 9 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: C 150 THR cc_start: 0.9055 (p) cc_final: 0.8767 (p) REVERT: C 299 ASP cc_start: 0.7811 (p0) cc_final: 0.7536 (p0) REVERT: D 72 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7403 (mtp85) REVERT: D 294 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6738 (tp30) REVERT: E 64 MET cc_start: 0.8790 (mmm) cc_final: 0.8564 (mmt) REVERT: F 282 GLN cc_start: 0.9184 (pm20) cc_final: 0.8139 (pm20) REVERT: G 59 ASN cc_start: 0.7662 (p0) cc_final: 0.6154 (t0) REVERT: H 11 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8432 (mmmt) REVERT: Z 92 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7421 (pp) REVERT: 6 75 ILE cc_start: 0.7703 (mm) cc_final: 0.7449 (mm) REVERT: 6 80 LEU cc_start: 0.7778 (mt) cc_final: 0.7554 (tp) REVERT: 6 87 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6431 (mm-30) REVERT: 8 34 MET cc_start: 0.7964 (ppp) cc_final: 0.7503 (ppp) REVERT: X 76 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6937 (tm-30) outliers start: 168 outliers final: 125 residues processed: 838 average time/residue: 0.4801 time to fit residues: 669.3316 Evaluate side-chains 795 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 663 time to evaluate : 4.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 48 PHE Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 9 TYR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 43 ILE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 76 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 341 GLU Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 9 LYS Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 157 LYS Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain 8 residue 13 LEU Chi-restraints excluded: chain X residue 67 ASP Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 207 VAL Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 219 ILE Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 0.9980 chunk 435 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 483 optimal weight: 9.9990 chunk 401 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 ASN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN A 145 HIS ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 ASN ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 62 GLN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 185 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39511 Z= 0.287 Angle : 0.690 11.194 53548 Z= 0.343 Chirality : 0.044 0.215 6352 Planarity : 0.004 0.072 6846 Dihedral : 6.580 83.750 5567 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.22 % Favored : 94.63 % Rotamer: Outliers : 5.02 % Allowed : 19.66 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.01 (0.12), residues: 5062 helix: 0.01 (0.10), residues: 2639 sheet: -1.05 (0.22), residues: 532 loop : -1.41 (0.15), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP X 126 HIS 0.009 0.001 HIS Z 99 PHE 0.051 0.002 PHE P 64 TYR 0.035 0.002 TYR Q 9 ARG 0.008 0.001 ARG 8 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 702 time to evaluate : 4.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 71 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8257 (mm) REVERT: L 5 LEU cc_start: 0.5980 (pt) cc_final: 0.5755 (pt) REVERT: L 43 ILE cc_start: 0.8368 (mm) cc_final: 0.8143 (tp) REVERT: N 72 LEU cc_start: 0.7022 (tp) cc_final: 0.6712 (tp) REVERT: Q 40 ASN cc_start: 0.8035 (t0) cc_final: 0.7723 (t0) REVERT: Q 59 GLU cc_start: 0.8107 (pt0) cc_final: 0.7823 (pt0) REVERT: R 52 ILE cc_start: 0.9211 (tp) cc_final: 0.8884 (tp) REVERT: R 53 LEU cc_start: 0.8298 (tt) cc_final: 0.7722 (mt) REVERT: R 70 PHE cc_start: 0.6980 (t80) cc_final: 0.6652 (t80) REVERT: S 43 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7108 (tp) REVERT: Y 77 THR cc_start: 0.6577 (OUTLIER) cc_final: 0.6291 (m) REVERT: Y 113 ASP cc_start: 0.8146 (p0) cc_final: 0.7871 (p0) REVERT: A 30 THR cc_start: 0.7434 (p) cc_final: 0.7041 (p) REVERT: A 272 ASP cc_start: 0.7692 (p0) cc_final: 0.6971 (p0) REVERT: A 274 SER cc_start: 0.8669 (m) cc_final: 0.8128 (p) REVERT: B 281 