Starting phenix.real_space_refine on Fri Feb 23 14:39:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/02_2024/6cp6_7548_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/02_2024/6cp6_7548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/02_2024/6cp6_7548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/02_2024/6cp6_7548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/02_2024/6cp6_7548_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/02_2024/6cp6_7548_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 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 24827 2.51 5 N 6557 2.21 5 O 7364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y GLU 127": "OE1" <-> "OE2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "D PHE 326": "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-5238/modules/chem_data/mon_lib" Total number of atoms: 38853 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: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 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: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 523 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 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: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1333 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 180} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3858 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Chain: "B" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3830 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3861 Classifications: {'peptide': 508} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 486} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1221 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1357 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 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: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1760 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 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: 19.57, per 1000 atoms: 0.50 Number of scatterers: 38853 At special positions: 0 Unit cell: (125.46, 151.29, 244.77, 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 7364 8.00 N 6557 7.00 C 24827 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: 15.37 Conformation dependent library (CDL) restraints added in 6.9 seconds 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 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: 198 helices and 24 sheets defined 52.2% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.26 Creating SS restraints... Processing helix chain 'K' and resid 3 through 39 removed outlier: 4.062A pdb=" N LYS K 8 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE K 17 " --> pdb=" O GLY K 13 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLY K 18 " --> pdb=" O ILE K 14 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU K 19 " --> pdb=" O SER K 15 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY K 21 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE K 28 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL K 29 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU K 33 " --> pdb=" O VAL K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 73 removed outlier: 3.596A pdb=" N LYS K 44 " --> pdb=" O PRO K 41 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP K 45 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE K 48 " --> pdb=" O ASP K 45 " (cutoff:3.500A) Proline residue: K 49 - end of helix removed outlier: 4.040A pdb=" N PHE K 55 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU K 57 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA K 60 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR K 61 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.008A 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 23 Processing helix chain 'L' and resid 25 through 38 removed outlier: 3.566A pdb=" N VAL L 29 " --> pdb=" O GLY L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 43 No H-bonds generated for 'chain 'L' and resid 41 through 43' Processing helix chain 'L' and resid 45 through 73 Proline residue: L 49 - end of helix removed outlier: 3.842A pdb=" N LEU L 57 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER L 58 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY L 62 " --> pdb=" O SER L 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS L 65 " --> pdb=" O THR L 61 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU L 66 " --> pdb=" O GLY L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 14 Processing helix chain 'M' and resid 17 through 23 Processing helix chain 'M' and resid 25 through 37 Processing helix chain 'M' and resid 44 through 73 Proline residue: M 49 - end of helix removed outlier: 3.788A pdb=" N LEU M 57 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER M 58 " --> pdb=" O GLY M 54 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY M 62 " --> pdb=" O SER M 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS M 65 " --> pdb=" O THR M 61 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU M 66 " --> pdb=" O GLY M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 14 Processing helix chain 'N' and resid 16 through 37 removed outlier: 3.990A pdb=" N LEU N 19 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLY N 21 " --> pdb=" O GLY N 18 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA N 22 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE N 26 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL N 37 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 73 removed outlier: 3.927A pdb=" N LYS N 44 " --> pdb=" O PRO N 41 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP N 45 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE N 48 " --> pdb=" O ASP N 45 " (cutoff:3.500A) Proline residue: N 49 - end of helix removed outlier: 3.656A pdb=" N LEU N 57 " --> pdb=" O GLY N 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER N 58 " --> pdb=" O PHE N 55 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA N 60 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR N 61 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 14 Processing helix chain 'O' and resid 17 through 37 removed outlier: 5.909A pdb=" N GLY O 21 " --> pdb=" O GLY O 18 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE O 26 " --> pdb=" O GLY O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 54 removed outlier: 3.806A pdb=" N LYS O 44 " --> pdb=" O PRO O 41 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP O 45 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE O 48 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Proline residue: O 49 - end of helix Processing helix chain 'O' and resid 59 through 71 removed outlier: 3.863A pdb=" N CYS O 65 " --> pdb=" O THR O 61 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU O 66 " --> pdb=" O GLY O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 14 Processing helix chain 'P' and resid 19 through 39 removed outlier: 4.676A pdb=" N ALA P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 73 removed outlier: 3.781A pdb=" N THR P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 4.362A 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 39 removed outlier: 3.839A pdb=" N GLY Q 21 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE Q 26 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER Q 38 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 73 removed outlier: 3.999A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 4.486A 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: 4.009A pdb=" N GLY R 21 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE R 24 " --> pdb=" O GLY R 21 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE R 26 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL R 37 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 74 removed outlier: 3.727A pdb=" N LYS R 44 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP R 45 " --> pdb=" O SER R 42 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE R 48 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Proline residue: R 49 - end of helix removed outlier: 5.918A pdb=" N LEU R 57 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA R 60 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR R 61 " --> pdb=" O SER R 58 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU R 72 " --> pdb=" O SER R 69 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU R 73 " --> pdb=" O PHE R 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 14 Processing helix chain 'S' and resid 16 through 37 removed outlier: 3.580A pdb=" N LEU S 19 " --> pdb=" O THR S 16 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE S 24 " --> pdb=" O GLY S 21 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE S 26 " --> pdb=" O GLY S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 43 No H-bonds generated for 'chain 'S' and resid 41 through 43' Processing helix chain 'S' and resid 46 through 64 removed outlier: 4.299A pdb=" N MET S 50 " --> pdb=" O THR S 46 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE S 52 " --> pdb=" O PHE S 48 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY S 54 " --> pdb=" O MET S 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 73 removed outlier: 3.726A pdb=" N LEU S 72 " --> 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: 4.788A pdb=" N GLY T 21 " --> pdb=" O GLY T 18 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE T 26 " --> pdb=" O GLY T 23 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL T 37 " --> pdb=" O ILE T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 61 removed outlier: 6.378A pdb=" N ASP T 45 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL T 47 " --> pdb=" O LYS T 44 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N PHE T 48 " --> pdb=" O ASP T 45 " (cutoff:3.500A) Proline residue: T 49 - end of helix removed outlier: 3.643A pdb=" N ILE T 52 " --> pdb=" O PRO T 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE T 55 " --> pdb=" O ILE T 52 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU T 57 " --> pdb=" O GLY T 54 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR T 61 " --> 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 30 removed outlier: 4.111A pdb=" N LYS Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN Y 30 " --> pdb=" O ALA Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 49 Processing helix chain 'Y' and resid 65 through 76 Processing helix chain 'Y' and resid 83 through 95 removed outlier: 3.801A pdb=" N VAL Y 86 " --> pdb=" O GLY Y 83 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU Y 88 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER Y 93 " --> pdb=" O LYS Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 102 through 116 Processing helix chain 'Y' and resid 131 through 143 Processing helix chain 'Y' and resid 181 through 192 removed outlier: 3.694A pdb=" N LEU Y 191 " --> pdb=" O LEU Y 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 17 removed outlier: 3.603A pdb=" N GLU A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) 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 153 through 158 Processing helix chain 'A' and resid 177 through 192 removed outlier: 4.248A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 242 through 262 Proline residue: A 249 - end of helix removed outlier: 3.618A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (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: 4.074A pdb=" N PHE A 301 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 305 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU A 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 4.582A 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 356 through 360 Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 383 through 407 removed outlier: 3.974A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 440 through 451 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 463 through 477 Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'B' and resid 5 through 20 removed outlier: 5.094A pdb=" N GLY B 20 " --> pdb=" O GLU B 15 " (cutoff:3.500A) 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 177 through 192 removed outlier: 3.983A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.804A 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 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix Processing helix chain 'B' and resid 273 through 286 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 298 through 308 removed outlier: 4.014A pdb=" N PHE B 301 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS B 304 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 305 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 307 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 377 through 380 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 390 through 408 removed outlier: 4.514A pdb=" N LEU B 394 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N PHE B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) 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 461 through 476 removed outlier: 3.956A pdb=" N GLY B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 467 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 468 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 475 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 493 through 508 removed outlier: 3.739A 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 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.758A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 225 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 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 298 through 310 removed outlier: 4.294A pdb=" N PHE C 301 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 306 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 308 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU C 309 " --> pdb=" O ARG C 306 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 310 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 345 Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 377 through 380 Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 392 through 408 removed outlier: 4.001A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 429 Processing helix chain 'C' and resid 440 through 451 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 460 through 476 removed outlier: 4.638A pdb=" N GLY C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 476 " --> pdb=" O SER C 472 " (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 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 139 through 144 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: 5.107A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 269 removed outlier: 3.848A pdb=" N THR D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 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: 3.621A 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 388 removed outlier: 4.754A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 420 through 425 removed outlier: 4.035A pdb=" N VAL D 423 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 425 " --> pdb=" O GLU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 463 through 474 removed outlier: 3.641A 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 139 through 143 Processing helix chain 'E' and resid 163 through 177 Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 226 through 229 No H-bonds generated for 'chain 'E' and resid 226 through 229' Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 258 through 271 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 285 through 293 removed outlier: 3.740A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 327 removed outlier: 3.838A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 360 through 390 removed outlier: 7.450A pdb=" N GLN E 365 " --> pdb=" O ALA E 361 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N GLU E 366 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N HIS E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 389 " --> pdb=" O GLN E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 Processing helix chain 'E' and resid 434 through 446 Processing helix chain 'E' and resid 454 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 Processing helix chain 'F' and resid 163 through 174 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 Processing helix chain 'F' and resid 258 through 267 removed outlier: 3.664A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 295 removed outlier: 4.022A pdb=" N ARG F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) 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: 4.004A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 365 through 390 removed outlier: 4.803A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.138A 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 398 through 414 Processing helix chain 'F' and resid 420 through 425 removed outlier: 4.332A pdb=" N VAL F 423 " --> pdb=" O VAL F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 476 Processing helix chain 'G' and resid 3 through 54 removed outlier: 4.091A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 101 removed outlier: 3.783A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 121 removed outlier: 3.731A pdb=" N ARG G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'G' and resid 185 through 189 Processing helix chain 'G' and resid 192 through 194 No H-bonds generated for 'chain 'G' and resid 192 through 194' Processing helix chain 'G' and resid 201 through 203 No H-bonds generated for 'chain 'G' and resid 201 through 203' Processing helix chain 'G' and resid 205 through 275 removed outlier: 4.402A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE G 253 " --> pdb=" O ASN G 