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8150 (ttt180) REVERT: B 335 ASP cc_start: 0.8484 (t70) cc_final: 0.7951 (p0) REVERT: C 9 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: C 299 ASP cc_start: 0.7917 (p0) cc_final: 0.7625 (p0) REVERT: D 72 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7467 (mtp85) REVERT: D 294 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6471 (tp30) REVERT: E 64 MET cc_start: 0.8813 (mmm) cc_final: 0.8456 (mmt) REVERT: E 353 SER cc_start: 0.8473 (m) cc_final: 0.7935 (p) REVERT: G 59 ASN cc_start: 0.7718 (p0) cc_final: 0.6157 (t0) REVERT: G 117 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: H 11 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8391 (mmmt) REVERT: Z 57 ILE cc_start: 0.4759 (mt) cc_final: 0.4334 (tt) REVERT: Z 179 ARG cc_start: 0.5843 (mpp80) cc_final: 0.4519 (mmp80) REVERT: 6 75 ILE cc_start: 0.7758 (mm) cc_final: 0.7522 (mm) REVERT: 6 87 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6395 (mm-30) REVERT: U 64 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7535 (mmtt) REVERT: 8 34 MET cc_start: 0.8125 (ppp) cc_final: 0.7679 (ppp) REVERT: X 76 GLN cc_start: 0.7389 (tm-30) cc_final: 0.7077 (tm-30) REVERT: J 13 TYR cc_start: 0.4743 (m-10) cc_final: 0.4485 (m-10) outliers start: 206 outliers final: 158 residues processed: 827 average time/residue: 0.4699 time to fit residues: 649.8629 Evaluate side-chains 829 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 664 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 48 PHE Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 43 ILE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 65 LYS Chi-restraints excluded: chain Y residue 76 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 341 GLU Chi-restraints excluded: chain F residue 352 ASP Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 184 ASN Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 115 ASN Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 9 LYS Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 130 PHE Chi-restraints excluded: chain 7 residue 157 LYS Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 55 TYR Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 175 LEU Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 207 VAL Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 219 ILE Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 466 optimal weight: 0.0030 chunk 54 optimal weight: 6.9990 chunk 275 optimal weight: 0.9980 chunk 353 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 chunk 407 optimal weight: 4.9990 chunk 270 optimal weight: 0.8980 chunk 481 optimal weight: 5.9990 chunk 301 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 chunk 222 optimal weight: 0.7980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 2 GLN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN A 262 ASN A 304 HIS ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN D 221 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 HIS G 217 GLN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN ** Z 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 39511 Z= 0.178 Angle : 0.672 18.407 53548 Z= 0.327 Chirality : 0.043 0.326 6352 Planarity : 0.004 0.070 6846 Dihedral : 6.336 86.749 5567 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.62 % Favored : 95.22 % Rotamer: Outliers : 3.37 % Allowed : 21.54 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.75 (0.12), residues: 5062 helix: 0.17 (0.10), residues: 2658 sheet: -0.78 (0.22), residues: 521 loop : -1.26 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP X 126 HIS 0.008 0.001 HIS Z 99 PHE 0.050 0.002 PHE P 64 TYR 0.024 0.001 TYR D 381 ARG 0.009 0.000 ARG 8 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 747 time to evaluate : 4.