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 114 removed outlier: 3.524A pdb=" N LEU H 104 " --> pdb=" O ASN H 100 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 105 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 137 removed outlier: 3.850A pdb=" N GLU H 122 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER H 135 " --> pdb=" O GLU H 131 " (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: 4.881A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.628A pdb=" N ARG Z 96 " --> pdb=" O LEU Z 92 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU Z 113 " --> pdb=" O SER Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 132 removed outlier: 4.246A pdb=" N VAL Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP Z 125 " --> pdb=" O LYS Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 135 through 184 removed outlier: 3.570A pdb=" N LYS Z 143 " --> pdb=" O GLU Z 139 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 206 removed outlier: 4.252A pdb=" N VAL Z 193 " --> pdb=" O PHE Z 189 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 20 removed outlier: 5.009A pdb=" N ARG 7 20 " --> pdb=" O ILE 7 16 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 47 Processing helix chain '7' and resid 58 through 61 No H-bonds generated for 'chain '7' and resid 58 through 61' Processing helix chain '7' and resid 68 through 77 Processing helix chain '7' and resid 91 through 126 removed outlier: 4.161A pdb=" N LYS 7 115 " --> pdb=" O SER 7 111 " (cutoff:3.500A) removed outlier: 3.539A 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 16 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 43 through 50 Proline residue: 6 47 - end of helix Processing helix chain '6' and resid 78 through 91 Processing helix chain 'U' and resid 18 through 31 removed outlier: 4.050A pdb=" N VAL U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 55 Processing helix chain 'U' and resid 63 through 84 removed outlier: 4.585A pdb=" N GLY U 77 " --> pdb=" O ILE U 74 " (cutoff:3.500A) removed outlier: 4.987A 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 46 removed outlier: 4.123A 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 76 removed outlier: 3.890A pdb=" N SER X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET X 72 " --> pdb=" O THR X 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY X 75 " --> pdb=" O ASN X 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 99 Proline residue: X 87 - end of helix removed outlier: 4.399A pdb=" N LEU X 92 " --> pdb=" O ILE X 89 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET X 94 " --> pdb=" O THR X 91 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE X 95 " --> pdb=" O LEU X 92 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA X 99 " --> pdb=" O ILE X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 136 Processing helix chain 'X' and resid 140 through 145 removed outlier: 3.596A pdb=" N PHE X 145 " --> pdb=" O PHE X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 176 Proline residue: X 156 - end of helix removed outlier: 4.027A pdb=" N ILE X 161 " --> pdb=" O LEU X 158 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU X 164 " --> pdb=" O ILE X 161 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE X 167 " --> pdb=" O LEU X 164 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG X 169 " --> pdb=" O TYR X 166 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE X 171 " --> pdb=" O ALA X 168 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER X 172 " --> pdb=" O ARG X 169 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU X 173 " --> pdb=" O ALA X 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY X 174 " --> pdb=" O ILE X 171 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG X 176 " --> pdb=" O LEU X 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 178 through 198 removed outlier: 4.032A pdb=" N LEU X 186 " --> pdb=" O LEU X 182 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU X 187 " --> pdb=" O ALA X 183 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA X 192 " --> pdb=" O MET X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 205 No H-bonds generated for 'chain 'X' and resid 203 through 205' Processing helix chain 'X' and resid 211 through 246 removed outlier: 4.403A pdb=" N GLN X 230 " --> pdb=" O ILE X 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 31 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 89 through 91 removed outlier: 6.898A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN A 95 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLU A 56 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 93 " --> pdb=" O GLU A 56 " (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 108 through 110 removed outlier: 4.127A pdb=" N ARG A 108 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A 326 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 167 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.546A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN B 95 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLU B 56 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR B 93 " --> pdb=" O GLU B 56 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= G, first strand: chain 'B' and resid 351 through 353 removed outlier: 6.996A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 231 through 236 removed outlier: 6.881A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER B 322 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE B 268 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N THR B 324 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N TYR B 270 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU B 326 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 89 through 91 removed outlier: 6.649A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN C 67 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN C 95 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLU C 56 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR C 93 " --> pdb=" O GLU C 56 " (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 351 through 354 removed outlier: 6.399A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 231 through 236 removed outlier: 6.761A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N TYR C 270 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 326 " --> pdb=" O TYR C 270 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.521A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.451A 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 331 through 334 removed outlier: 7.719A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLY D 157 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL D 310 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE D 181 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE D 254 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.478A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.235A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 331 through 333 removed outlier: 8.773A pdb=" N ILE E 153 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N SER E 306 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU E 155 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN E 308 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 11 through 17 removed outlier: 6.428A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 331 through 335 removed outlier: 7.623A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 126 through 130 removed outlier: 7.852A pdb=" N ILE G 107 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER G 129 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 109 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA G 76 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS G 161 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL G 75 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER G 163 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ILE G 77 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE G 165 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 49 through 52 removed outlier: 6.132A pdb=" N LYS H 11 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL H 85 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE H 14 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER H 23 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 37 through 41 removed outlier: 6.872A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) 1885 hydrogen bonds defined for protein. 4836 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: 13.68 Time building geometry restraints manager: 16.