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 5 LEU cc_start: 0.5889 (pt) cc_final: 0.5667 (pt) REVERT: L 70 PHE cc_start: 0.7639 (m-80) cc_final: 0.7439 (m-80) REVERT: N 30 PHE cc_start: 0.8040 (m-80) cc_final: 0.7776 (m-80) REVERT: N 72 LEU cc_start: 0.7000 (tp) cc_final: 0.6633 (tp) REVERT: P 5 LEU cc_start: 0.7774 (pt) cc_final: 0.7359 (tp) REVERT: Q 40 ASN cc_start: 0.8069 (t0) cc_final: 0.7687 (t0) REVERT: Q 59 GLU cc_start: 0.8066 (pt0) cc_final: 0.7709 (pt0) REVERT: R 52 ILE cc_start: 0.9151 (tp) cc_final: 0.8799 (tp) REVERT: R 53 LEU cc_start: 0.8190 (tt) cc_final: 0.7669 (mt) REVERT: R 70 PHE cc_start: 0.6812 (t80) cc_final: 0.6477 (t80) REVERT: T 57 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8438 (mt) REVERT: Y 77 THR cc_start: 0.6324 (OUTLIER) cc_final: 0.6076 (m) REVERT: Y 113 ASP cc_start: 0.7987 (p0) cc_final: 0.7719 (p0) REVERT: Y 185 GLN cc_start: 0.8661 (tp40) cc_final: 0.8341 (tm-30) REVERT: A 27 LEU cc_start: 0.7236 (mt) cc_final: 0.6971 (mt) REVERT: A 30 THR cc_start: 0.7375 (p) cc_final: 0.6961 (p) REVERT: A 272 ASP cc_start: 0.7745 (p0) cc_final: 0.6924 (p0) REVERT: A 274 SER cc_start: 0.8541 (m) cc_final: 0.7977 (p) REVERT: B 281 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8136 (ttt180) REVERT: B 293 ARG cc_start: 0.8838 (ttm-80) cc_final: 0.8593 (mtp85) REVERT: B 335 ASP cc_start: 0.8453 (t70) cc_final: 0.8063 (p0) REVERT: C 299 ASP cc_start: 0.7742 (p0) cc_final: 0.7392 (p0) REVERT: D 72 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7369 (mtp85) REVERT: D 294 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6521 (tp30) REVERT: F 282 GLN cc_start: 0.9162 (pm20) cc_final: 0.8134 (pm20) REVERT: G 59 ASN cc_start: 0.7654 (p0) cc_final: 0.6224 (t0) REVERT: H 11 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8399 (mmmt) REVERT: Z 57 ILE cc_start: 0.4306 (mt) cc_final: 0.3949 (tt) REVERT: Z 92 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7446 (pp) REVERT: 7 157 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.6275 (mtmt) REVERT: U 64 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7654 (mmtt) REVERT: 8 34 MET cc_start: 0.7987 (ppp) cc_final: 0.7595 (ppp) REVERT: X 32 TYR cc_start: 0.6725 (m-10) cc_final: 0.6441 (m-80) outliers start: 138 outliers final: 102 residues processed: 825 average time/residue: 0.4747 time to fit residues: 653.2574 Evaluate side-chains 793 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 685 time to evaluate : 4.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 48 PHE Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 9 TYR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 76 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 352 ASP Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 157 LYS Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 172 SER Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 219 ILE Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 298 optimal weight: 4.9990 chunk 192 optimal weight: 0.1980 chunk 287 optimal weight: 0.0980 chunk 145 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 328 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 378 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 28 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN G 141 GLN ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39511 Z= 0.179 Angle : 0.673 13.998 53548 Z= 0.327 Chirality : 0.043 0.349 6352 Planarity : 0.004 0.071 6846 Dihedral : 6.181 89.126 5567 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.40 % Rotamer: Outliers : 3.34 % Allowed : 22.10 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.58 (0.12), residues: 5062 helix: 0.30 (0.10), residues: 2635 sheet: -0.71 (0.22), residues: 535 loop : -1.15 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP X 126 HIS 0.008 0.001 HIS Z 99 PHE 0.048 0.002 PHE P 64 TYR 0.027 0.001 TYR D 381 ARG 0.008 0.000 ARG 8 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 729 time to evaluate : 4.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 PHE cc_start: 0.7436 (m-80) cc_final: 0.7208 (m-80) REVERT: N 72 LEU cc_start: 0.6997 (tp) cc_final: 0.6624 (tp) REVERT: P 5 LEU cc_start: 0.7551 (pt) cc_final: 0.7227 (tp) REVERT: P 46 THR cc_start: 0.6160 (m) cc_final: 0.5918 (m) REVERT: Q 40 ASN cc_start: 0.8148 (t0) cc_final: 0.7899 (t0) REVERT: Q 59 GLU cc_start: 0.8029 (pt0) cc_final: 0.7705 (pt0) REVERT: R 53 LEU cc_start: 0.8155 (tt) cc_final: 0.7661 (mt) REVERT: R 70 PHE cc_start: 0.6826 (t80) cc_final: 0.6512 (t80) REVERT: Y 113 ASP cc_start: 0.8003 (p0) cc_final: 0.7735 (p0) REVERT: Y 185 GLN cc_start: 0.8684 (tp40) cc_final: 0.8377 (tm-30) REVERT: A 27 LEU cc_start: 0.7076 (mt) cc_final: 0.6851 (mt) REVERT: A 30 THR cc_start: 0.7427 (p) cc_final: 0.6986 (p) REVERT: A 272 ASP cc_start: 0.7755 (p0) cc_final: 0.6905 (p0) REVERT: A 274 SER cc_start: 0.8572 (m) cc_final: 0.7947 (p) REVERT: B 281 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8055 (ttt180) REVERT: B 335 ASP cc_start: 0.8428 (t70) cc_final: 0.8036 (p0) REVERT: C 299 ASP cc_start: 0.7751 (p0) cc_final: 0.7436 (p0) REVERT: D 72 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7424 (mtp85) REVERT: D 294 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6557 (tp30) REVERT: E 105 GLU cc_start: 0.6846 (tp30) cc_final: 0.6599 (tp30) REVERT: E 263 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7931 (tp-100) REVERT: F 242 TYR cc_start: 0.7316 (t80) cc_final: 0.7106 (t80) REVERT: F 282 GLN cc_start: 0.9110 (pm20) cc_final: 0.8105 (pm20) REVERT: G 59 ASN cc_start: 0.7668 (p0) cc_final: 0.6172 (t0) REVERT: G 117 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6831 (tm-30) REVERT: H 11 LYS cc_start: 0.8714 (mtpp) cc_final: 0.8407 (mmmt) REVERT: Z 57 ILE cc_start: 0.4329 (mt) cc_final: 0.3972 (tt) REVERT: Z 133 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6843 (tt) REVERT: 7 157 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6236 (mtmt) REVERT: 6 75 ILE cc_start: 0.7705 (mm) cc_final: 0.7503 (mm) REVERT: U 64 LYS cc_start: 0.7824 (mtmt) cc_final: 0.7582 (mmtt) REVERT: 8 34 MET cc_start: 0.7890 (ppp) cc_final: 0.7527 (ppp) REVERT: X 32 TYR cc_start: 0.6626 (m-10) cc_final: 0.6344 (m-80) outliers start: 137 outliers final: 110 residues processed: 811 average time/residue: 0.4711 time to fit residues: 635.6195 Evaluate side-chains 797 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 682 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 9 TYR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 352 ASP Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 9 LYS Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 157 LYS Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 60 ASN Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 175 LEU Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 219 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 438 optimal weight: 0.9980 chunk 461 optimal weight: 20.0000 chunk 421 optimal weight: 2.9990 chunk 449 optimal weight: 5.9990 chunk 270 optimal weight: 0.8980 chunk 195 optimal weight: 0.8980 chunk 352 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 405 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 447 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN A 145 HIS ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN H 51 GLN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 230 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39511 Z= 0.199 Angle : 0.686 14.249 53548 Z= 0.332 Chirality : 0.044 0.367 6352 Planarity : 0.004 0.071 6846 Dihedral : 6.090 85.836 5565 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.36 % Rotamer: Outliers : 3.46 % Allowed : 22.17 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.51 (0.12), residues: 5062 helix: 0.32 (0.10), residues: 2647 sheet: -0.58 (0.22), residues: 525 loop : -1.07 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP X 126 HIS 0.008 0.001 HIS Z 99 PHE 0.049 0.002 PHE P 64 TYR 0.038 0.002 TYR Q 9 ARG 0.008 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 704 time to evaluate : 4.