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6560 1.31 - 1.43: 9444 1.43 - 1.56: 23285 1.56 - 1.68: 24 1.68 - 1.81: 168 Bond restraints: 39481 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.93e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.34e+01 ... (remaining 39476 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.48: 1046 106.48 - 113.94: 23362 113.94 - 121.40: 19695 121.40 - 128.86: 9231 128.86 - 136.31: 173 Bond angle restraints: 53507 Sorted by residual: angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 112.71 24.12 1.00e+00 1.00e+00 5.82e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 113.25 23.58 1.00e+00 1.00e+00 5.56e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 118.01 21.86 1.00e+00 1.00e+00 4.78e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 118.20 21.67 1.00e+00 1.00e+00 4.69e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.64 21.23 1.00e+00 1.00e+00 4.51e+02 ... (remaining 53502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 23568 33.93 - 67.87: 252 67.87 - 101.80: 27 101.80 - 135.73: 1 135.73 - 169.67: 1 Dihedral angle restraints: 23849 sinusoidal: 9246 harmonic: 14603 Sorted by residual: dihedral pdb=" C5' ADP F 600 " pdb=" O5' ADP F 600 " pdb=" PA ADP F 600 " pdb=" O2A ADP F 600 " ideal model delta sinusoidal sigma weight residual 300.00 130.34 169.67 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 177.34 122.66 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" CA PHE R 55 " pdb=" C PHE R 55 " pdb=" N ALA R 56 " pdb=" CA ALA R 56 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 23846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 5865 0.097 - 0.193: 467 0.193 - 0.290: 15 0.290 - 0.386: 1 0.386 - 0.483: 1 Chirality restraints: 6349 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 2.16 0.48 2.00e-01 2.50e+01 5.82e+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 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CB ILE Q 14 " pdb=" CA ILE Q 14 " pdb=" CG1 ILE Q 14 " pdb=" CG2 ILE Q 14 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 6346 not shown) Planarity restraints: 6839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA 6 17 " -0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO 6 18 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO 6 18 " -0.044 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 ALA D 321 " -0.050 5.00e-02 4.00e+02 7.58e-02 9.19e+00 pdb=" N PRO D 322 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 53 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C LEU R 53 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU R 53 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY R 54 " -0.017 2.00e-02 2.50e+03 ... (remaining 6836 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3739 2.74 - 3.28: 41153 3.28 - 3.82: 70053 3.82 - 4.36: 82270 4.36 - 4.90: 133143 Nonbonded interactions: 330358 Sorted by model distance: nonbonded pdb=" O GLY Y 172 " pdb=" OD1 ASP Y 173 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASP B 172 " pdb=" OG1 THR B 331 " model vdw 2.235 2.440 nonbonded pdb=" O VAL E 87 " pdb=" OG SER E 111 " model vdw 2.239 2.440 nonbonded pdb=" OD1 ASP Y 193 " pdb=" N SER Y 194 " model vdw 2.246 2.520 nonbonded pdb=" CB GLU B 29 " pdb=" CG ARG B 92 " model vdw 2.255 3.840 ... (remaining 330353 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 18 or resid 20 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 \ 509 or resid 600)) selection = chain 'B' selection = (chain 'C' and (resid 4 through 18 or resid 20 through 22 or (resid 23 and (name \ N or name CA or name C or name O or name CB )) or resid 24 through 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 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = (chain 'L' and (resid 1 through 18 or (resid 19 through 20 and (name N or name C \ A or name C or name O or name CB )) or resid 21 through 56 or (resid 57 and (nam \ e N or name CA or name C or name O or name CB )) or resid 58 through 74)) 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 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = (chain 'N' and (resid 1 through 18 or (resid 19 through 20 and (name N or name C \ A or name C or name O or name CB )) or resid 21 through 74)) 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 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 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 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 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 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = (chain 'S' and (resid 1 through 18 or (resid 19 through 20 and (name N or name C \ A or name C or name O or name CB )) or resid 21 through 56 or (resid 57 and (nam \ e N or name CA or name C or name O or name CB )) or resid 58 through 74)) 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 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 12.780 Check model and map are aligned: 0.510 Set scattering table: 0.330 Process input model: 97.950 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.007 0.090 39481 Z= 0.450 Angle : 1.088 24.118 53507 Z= 0.648 Chirality : 0.054 0.483 6349 Planarity : 0.007 0.086 6839 Dihedral : 10.954 169.666 14473 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.51 % Favored : 94.17 % Rotamer: Outliers : 0.66 % Allowed : 4.03 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.10), residues: 5060 helix: -2.04 (0.08), residues: 2508 sheet: -1.67 (0.21), residues: 568 loop : -1.88 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 258 HIS 0.020 0.003 HIS 6 92 PHE 0.035 0.003 PHE 7 95 TYR 0.028 0.003 TYR 7 58 ARG 0.016 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1168 time to evaluate : 4.224 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: K 19 LEU cc_start: 0.4059 (pp) cc_final: 0.2789 (mt) REVERT: K 43 ILE cc_start: 0.7698 (tp) cc_final: 0.7211 (tt) REVERT: K 53 LEU cc_start: 0.8160 (tm) cc_final: 0.7745 (mt) REVERT: K 61 THR cc_start: 0.6798 (p) cc_final: 0.6513 (p) REVERT: M 46 THR cc_start: 0.6797 (m) cc_final: 0.6513 (m) REVERT: M 50 MET cc_start: 0.8248 (mtm) cc_final: 0.7952 (tpp) REVERT: N 29 VAL cc_start: 0.8391 (t) cc_final: 0.8012 (t) REVERT: N 30 PHE cc_start: 0.7615 (m-80) cc_final: 0.7177 (m-80) REVERT: N 67 MET cc_start: 0.5001 (pp-130) cc_final: 0.4698 (ttt) REVERT: N 70 PHE cc_start: 0.6687 (t80) cc_final: 0.6432 (t80) REVERT: O 16 THR cc_start: 0.4051 (m) cc_final: 0.3721 (m) REVERT: P 5 LEU cc_start: 0.8510 (pt) cc_final: 0.8282 (tp) REVERT: P 39 ARG cc_start: 0.7691 (mtp180) cc_final: 0.7258 (mtp180) REVERT: P 47 VAL cc_start: 0.7906 (m) cc_final: 0.7588 (m) REVERT: P 67 MET cc_start: 0.6089 (pp-130) cc_final: 0.5786 (ppp) REVERT: Q 63 LEU cc_start: 0.7625 (mt) cc_final: 0.7394 (tt) REVERT: Q 67 MET cc_start: 0.3905 (pp-130) cc_final: 0.3546 (ptp) REVERT: Q 68 VAL cc_start: 0.8410 (t) cc_final: 0.8185 (t) REVERT: R 4 VAL cc_start: 0.3447 (p) cc_final: 0.2919 (t) REVERT: R 34 ILE cc_start: 0.8372 (mt) cc_final: 0.8028 (mm) REVERT: R 53 LEU cc_start: 0.8114 (tm) cc_final: 0.7861 (mt) REVERT: R 72 LEU cc_start: 0.6239 (tp) cc_final: 0.5929 (tp) REVERT: S 5 LEU cc_start: 0.8281 (pt) cc_final: 0.7923 (pt) REVERT: S 45 ASP cc_start: 0.8853 (m-30) cc_final: 0.8380 (t0) REVERT: S 47 VAL cc_start: 0.8653 (m) cc_final: 0.8416 (p) REVERT: S 70 PHE cc_start: 0.8147 (m-10) cc_final: 0.7777 (m-80) REVERT: S 72 LEU cc_start: 0.6957 (tp) cc_final: 0.6714 (tp) REVERT: T 17 ILE cc_start: 0.6920 (pp) cc_final: 0.6464 (mm) REVERT: T 57 LEU cc_start: 0.6750 (mm) cc_final: 0.6483 (mm) REVERT: Y 34 ASP cc_start: 0.9249 (m-30) cc_final: 0.8986 (t0) REVERT: Y 44 GLU cc_start: 0.8664 (tp30) cc_final: 0.7747 (tp30) REVERT: Y 103 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.6204 (mttt) REVERT: A 124 ASP cc_start: 0.8576 (m-30) cc_final: 0.8011 (p0) REVERT: A 228 MET cc_start: 0.8633 (mmm) cc_final: 0.8394 (mmm) REVERT: A 260 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8311 (ttp-170) REVERT: A 271 ASP cc_start: 0.8446 (t70) cc_final: 0.8094 (t0) REVERT: A 272 ASP cc_start: 0.7880 (p0) cc_final: 0.7306 (p0) REVERT: A 274 SER cc_start: 0.7824 (m) cc_final: 0.7558 (p) REVERT: A 383 LYS cc_start: 0.9100 (mttt) cc_final: 0.8866 (tppt) REVERT: A 442 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8456 (mt-10) REVERT: B 52 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7926 (tt0) REVERT: B 62 LYS cc_start: 0.8398 (mttt) cc_final: 0.8130 (mmtt) REVERT: B 84 VAL cc_start: 0.8360 (t) cc_final: 0.8143 (p) REVERT: B 275 LYS cc_start: 0.8276 (mttm) cc_final: 0.8030 (mptt) REVERT: B 330 GLU cc_start: 0.8700 (tt0) cc_final: 0.8029 (tm-30) REVERT: B 355 GLU cc_start: 0.7984 (tt0) cc_final: 0.7061 (tp30) REVERT: B 475 LYS cc_start: 0.9247 (mttm) cc_final: 0.9007 (tptm) REVERT: C 16 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: C 146 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8077 (mp0) REVERT: C 271 ASP cc_start: 0.8147 (t0) cc_final: 0.7882 (t70) REVERT: C 272 ASP cc_start: 0.7476 (p0) cc_final: 0.7193 (p0) REVERT: C 471 LEU cc_start: 0.9170 (mt) cc_final: 0.8776 (mm) REVERT: D 38 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7896 (mm-30) REVERT: D 50 VAL cc_start: 0.7916 (t) cc_final: 0.7669 (t) REVERT: D 61 THR cc_start: 0.9166 (p) cc_final: 0.8749 (t) REVERT: D 65 ASP cc_start: 0.8303 (t70) cc_final: 0.7698 (m-30) REVERT: D 198 TYR cc_start: 0.8676 (t80) cc_final: 0.8451 (t80) REVERT: D 208 ASN cc_start: 0.7802 (t0) cc_final: 0.7577 (t0) REVERT: D 291 LEU cc_start: 0.8937 (mt) cc_final: 0.8736 (mp) REVERT: D 459 MET cc_start: 0.8256 (tpp) cc_final: 0.8048 (mmm) REVERT: E 22 ASP cc_start: 0.8279 (m-30) cc_final: 0.8044 (m-30) REVERT: E 153 ILE cc_start: 0.9487 (mp) cc_final: 0.9058 (mm) REVERT: E 208 ASN cc_start: 0.7923 (t0) cc_final: 0.7607 (t0) REVERT: E 256 ASP cc_start: 0.7229 (t70) cc_final: 0.6991 (t0) REVERT: E 262 THR cc_start: 0.8740 (m) cc_final: 0.8503 (m) REVERT: E 277 SER cc_start: 0.8319 (t) cc_final: 0.7682 (p) REVERT: E 319 ASP cc_start: 0.7838 (t0) cc_final: 0.7309 (t0) REVERT: E 341 GLU cc_start: 0.9454 (tt0) cc_final: 0.9100 (tm-30) REVERT: E 349 ASP cc_start: 0.8705 (t70) cc_final: 0.8097 (t0) REVERT: E 396 LEU cc_start: 0.7709 (mt) cc_final: 0.7328 (mt) REVERT: E 458 TYR cc_start: 0.8005 (t80) cc_final: 0.7435 (t80) REVERT: E 465 ASP cc_start: 0.8365 (m-30) cc_final: 0.8009 (t0) REVERT: E 467 VAL cc_start: 0.8079 (t) cc_final: 0.7767 (m) REVERT: E 472 LYS cc_start: 0.8634 (mttt) cc_final: 0.8303 (pttt) REVERT: F 56 GLU cc_start: 0.8303 (tt0) cc_final: 0.7933 (tm-30) REVERT: F 62 ILE cc_start: 0.9044 (mt) cc_final: 0.8682 (tt) REVERT: F 64 MET cc_start: 0.8504 (mmp) cc_final: 0.8164 (mmp) REVERT: F 282 GLN cc_start: 0.9212 (pm20) cc_final: 0.8521 (pm20) REVERT: F 284 THR cc_start: 0.8885 (p) cc_final: 0.8029 (t) REVERT: F 288 ASP cc_start: 0.8841 (m-30) cc_final: 0.8506 (m-30) REVERT: F 316 ASP cc_start: 0.8142 (t70) cc_final: 0.7884 (t0) REVERT: F 352 ASP cc_start: 0.8142 (t70) cc_final: 0.7814 (t0) REVERT: F 368 TYR cc_start: 0.9385 (t80) cc_final: 0.8956 (t80) REVERT: F 393 MET cc_start: 0.8321 (mtp) cc_final: 0.7006 (mmm) REVERT: F 401 LYS cc_start: 0.8277 (tttt) cc_final: 0.7684 (mttm) REVERT: F 449 TYR cc_start: 0.8919 (m-80) cc_final: 0.8646 (m-80) REVERT: F 459 MET cc_start: 0.8067 (tpp) cc_final: 0.7675 (tpp) REVERT: G 53 LYS cc_start: 0.9023 (mmpt) cc_final: 0.8659 (pttt) REVERT: G 90 GLN cc_start: 0.8206 (tp40) cc_final: 0.7895 (tp-100) REVERT: G 135 LYS cc_start: 0.7007 (pttm) cc_final: 0.6467 (tppt) REVERT: G 142 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8937 (mt-10) REVERT: G 166 TYR cc_start: 0.7293 (p90) cc_final: 0.6459 (p90) REVERT: G 168 ASP cc_start: 0.7670 (t0) cc_final: 0.7258 (t0) REVERT: G 218 MET cc_start: 0.6637 (ttm) cc_final: 0.6191 (ttm) REVERT: G 246 ASP cc_start: 0.8771 (t70) cc_final: 0.8383 (t0) REVERT: H 29 GLN cc_start: 0.8486 (tt0) cc_final: 0.8280 (tp40) REVERT: H 32 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6876 (pp) REVERT: H 51 GLN cc_start: 0.7258 (pt0) cc_final: 0.6999 (pt0) REVERT: H 66 LYS cc_start: 0.7562 (mttp) cc_final: 0.7322 (mptt) REVERT: H 116 ASP cc_start: 0.8102 (m-30) cc_final: 0.7604 (p0) REVERT: H 118 ARG cc_start: 0.7089 (mmm160) cc_final: 0.6722 (mmm-85) REVERT: I 13 TYR cc_start: 0.8823 (t80) cc_final: 0.8195 (t80) REVERT: I 36 ASN cc_start: 0.8317 (m-40) cc_final: 0.7943 (t0) REVERT: I 38 SER cc_start: 0.9059 (t) cc_final: 0.8682 (p) REVERT: I 41 ASP cc_start: 0.8221 (m-30) cc_final: 0.7916 (m-30) REVERT: Z 139 GLU cc_start: 0.3482 (mm-30) cc_final: 0.2348 (tm-30) REVERT: Z 151 LYS cc_start: 0.8361 (tmtm) cc_final: 0.8113 (mmmt) REVERT: Z 195 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8710 (mm-40) REVERT: 7 24 SER cc_start: 0.4129 (p) cc_final: 0.3921 (m) REVERT: 7 42 GLN cc_start: 0.6179 (pp30) cc_final: 0.5658 (tm-30) REVERT: 7 58 TYR cc_start: 0.6218 (t80) cc_final: 0.5895 (t80) REVERT: 7 68 ILE cc_start: 0.5907 (mt) cc_final: 0.5658 (mt) REVERT: 7 107 GLU cc_start: 0.8542 (tt0) cc_final: 0.8024 (tp30) REVERT: 7 115 LYS cc_start: 0.6966 (mttt) cc_final: 0.6747 (tppt) REVERT: 7 125 GLN cc_start: 0.7236 (tp-100) cc_final: 0.7034 (mt0) REVERT: 7 173 MET cc_start: 0.5784 (pp-130) cc_final: 0.5023 (mpp) REVERT: 8 20 MET cc_start: 0.6734 (mmt) cc_final: 0.6284 (ptt) REVERT: X 46 LEU cc_start: 0.7334 (pp) cc_final: 0.6905 (mm) REVERT: X 47 THR cc_start: 0.7826 (m) cc_final: 0.6542 (m) REVERT: X 67 ASP cc_start: 0.8994 (m-30) cc_final: 0.8354 (t70) REVERT: X 69 ILE cc_start: 0.8897 (mt) cc_final: 0.8685 (tp) REVERT: X 70 MET cc_start: 0.8410 (ttt) cc_final: 0.8136 (tmm) REVERT: X 82 TRP cc_start: 0.6641 (p-90) cc_final: 0.6127 (p-90) REVERT: X 89 ILE cc_start: 0.8649 (tp) cc_final: 0.8055 (pt) REVERT: X 102 ILE cc_start: 0.8285 (mt) cc_final: 0.8066 (mm) REVERT: X 169 ARG cc_start: 0.7343 (ttm170) cc_final: 0.6774 (mtp180) REVERT: X 220 MET cc_start: 0.7428 (ttm) cc_final: 0.7132 (mmm) REVERT: X 237 LEU cc_start: 0.9332 (mp) cc_final: 0.9079 (tp) REVERT: X 246 VAL cc_start: 0.4798 (t) cc_final: 0.4549 (m) REVERT: J 1 MET cc_start: 0.2242 (ttp) cc_final: 0.1953 (tpt) REVERT: J 4 ARG cc_start: 0.5060 (ttt180) cc_final: 0.4580 (mtp85) outliers start: 27 outliers final: 6 residues processed: 1190 average time/residue: 0.5428 time to fit residues: 1029.2297 Evaluate side-chains 624 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 615 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain H residue 32 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 422 optimal weight: 5.9990 chunk 378 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 255 optimal weight: 9.9990 chunk 202 optimal weight: 0.2980 chunk 391 optimal weight: 20.0000 chunk 151 optimal weight: 0.0980 chunk 238 optimal weight: 4.9990 chunk 291 optimal weight: 0.0470 chunk 454 optimal weight: 20.0000 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 2 GLN K 35 ASN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 ASN Y 95 ASN Y 112 ASN A 26 ASN A 145 HIS A 193 ASN A 332 GLN A 428 GLN A 432 GLN B 145 HIS B 192 ASN B 217 GLN B 304 HIS B 332 GLN B 351 GLN C 187 ASN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 173 ASN D 221 GLN D 379 GLN D 385 GLN E 293 GLN F 52 GLN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN F 455 HIS G 217 GLN H 44 ASN H 51 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** Z 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 171 GLN Z 203 GLN 7 123 ASN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 27 ASN 6 38 ASN U 14 ASN ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 11 ASN X 71 ASN X 76 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39481 Z= 0.200 Angle : 0.674 11.759 53507 Z= 0.339 Chirality : 0.043 0.224 6349 Planarity : 0.005 0.064 6839 Dihedral : 8.068 169.410 5582 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 2.76 % Allowed : 11.39 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.11), residues: 5060 helix: -0.75 (0.09), residues: 2625 sheet: -1.22 (0.21), residues: 573 loop : -1.30 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 234 HIS 0.006 0.001 HIS Z 99 PHE 0.022 0.002 PHE H 91 TYR 0.015 0.002 TYR U 31 ARG 0.008 0.001 ARG B 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 721 time to evaluate : 4.723 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: K 17 ILE cc_start: 0.2544 (OUTLIER) cc_final: 0.1984 (pp) REVERT: K 20 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6354 (mt) REVERT: K 34 ILE cc_start: 0.6789 (mt) cc_final: 0.6572 (mp) REVERT: K 43 ILE cc_start: 0.7493 (tp) cc_final: 0.7288 (tt) REVERT: K 53 LEU cc_start: 0.8121 (tm) cc_final: 0.7688 (mt) REVERT: K 73 LEU cc_start: 0.4311 (tp) cc_final: 0.3947 (mt) REVERT: N 29 VAL cc_start: 0.8113 (t) cc_final: 0.7833 (t) REVERT: N 30 PHE cc_start: 0.7386 (m-80) cc_final: 0.7062 (m-80) REVERT: N 67 MET cc_start: 0.4796 (pp-130) cc_final: 0.4376 (ttt) REVERT: O 66 LEU cc_start: 0.5480 (OUTLIER) cc_final: 0.5117 (mt) REVERT: Q 68 VAL cc_start: 0.8132 (t) cc_final: 0.7870 (t) REVERT: R 4 VAL cc_start: 0.3141 (p) cc_final: 0.2700 (t) REVERT: R 50 MET cc_start: 0.7493 (ttt) cc_final: 0.6988 (ptm) REVERT: S 45 ASP cc_start: 0.8868 (m-30) cc_final: 0.8318 (t0) REVERT: S 70 PHE cc_start: 0.8351 (m-10) cc_final: 0.7958 (m-80) REVERT: Y 25 GLN cc_start: 0.8310 (tm-30) cc_final: 0.8094 (tp40) REVERT: Y 34 ASP cc_start: 0.9285 (m-30) cc_final: 0.8959 (t0) REVERT: Y 44 GLU cc_start: 0.8514 (tp30) cc_final: 0.8186 (tp30) REVERT: Y 50 ASN cc_start: 0.8383 (t0) cc_final: 0.8136 (t0) REVERT: Y 103 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.5913 (mttt) REVERT: A 124 ASP cc_start: 0.8622 (m-30) cc_final: 0.8039 (p0) REVERT: A 220 GLN cc_start: 0.9240 (tt0) cc_final: 0.8897 (mt0) REVERT: A 228 MET cc_start: 0.8662 (mmm) cc_final: 0.8403 (mmm) REVERT: A 260 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8268 (ttp-170) REVERT: A 271 ASP cc_start: 0.8350 (t70) cc_final: 0.8072 (t0) REVERT: B 62 LYS cc_start: 0.8551 (mttt) cc_final: 0.8317 (mmtt) REVERT: B 228 MET cc_start: 0.8561 (mmm) cc_final: 0.8043 (mmm) REVERT: B 240 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7985 (mt-10) REVERT: B 275 LYS cc_start: 0.8250 (mttm) cc_final: 0.7855 (mttp) REVERT: B 330 GLU cc_start: 0.8675 (tt0) cc_final: 0.7943 (tm-30) REVERT: B 343 ASN cc_start: 0.7921 (m-40) cc_final: 0.7677 (m-40) REVERT: B 357 GLU cc_start: 0.8765 (pt0) cc_final: 0.8482 (tp30) REVERT: B 475 LYS cc_start: 0.9239 (mttm) cc_final: 0.8736 (tppt) REVERT: C 64 MET cc_start: 0.8490 (ttp) cc_final: 0.8281 (ttp) REVERT: C 275 LYS cc_start: 0.8377 (mmtp) cc_final: 0.8172 (mmtp) REVERT: C 490 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8255 (mp0) REVERT: D 38 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7838 (mm-30) REVERT: D 50 VAL cc_start: 0.8355 (t) cc_final: 0.8057 (t) REVERT: D 65 ASP cc_start: 0.8246 (t70) cc_final: 0.7644 (m-30) REVERT: D 294 GLU cc_start: 0.8760 (mm-30) cc_final: 0.7905 (mm-30) REVERT: D 388 ILE cc_start: 0.8511 (mt) cc_final: 0.8098 (mp) REVERT: D 393 MET cc_start: 0.7498 (mpp) cc_final: 0.7041 (mpp) REVERT: D 459 MET cc_start: 0.8287 (tpp) cc_final: 0.8051 (mmm) REVERT: E 22 ASP cc_start: 0.8312 (m-30) cc_final: 0.8042 (m-30) REVERT: E 153 ILE cc_start: 0.9468 (mp) cc_final: 0.9024 (mm) REVERT: E 201 MET cc_start: 0.8667 (mtt) cc_final: 0.8391 (mtt) REVERT: E 203 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8060 (pp20) REVERT: E 208 ASN cc_start: 0.7882 (t0) cc_final: 0.7526 (t0) REVERT: E 277 SER cc_start: 0.8110 (t) cc_final: 0.7115 (p) REVERT: E 279 VAL cc_start: 0.8223 (t) cc_final: 0.7905 (t) REVERT: E 288 ASP cc_start: 0.8016 (m-30) cc_final: 0.7768 (m-30) REVERT: E 289 MET cc_start: 0.8288 (mmm) cc_final: 0.7996 (mmm) REVERT: E 308 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: E 341 GLU cc_start: 0.9428 (tt0) cc_final: 0.9039 (tm-30) REVERT: E 349 ASP cc_start: 0.8628 (t70) cc_final: 0.8415 (t70) REVERT: E 458 TYR cc_start: 0.7846 (t80) cc_final: 0.7125 (t80) REVERT: E 465 ASP cc_start: 0.8475 (m-30) cc_final: 0.8213 (t0) REVERT: E 472 LYS cc_start: 0.8672 (mttt) cc_final: 0.8362 (pttt) REVERT: F 62 ILE cc_start: 0.9027 (mt) cc_final: 0.8647 (tt) REVERT: F 64 MET cc_start: 0.8474 (mmp) cc_final: 0.8092 (mmm) REVERT: F 105 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8779 (pm20) REVERT: F 218 VAL cc_start: 0.8506 (t) cc_final: 0.8285 (p) REVERT: F 282 GLN cc_start: 0.9255 (pm20) cc_final: 0.8402 (pm20) REVERT: F 284 THR cc_start: 0.9025 (p) cc_final: 0.8175 (t) REVERT: F 288 ASP cc_start: 0.8878 (m-30) cc_final: 0.8379 (m-30) REVERT: F 316 ASP cc_start: 0.8180 (t70) cc_final: 0.7930 (t0) REVERT: F 341 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8293 (tm-30) REVERT: F 368 TYR cc_start: 0.9278 (t80) cc_final: 0.8900 (t80) REVERT: F 458 TYR cc_start: 0.8330 (t80) cc_final: 0.8097 (t80) REVERT: F 459 MET cc_start: 0.8224 (tpp) cc_final: 0.7810 (tpp) REVERT: G 23 MET cc_start: 0.8492 (tpp) cc_final: 0.8283 (ttm) REVERT: G 53 LYS cc_start: 0.8848 (mmpt) cc_final: 0.8615 (pttt) REVERT: G 90 GLN cc_start: 0.8334 (tp40) cc_final: 0.7776 (tp-100) REVERT: G 135 LYS cc_start: 0.6883 (pttm) cc_final: 0.6422 (tppt) REVERT: G 142 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8857 (pt0) REVERT: G 166 TYR cc_start: 0.7384 (p90) cc_final: 0.6783 (p90) REVERT: G 168 ASP cc_start: 0.7298 (t0) cc_final: 0.6963 (p0) REVERT: G 196 LYS cc_start: 0.9014 (ptpt) cc_final: 0.8683 (ptmt) REVERT: G 218 MET cc_start: 0.6788 (ttm) cc_final: 0.6449 (ttm) REVERT: G 246 ASP cc_start: 0.8838 (t70) cc_final: 0.8515 (t0) REVERT: G 250 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7564 (ttp80) REVERT: H 44 ASN cc_start: 0.7588 (t0) cc_final: 0.7332 (t0) REVERT: H 66 LYS cc_start: 0.7689 (mttp) cc_final: 0.7413 (mptt) REVERT: H 133 LEU cc_start: 0.7885 (mt) cc_final: 0.7236 (tp) REVERT: I 13 TYR cc_start: 0.8732 (t80) cc_final: 0.8101 (t80) REVERT: I 36 ASN cc_start: 0.8333 (m-40) cc_final: 0.7939 (t0) REVERT: Z 65 PHE cc_start: 0.6562 (t80) cc_final: 0.6306 (t80) REVERT: Z 139 GLU cc_start: 0.3052 (mm-30) cc_final: 0.2341 (tm-30) REVERT: Z 166 GLN cc_start: 0.8092 (mm110) cc_final: 0.7643 (tm-30) REVERT: 7 24 SER cc_start: 0.4884 (p) cc_final: 0.4664 (m) REVERT: 7 83 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5206 (pp) REVERT: 7 107 GLU cc_start: 0.8567 (tt0) cc_final: 0.8072 (tp30) REVERT: 7 125 GLN cc_start: 0.7191 (tp-100) cc_final: 0.6967 (mt0) REVERT: 7 151 GLU cc_start: 0.8102 (tp30) cc_final: 0.7549 (pt0) REVERT: 7 163 TYR cc_start: 0.5040 (t80) cc_final: 0.4698 (t80) REVERT: 7 173 MET cc_start: 0.5671 (pp-130) cc_final: 0.5166 (mmt) REVERT: 6 71 GLU cc_start: 0.3647 (mp0) cc_final: 0.3041 (pt0) REVERT: U 9 VAL cc_start: 0.4291 (OUTLIER) cc_final: 0.3940 (p) REVERT: 8 20 MET cc_start: 0.6573 (mmt) cc_final: 0.6291 (ppp) REVERT: X 47 THR cc_start: 0.7413 (m) cc_final: 0.5478 (m) REVERT: X 57 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7263 (mtm-85) REVERT: X 58 TRP cc_start: 0.7262 (t-100) cc_final: 0.6973 (t-100) REVERT: X 70 MET cc_start: 0.8560 (ttt) cc_final: 0.8333 (ppp) REVERT: X 89 ILE cc_start: 0.8594 (tp) cc_final: 0.8221 (pt) REVERT: X 122 SER cc_start: 0.8006 (t) cc_final: 0.7667 (p) REVERT: X 166 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: X 169 ARG cc_start: 0.7005 (ttm170) cc_final: 0.6664 (mtp180) outliers start: 113 outliers final: 55 residues processed: 789 average time/residue: 0.4912 time to fit residues: 639.3646 Evaluate side-chains 609 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 544 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 65 CYS Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 308 GLN Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 83 ILE Chi-restraints excluded: chain 7 residue 138 LEU Chi-restraints excluded: chain 6 residue 59 GLU Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 13 LEU Chi-restraints excluded: chain 8 residue 38 LEU Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 166 TYR Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain J residue 9 ILE 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: 8.9990 chunk 377 optimal weight: 0.9980 chunk 309 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 454 optimal weight: 40.0000 chunk 491 optimal weight: 8.9990 chunk 405 optimal weight: 20.0000 chunk 451 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 364 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 59 ASN A 26 ASN B 145 HIS ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS D 365 GLN F 249 GLN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 203 GLN 7 47 GLN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39481 Z= 0.251 Angle : 0.656 13.322 53507 Z= 0.329 Chirality : 0.043 0.317 6349 Planarity : 0.004 0.068 6839 Dihedral : 7.586 165.737 5575 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.81 % Rotamer: Outliers : 3.18 % Allowed : 12.51 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.12), residues: 5060 helix: -0.04 (0.10), residues: 2626 sheet: -1.01 (0.21), residues: 581 loop : -1.08 (0.15), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP X 234 HIS 0.005 0.001 HIS 6 92 PHE 0.033 0.002 PHE 7 95 TYR 0.034 0.002 TYR S 9 ARG 0.005 0.001 ARG B 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 593 time to evaluate : 4.737 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: K 17 ILE cc_start: 0.1418 (OUTLIER) cc_final: 0.1148 (pp) REVERT: K 20 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6391 (mt) REVERT: K 43 ILE cc_start: 0.7578 (tp) cc_final: 0.7331 (tt) REVERT: K 55 PHE cc_start: 0.8200 (t80) cc_final: 0.7967 (m-80) REVERT: K 73 LEU cc_start: 0.4441 (tp) cc_final: 0.4176 (mt) REVERT: L 67 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5643 (tmm) REVERT: O 66 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5727 (mt) REVERT: S 45 ASP cc_start: 0.8786 (m-30) cc_final: 0.8223 (t0) REVERT: S 70 PHE cc_start: 0.8267 (m-10) cc_final: 0.7920 (m-80) REVERT: T 9 TYR cc_start: 0.8546 (m-10) cc_final: 0.8278 (m-80) REVERT: T 67 MET cc_start: 0.7983 (tmm) cc_final: 0.7657 (ptt) REVERT: Y 34 ASP cc_start: 0.9265 (m-30) cc_final: 0.8979 (t70) REVERT: Y 44 GLU cc_start: 0.8664 (tp30) cc_final: 0.8324 (tp30) REVERT: Y 103 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.5994 (mttt) REVERT: Y 123 VAL cc_start: 0.7710 (m) cc_final: 0.7398 (t) REVERT: A 40 ILE cc_start: 0.8260 (mt) cc_final: 0.8059 (mt) REVERT: A 69 GLU cc_start: 0.7877 (mp0) cc_final: 0.7549 (mp0) REVERT: A 124 ASP cc_start: 0.8606 (m-30) cc_final: 0.8062 (p0) REVERT: A 260 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8174 (ttp-170) REVERT: A 271 ASP cc_start: 0.8510 (t70) cc_final: 0.8235 (t0) REVERT: A 424 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8397 (mm-30) REVERT: B 228 MET cc_start: 0.8602 (mmm) cc_final: 0.8111 (mmm) REVERT: B 240 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8051 (mt-10) REVERT: B 330 GLU cc_start: 0.8652 (tt0) cc_final: 0.7899 (tm-30) REVERT: B 357 GLU cc_start: 0.8840 (pt0) cc_final: 0.8406 (tp30) REVERT: D 38 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8140 (mp0) REVERT: D 56 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8371 (tm-30) REVERT: D 61 THR cc_start: 0.9238 (p) cc_final: 0.8836 (t) REVERT: D 65 ASP cc_start: 0.8321 (t70) cc_final: 0.7600 (m-30) REVERT: D 84 SER cc_start: 0.8473 (m) cc_final: 0.8097 (t) REVERT: D 306 SER cc_start: 0.8308 (t) cc_final: 0.7967 (p) REVERT: D 388 ILE cc_start: 0.8539 (mt) cc_final: 0.8314 (mp) REVERT: D 393 MET cc_start: 0.7271 (mpp) cc_final: 0.6912 (mpp) REVERT: D 459 MET cc_start: 0.8327 (tpp) cc_final: 0.8019 (mmp) REVERT: E 22 ASP cc_start: 0.8314 (m-30) cc_final: 0.8040 (m-30) REVERT: E 57 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7568 (t0) REVERT: E 201 MET cc_start: 0.8673 (mtt) cc_final: 0.8334 (mtt) REVERT: E 203 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7947 (pp20) REVERT: E 288 ASP cc_start: 0.7986 (m-30) cc_final: 0.7694 (m-30) REVERT: E 308 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: E 341 GLU cc_start: 0.9451 (tt0) cc_final: 0.8964 (tm-30) REVERT: E 349 ASP cc_start: 0.8462 (t70) cc_final: 0.8175 (t0) REVERT: E 465 ASP cc_start: 0.8493 (m-30) cc_final: 0.8260 (t0) REVERT: E 472 LYS cc_start: 0.8620 (mttt) cc_final: 0.8304 (pttt) REVERT: F 62 ILE cc_start: 0.8986 (mt) cc_final: 0.8742 (tt) REVERT: F 64 MET cc_start: 0.8434 (mmp) cc_final: 0.8088 (mmm) REVERT: F 201 MET cc_start: 0.9540 (mmp) cc_final: 0.9293 (mmm) REVERT: F 282 GLN cc_start: 0.9381 (pm20) cc_final: 0.8498 (pm20) REVERT: F 284 THR cc_start: 0.9223 (p) cc_final: 0.8961 (t) REVERT: F 341 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8389 (tm-30) REVERT: F 368 TYR cc_start: 0.9287 (t80) cc_final: 0.9000 (t80) REVERT: F 393 MET cc_start: 0.8507 (tpp) cc_final: 0.8256 (tpp) REVERT: G 53 LYS cc_start: 0.8902 (mmpt) cc_final: 0.8658 (ttpt) REVERT: G 90 GLN cc_start: 0.8408 (tp40) cc_final: 0.7827 (tp-100) REVERT: G 166 TYR cc_start: 0.7368 (p90) cc_final: 0.6693 (p90) REVERT: H 44 ASN cc_start: 0.7895 (t0) cc_final: 0.7665 (t0) REVERT: H 66 LYS cc_start: 0.7679 (mttp) cc_final: 0.7433 (mptt) REVERT: I 13 TYR cc_start: 0.8723 (t80) cc_final: 0.8271 (t80) REVERT: I 36 ASN cc_start: 0.8309 (m-40) cc_final: 0.7911 (t0) REVERT: Z 139 GLU cc_start: 0.3624 (mm-30) cc_final: 0.3060 (tm-30) REVERT: Z 157 TRP cc_start: 0.6331 (m100) cc_final: 0.6121 (m100) REVERT: Z 202 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8997 (tm-30) REVERT: Z 203 GLN cc_start: 0.8355 (tp40) cc_final: 0.8089 (tp-100) REVERT: 7 24 SER cc_start: 0.4962 (p) cc_final: 0.4591 (m) REVERT: 7 45 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: 7 83 ILE cc_start: 0.5627 (OUTLIER) cc_final: 0.5191 (pp) REVERT: 7 107 GLU cc_start: 0.8582 (tt0) cc_final: 0.8096 (tp30) REVERT: 7 125 GLN cc_start: 0.7180 (tp-100) cc_final: 0.6941 (mt0) REVERT: 7 151 GLU cc_start: 0.7958 (tp30) cc_final: 0.7427 (pt0) REVERT: 7 163 TYR cc_start: 0.5185 (t80) cc_final: 0.4858 (t80) REVERT: 6 7 TYR cc_start: 0.7760 (t80) cc_final: 0.7543 (t80) REVERT: 8 10 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6480 (tmm) REVERT: 8 20 MET cc_start: 0.6760 (mmt) cc_final: 0.6464 (ppp) REVERT: X 30 SER cc_start: 0.2976 (OUTLIER) cc_final: 0.2678 (m) REVERT: X 47 THR cc_start: 0.5950 (m) cc_final: 0.4988 (m) REVERT: X 58 TRP cc_start: 0.7414 (t-100) cc_final: 0.7017 (t-100) REVERT: X 62 GLN cc_start: 0.7067 (mt0) cc_final: 0.6653 (mt0) REVERT: X 89 ILE cc_start: 0.8632 (tp) cc_final: 0.8391 (pt) REVERT: X 94 MET cc_start: 0.7904 (tpp) cc_final: 0.7439 (mmm) REVERT: X 104 MET cc_start: 0.4235 (ptt) cc_final: 0.3802 (ttp) REVERT: X 122 SER cc_start: 0.8164 (t) cc_final: 0.7873 (p) REVERT: X 166 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: J 1 MET cc_start: 0.3422 (tmm) cc_final: 0.3219 (tpt) REVERT: J 4 ARG cc_start: 0.4727 (ttt180) cc_final: 0.4253 (mtt90) REVERT: J 27 MET cc_start: 0.3662 (tpp) cc_final: 0.3223 (tmm) outliers start: 130 outliers final: 66 residues processed: 672 average time/residue: 0.4745 time to fit residues: 533.2284 Evaluate side-chains 592 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 513 time to evaluate : 4.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain Y residue 106 SER Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 308 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 45 GLU Chi-restraints excluded: chain 7 residue 83 ILE Chi-restraints excluded: chain 7 residue 138 LEU Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain 6 residue 59 GLU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 13 LEU Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain X residue 166 TYR Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 222 LEU Chi-restraints excluded: chain X residue 238 THR Chi-restraints excluded: chain J residue 9 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 449 optimal weight: 2.9990 chunk 341 optimal weight: 0.0030 chunk 236 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 chunk 456 optimal weight: 6.9990 chunk 483 optimal weight: 9.9990 chunk 238 optimal weight: 0.1980 chunk 432 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 overall best weight: 2.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 96 ASN Y 112 ASN B 217 GLN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 98 HIS 7 123 ASN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39481 Z= 0.235 Angle : 0.623 13.839 53507 Z= 0.311 Chirality : 0.042 0.246 6349 Planarity : 0.004 0.063 6839 Dihedral : 7.385 163.270 5571 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 3.13 % Allowed : 13.86 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.12), residues: 5060 helix: 0.26 (0.10), residues: 2656 sheet: -0.82 (0.22), residues: 568 loop : -1.08 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP X 234 HIS 0.004 0.001 HIS Z 99 PHE 0.036 0.002 PHE S 64 TYR 0.023 0.001 TYR E 458 ARG 0.006 0.000 ARG G 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 558 time to evaluate : 4.477 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 35 ASN cc_start: 0.8481 (m-40) cc_final: 0.8279 (m-40) REVERT: K 43 ILE cc_start: 0.7526 (tp) cc_final: 0.7278 (tt) REVERT: K 50 MET cc_start: 0.6673 (ttp) cc_final: 0.6447 (ptm) REVERT: K 59 GLU cc_start: 0.8410 (tp30) cc_final: 0.7625 (mp0) REVERT: L 67 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.6048 (tmm) REVERT: N 17 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7603 (tt) REVERT: O 16 THR cc_start: 0.2133 (t) cc_final: 0.1776 (p) REVERT: O 66 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5726 (mt) REVERT: P 53 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7075 (mp) REVERT: S 45 ASP cc_start: 0.8719 (m-30) cc_final: 0.8175 (t0) REVERT: S 70 PHE cc_start: 0.8233 (m-10) cc_final: 0.8002 (m-80) REVERT: T 9 TYR cc_start: 0.8508 (m-10) cc_final: 0.8103 (m-80) REVERT: T 67 MET cc_start: 0.7844 (tmm) cc_final: 0.7475 (ptt) REVERT: Y 44 GLU cc_start: 0.8750 (tp30) cc_final: 0.8381 (tp30) REVERT: Y 123 VAL cc_start: 0.7988 (m) cc_final: 0.7630 (t) REVERT: A 40 ILE cc_start: 0.8279 (mt) cc_final: 0.7983 (mm) REVERT: A 69 GLU cc_start: 0.8016 (mp0) cc_final: 0.7607 (mp0) REVERT: A 124 ASP cc_start: 0.8669 (m-30) cc_final: 0.8114 (p0) REVERT: A 260 ARG cc_start: 0.8565 (ttp80) cc_final: 0.8153 (ttp-170) REVERT: A 271 ASP cc_start: 0.8531 (t70) cc_final: 0.8284 (t0) REVERT: A 484 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8646 (mm-30) REVERT: B 228 MET cc_start: 0.8561 (mmm) cc_final: 0.8112 (mmm) REVERT: B 281 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7357 (ptt-90) REVERT: B 330 GLU cc_start: 0.8754 (tt0) cc_final: 0.7868 (tm-30) REVERT: B 357 GLU cc_start: 0.8853 (pt0) cc_final: 0.8573 (tp30) REVERT: C 228 MET cc_start: 0.8080 (mmm) cc_final: 0.7816 (mmm) REVERT: D 38 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8183 (mt-10) REVERT: D 65 ASP cc_start: 0.8395 (t70) cc_final: 0.7651 (m-30) REVERT: D 393 MET cc_start: 0.7157 (mpp) cc_final: 0.6852 (mpp) REVERT: D 459 MET cc_start: 0.8333 (tpp) cc_final: 0.7924 (mmp) REVERT: E 22 ASP cc_start: 0.8297 (m-30) cc_final: 0.8053 (m-30) REVERT: E 57 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7552 (t0) REVERT: E 201 MET cc_start: 0.8610 (mtt) cc_final: 0.8240 (mtt) REVERT: E 203 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8052 (pp20) REVERT: E 288 ASP cc_start: 0.7944 (m-30) cc_final: 0.7712 (m-30) REVERT: E 308 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7445 (pm20) REVERT: E 311 TYR cc_start: 0.8999 (t80) cc_final: 0.8680 (t80) REVERT: E 341 GLU cc_start: 0.9451 (tt0) cc_final: 0.8957 (tm-30) REVERT: E 349 ASP cc_start: 0.8307 (t70) cc_final: 0.8039 (t0) REVERT: E 465 ASP cc_start: 0.8477 (m-30) cc_final: 0.7951 (t0) REVERT: E 472 LYS cc_start: 0.8614 (mttt) cc_final: 0.8300 (pttt) REVERT: F 64 MET cc_start: 0.8320 (mmp) cc_final: 0.7940 (mmm) REVERT: F 201 MET cc_start: 0.9560 (mmp) cc_final: 0.9310 (mmm) REVERT: F 282 GLN cc_start: 0.9398 (pm20) cc_final: 0.8531 (pm20) REVERT: F 284 THR cc_start: 0.9339 (p) cc_final: 0.9014 (t) REVERT: F 316 ASP cc_start: 0.8426 (t0) cc_final: 0.8093 (t0) REVERT: F 341 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8482 (tm-30) REVERT: F 368 TYR