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 PHE cc_start: 0.7450 (m-80) cc_final: 0.7230 (m-80) REVERT: O 50 MET cc_start: 0.6994 (ptt) cc_final: 0.6789 (mtm) REVERT: P 5 LEU cc_start: 0.7764 (pt) cc_final: 0.7395 (tp) REVERT: P 46 THR cc_start: 0.6240 (m) cc_final: 0.5990 (m) REVERT: Q 40 ASN cc_start: 0.8188 (t0) cc_final: 0.7909 (t0) REVERT: Q 59 GLU cc_start: 0.8036 (pt0) cc_final: 0.7741 (pt0) REVERT: R 53 LEU cc_start: 0.8162 (tt) cc_final: 0.7670 (mt) REVERT: R 70 PHE cc_start: 0.6815 (t80) cc_final: 0.6516 (t80) REVERT: Y 113 ASP cc_start: 0.8001 (p0) cc_final: 0.7739 (p0) REVERT: Y 185 GLN cc_start: 0.8700 (tp40) cc_final: 0.8344 (tm-30) REVERT: A 30 THR cc_start: 0.7410 (p) cc_final: 0.6973 (p) REVERT: A 272 ASP cc_start: 0.7772 (p0) cc_final: 0.6931 (p0) REVERT: A 274 SER cc_start: 0.8603 (m) cc_final: 0.7975 (p) REVERT: B 281 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8115 (ttt180) REVERT: B 335 ASP cc_start: 0.8390 (t70) cc_final: 0.8062 (p0) REVERT: C 299 ASP cc_start: 0.7768 (p0) cc_final: 0.7473 (p0) REVERT: C 401 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6301 (tm-30) REVERT: D 72 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7435 (mtp85) REVERT: D 294 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6604 (tp30) REVERT: E 30 LEU cc_start: 0.8042 (tt) cc_final: 0.7767 (tt) REVERT: E 263 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7918 (tp-100) REVERT: F 242 TYR cc_start: 0.7325 (t80) cc_final: 0.7125 (t80) REVERT: F 282 GLN cc_start: 0.9116 (pm20) cc_final: 0.8136 (pm20) REVERT: G 59 ASN cc_start: 0.7664 (p0) cc_final: 0.6156 (t0) REVERT: G 117 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6719 (tm-30) REVERT: H 11 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8396 (mmmt) REVERT: Z 57 ILE cc_start: 0.4356 (mt) cc_final: 0.4039 (tt) REVERT: Z 133 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6908 (tt) REVERT: U 64 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7623 (mmtt) REVERT: X 32 TYR cc_start: 0.6611 (m-10) cc_final: 0.6350 (m-80) outliers start: 142 outliers final: 124 residues processed: 788 average time/residue: 0.4520 time to fit residues: 598.0688 Evaluate side-chains 804 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 676 time to evaluate : 4.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 9 TYR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 67 MET Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 341 GLU Chi-restraints excluded: chain F residue 352 ASP Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 9 LYS Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 130 PHE Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 55 TYR Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 172 SER Chi-restraints excluded: chain X residue 175 LEU Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 219 ILE Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 294 optimal weight: 0.0060 chunk 474 optimal weight: 7.9990 chunk 289 optimal weight: 0.6980 chunk 225 optimal weight: 9.9990 chunk 330 optimal weight: 8.9990 chunk 498 optimal weight: 0.0770 chunk 458 optimal weight: 0.5980 chunk 396 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 306 optimal weight: 0.9990 chunk 243 optimal weight: 0.9990 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN D 328 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 39511 Z= 0.174 Angle : 0.694 21.485 53548 Z= 0.332 Chirality : 0.044 0.441 6352 Planarity : 0.004 0.071 6846 Dihedral : 5.959 83.887 5563 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.25 % Favored : 95.59 % Rotamer: Outliers : 3.10 % Allowed : 22.68 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.40 (0.12), residues: 5062 helix: 0.38 (0.11), residues: 2626 sheet: -0.47 (0.23), residues: 514 loop : -0.98 (0.15), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP X 126 HIS 0.009 0.001 HIS Z 99 PHE 0.050 0.001 PHE P 64 TYR 0.033 0.001 TYR D 381 ARG 0.007 0.000 ARG 8 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 718 time to evaluate : 4.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 PHE cc_start: 0.7333 (m-80) cc_final: 0.7131 (m-80) REVERT: N 72 LEU cc_start: 0.7014 (tp) cc_final: 0.6747 (tp) REVERT: O 43 ILE cc_start: 0.7547 (tp) cc_final: 0.7344 (tp) REVERT: P 5 LEU cc_start: 0.7683 (pt) cc_final: 0.7337 (tp) REVERT: P 46 THR cc_start: 0.6126 (m) cc_final: 0.5877 (m) REVERT: Q 40 ASN cc_start: 0.8159 (t0) cc_final: 0.7920 (t0) REVERT: Q 59 GLU cc_start: 0.7996 (pt0) cc_final: 0.7671 (pt0) REVERT: R 52 ILE cc_start: 0.9133 (tp) cc_final: 0.8931 (mm) REVERT: R 53 LEU cc_start: 0.8064 (tt) cc_final: 0.7661 (mt) REVERT: R 70 PHE cc_start: 0.6568 (t80) cc_final: 0.6299 (t80) REVERT: S 30 PHE cc_start: 0.7372 (m-80) cc_final: 0.6981 (m-80) REVERT: S 43 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7660 (tp) REVERT: Y 113 ASP cc_start: 0.7974 (p0) cc_final: 0.7722 (p0) REVERT: Y 185 GLN cc_start: 0.8655 (tp40) cc_final: 0.8351 (tm-30) REVERT: A 30 THR cc_start: 0.7308 (p) cc_final: 0.6914 (p) REVERT: A 272 ASP cc_start: 0.7839 (p0) cc_final: 0.7098 (p0) REVERT: A 274 SER cc_start: 0.8510 (m) cc_final: 0.7923 (p) REVERT: A 340 ILE cc_start: 0.9492 (mm) cc_final: 0.9243 (mt) REVERT: B 281 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8074 (ttt180) REVERT: B 335 ASP cc_start: 0.8385 (t70) cc_final: 0.8127 (p0) REVERT: C 299 ASP cc_start: 0.7741 (p0) cc_final: 0.7541 (p0) REVERT: C 401 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6353 (tm-30) REVERT: C 428 GLN cc_start: 0.8236 (tp40) cc_final: 0.7995 (tp40) REVERT: D 64 MET cc_start: 0.8617 (mmp) cc_final: 0.7977 (mmp) REVERT: D 72 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7395 (mtp85) REVERT: D 294 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6580 (tp30) REVERT: E 30 LEU cc_start: 0.8011 (tt) cc_final: 0.7731 (tt) REVERT: E 263 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7875 (tp-100) REVERT: E 316 ASP cc_start: 0.7274 (t0) cc_final: 0.6695 (m-30) REVERT: F 282 GLN cc_start: 0.9068 (pm20) cc_final: 0.8031 (pm20) REVERT: G 59 ASN cc_start: 0.7672 (p0) cc_final: 0.6165 (t0) REVERT: G 117 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: H 11 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8418 (mmmt) REVERT: H 14 PHE cc_start: 0.8003 (t80) cc_final: 0.7774 (t80) REVERT: Z 57 ILE cc_start: 0.4466 (mt) cc_final: 0.4108 (tt) REVERT: Z 133 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6838 (tt) REVERT: 8 39 TYR cc_start: 0.6719 (m-80) cc_final: 0.5581 (m-80) outliers start: 127 outliers final: 107 residues processed: 792 average time/residue: 0.4702 time to fit residues: 622.4591 Evaluate side-chains 796 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 684 time to evaluate : 4.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 9 TYR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain S residue 43 ILE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 67 MET Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 352 ASP Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 9 LYS Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 55 TYR Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 172 SER Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 219 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 315 optimal weight: 0.0070 chunk 422 optimal weight: 5.9990 chunk 121 optimal weight: 0.0870 chunk 365 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 397 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 407 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 62 HIS ** U 20 ASN ** 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 = 0.3728 r_free = 0.3728 target = 0.110430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.086711 restraints weight = 110804.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086853 restraints weight = 75419.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087168 restraints weight = 51597.539| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39511 Z= 0.170 Angle : 0.689 14.522 53548 Z= 0.330 Chirality : 0.043 0.340 6352 Planarity : 0.004 0.071 6846 Dihedral : 5.854 81.485 5563 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 3.17 % Allowed : 22.68 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 5062 helix: 0.44 (0.11), residues: 2635 sheet: -0.40 (0.23), residues: 496 loop : -0.87 (0.15), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP X 126 HIS 0.009 0.001 HIS Z 99 PHE 0.049 0.001 PHE P 64 TYR 0.053 0.001 TYR F 242 ARG 0.007 0.000 ARG 8 42 =============================================================================== Job complete usr+sys time: 10944.34 seconds wall clock time: 196 minutes 8.87 seconds (11768.87 seconds total)