cc_start: 0.9267 (t80) cc_final: 0.8991 (t80) REVERT: F 393 MET cc_start: 0.8494 (tpp) cc_final: 0.8153 (tpp) REVERT: F 459 MET cc_start: 0.8331 (tpp) cc_final: 0.8066 (tpp) REVERT: G 23 MET cc_start: 0.8556 (tpp) cc_final: 0.8264 (ttm) REVERT: G 53 LYS cc_start: 0.8921 (mmpt) cc_final: 0.8661 (ttpt) REVERT: G 60 LEU cc_start: 0.7791 (mp) cc_final: 0.7553 (mp) REVERT: G 90 GLN cc_start: 0.8456 (tp40) cc_final: 0.7891 (tp-100) REVERT: G 166 TYR cc_start: 0.7227 (p90) cc_final: 0.6446 (p90) REVERT: H 35 LYS cc_start: 0.8648 (tttt) cc_final: 0.7972 (pptt) REVERT: H 44 ASN cc_start: 0.7866 (t0) cc_final: 0.7629 (t0) REVERT: H 66 LYS cc_start: 0.7687 (mttp) cc_final: 0.7399 (mptt) REVERT: I 13 TYR cc_start: 0.8669 (t80) cc_final: 0.8198 (t80) REVERT: I 29 LEU cc_start: 0.7360 (mt) cc_final: 0.7151 (pp) REVERT: I 36 ASN cc_start: 0.8348 (m-40) cc_final: 0.7936 (t0) REVERT: Z 129 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: Z 202 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8991 (tm-30) REVERT: Z 203 GLN cc_start: 0.8281 (tp40) cc_final: 0.8067 (tp-100) REVERT: 7 83 ILE cc_start: 0.5621 (OUTLIER) cc_final: 0.5198 (pp) REVERT: 7 107 GLU cc_start: 0.8579 (tt0) cc_final: 0.8107 (tp30) REVERT: 7 151 GLU cc_start: 0.7925 (tp30) cc_final: 0.7376 (pt0) REVERT: 7 163 TYR cc_start: 0.5224 (t80) cc_final: 0.4918 (t80) REVERT: 6 71 GLU cc_start: 0.3681 (mp0) cc_final: 0.3176 (pt0) REVERT: 8 10 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6522 (tmm) REVERT: 8 20 MET cc_start: 0.6712 (mmt) cc_final: 0.6482 (ppp) REVERT: X 47 THR cc_start: 0.5908 (m) cc_final: 0.5169 (m) REVERT: X 57 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7355 (mtm-85) REVERT: X 58 TRP cc_start: 0.7492 (t-100) cc_final: 0.7269 (t-100) REVERT: X 62 GLN cc_start: 0.7414 (mt0) cc_final: 0.7102 (mt0) REVERT: X 67 ASP cc_start: 0.9051 (m-30) cc_final: 0.8542 (t70) REVERT: X 82 TRP cc_start: 0.6546 (p-90) cc_final: 0.6317 (p-90) REVERT: X 89 ILE cc_start: 0.8679 (tp) cc_final: 0.8432 (pt) REVERT: X 94 MET cc_start: 0.7834 (tpp) cc_final: 0.7485 (mmm) REVERT: X 104 MET cc_start: 0.4191 (ptt) cc_final: 0.3788 (tmm) REVERT: X 122 SER cc_start: 0.8158 (t) cc_final: 0.7925 (p) REVERT: X 166 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: X 169 ARG cc_start: 0.7153 (mtp180) cc_final: 0.6835 (mtp-110) REVERT: X 220 MET cc_start: 0.7501 (mmp) cc_final: 0.7064 (mmp) REVERT: J 4 ARG cc_start: 0.4850 (ttt180) cc_final: 0.4529 (mtp85) REVERT: J 27 MET cc_start: 0.3682 (tpp) cc_final: 0.3270 (tmm) outliers start: 128 outliers final: 75 residues processed: 638 average time/residue: 0.4818 time to fit residues: 512.9506 Evaluate side-chains 602 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 515 time to evaluate : 5.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 65 CYS Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 308 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 207 LYS Chi-restraints excluded: chain 7 residue 10 LEU Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 83 ILE Chi-restraints excluded: chain 7 residue 126 SER Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 13 LEU Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain X residue 166 TYR Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 222 LEU Chi-restraints excluded: chain J residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 402 optimal weight: 1.9990 chunk 274 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 359 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 chunk 412 optimal weight: 3.9990 chunk 334 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 246 optimal weight: 6.9990 chunk 433 optimal weight: 10.0000 chunk 121 optimal weight: 0.0770 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 2 GLN R 35 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 ASN A 47 ASN B 217 GLN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 39481 Z= 0.231 Angle : 0.619 10.510 53507 Z= 0.307 Chirality : 0.042 0.217 6349 Planarity : 0.004 0.061 6839 Dihedral : 7.225 162.253 5567 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 3.15 % Allowed : 15.15 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 5060 helix: 0.47 (0.10), residues: 2649 sheet: -0.72 (0.22), residues: 583 loop : -1.03 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP X 234 HIS 0.005 0.001 HIS Z 99 PHE 0.033 0.002 PHE S 64 TYR 0.021 0.001 TYR F 458 ARG 0.006 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 547 time to evaluate : 4.216 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: K 43 ILE cc_start: 0.7507 (tp) cc_final: 0.7261 (tt) REVERT: L 67 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5744 (tmm) REVERT: O 16 THR cc_start: 0.2201 (t) cc_final: 0.1781 (p) REVERT: O 66 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5690 (mt) REVERT: P 53 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7084 (mp) REVERT: R 50 MET cc_start: 0.7299 (ttt) cc_final: 0.6826 (ptm) REVERT: S 45 ASP cc_start: 0.8743 (m-30) cc_final: 0.8240 (t0) REVERT: S 70 PHE cc_start: 0.8120 (m-10) cc_final: 0.7686 (m-80) REVERT: T 50 MET cc_start: 0.5339 (ppp) cc_final: 0.5107 (ppp) REVERT: T 67 MET cc_start: 0.7778 (tmm) cc_final: 0.7552 (ptt) REVERT: Y 44 GLU cc_start: 0.8763 (tp30) cc_final: 0.8413 (tp30) REVERT: Y 123 VAL cc_start: 0.7961 (m) cc_final: 0.7730 (t) REVERT: Y 171 LEU cc_start: 0.8295 (tt) cc_final: 0.8066 (tp) REVERT: A 40 ILE cc_start: 0.8305 (mt) cc_final: 0.8026 (tp) REVERT: A 69 GLU cc_start: 0.8065 (mp0) cc_final: 0.7636 (mp0) REVERT: A 124 ASP cc_start: 0.8635 (m-30) cc_final: 0.8139 (p0) REVERT: A 260 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8154 (ttp-170) REVERT: A 271 ASP cc_start: 0.8433 (t70) cc_final: 0.8196 (t0) REVERT: A 484 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8658 (mm-30) REVERT: B 84 VAL cc_start: 0.8690 (t) cc_final: 0.8449 (p) REVERT: B 228 MET cc_start: 0.8605 (mmm) cc_final: 0.8127 (mmm) REVERT: B 240 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8039 (mt-10) REVERT: B 281 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7480 (ptt-90) REVERT: B 330 GLU cc_start: 0.8799 (tt0) cc_final: 0.7908 (tm-30) REVERT: B 357 GLU cc_start: 0.8858 (pt0) cc_final: 0.8568 (tp30) REVERT: C 210 GLN cc_start: 0.8008 (mt0) cc_final: 0.7732 (mt0) REVERT: D 38 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8215 (mt-10) REVERT: D 65 ASP cc_start: 0.8393 (t70) cc_final: 0.7616 (m-30) REVERT: D 198 TYR cc_start: 0.8796 (t80) cc_final: 0.8594 (t80) REVERT: D 393 MET cc_start: 0.7145 (mpp) cc_final: 0.6938 (mpp) REVERT: D 459 MET cc_start: 0.8382 (tpp) cc_final: 0.7942 (mmp) REVERT: E 22 ASP cc_start: 0.8288 (m-30) cc_final: 0.8032 (m-30) REVERT: E 57 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7601 (t0) REVERT: E 203 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8009 (pp20) REVERT: E 208 ASN cc_start: 0.8187 (t0) cc_final: 0.7786 (t0) REVERT: E 308 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: E 311 TYR cc_start: 0.8993 (t80) cc_final: 0.8683 (t80) REVERT: E 341 GLU cc_start: 0.9436 (tt0) cc_final: 0.8906 (tm-30) REVERT: E 349 ASP cc_start: 0.8249 (t70) cc_final: 0.7969 (t0) REVERT: E 402 LEU cc_start: 0.9265 (tp) cc_final: 0.8625 (pp) REVERT: E 465 ASP cc_start: 0.8444 (m-30) cc_final: 0.7906 (t0) REVERT: E 472 LYS cc_start: 0.8581 (mttt) cc_final: 0.8264 (pttt) REVERT: F 201 MET cc_start: 0.9468 (mmp) cc_final: 0.9237 (mmm) REVERT: F 282 GLN cc_start: 0.9422 (pm20) cc_final: 0.8597 (pm20) REVERT: F 284 THR cc_start: 0.9378 (p) cc_final: 0.9036 (t) REVERT: F 316 ASP cc_start: 0.8459 (t0) cc_final: 0.8109 (t0) REVERT: F 341 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8491 (tm-30) REVERT: F 393 MET cc_start: 0.8566 (tpp) cc_final: 0.8243 (tpp) REVERT: F 458 TYR cc_start: 0.8389 (t80) cc_final: 0.8127 (t80) REVERT: G 23 MET cc_start: 0.8544 (tpp) cc_final: 0.8230 (ttm) REVERT: G 53 LYS cc_start: 0.8908 (mmpt) cc_final: 0.8646 (ttpt) REVERT: G 90 GLN cc_start: 0.8441 (tp40) cc_final: 0.7856 (tp-100) REVERT: G 166 TYR cc_start: 0.7233 (p90) cc_final: 0.6424 (p90) REVERT: H 35 LYS cc_start: 0.8657 (tttt) cc_final: 0.7965 (pptt) REVERT: H 44 ASN cc_start: 0.7908 (t0) cc_final: 0.7680 (t0) REVERT: H 66 LYS cc_start: 0.7710 (mttp) cc_final: 0.7426 (mptt) REVERT: H 96 PHE cc_start: 0.4000 (t80) cc_final: 0.3718 (t80) REVERT: H 109 LYS cc_start: 0.9153 (mmmt) cc_final: 0.8914 (mmmt) REVERT: I 13 TYR cc_start: 0.8714 (t80) cc_final: 0.8225 (t80) REVERT: I 36 ASN cc_start: 0.8369 (m-40) cc_final: 0.7953 (t0) REVERT: Z 202 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8919 (tm-30) REVERT: Z 203 GLN cc_start: 0.8276 (tp40) cc_final: 0.8057 (tp-100) REVERT: 7 151 GLU cc_start: 0.7991 (tp30) cc_final: 0.7431 (pt0) REVERT: 7 163 TYR cc_start: 0.5184 (t80) cc_final: 0.4889 (t80) REVERT: 8 20 MET cc_start: 0.6729 (mmt) cc_final: 0.6433 (ppp) REVERT: X 43 LEU cc_start: 0.8087 (pp) cc_final: 0.7672 (tt) REVERT: X 47 THR cc_start: 0.5707 (m) cc_final: 0.4336 (m) REVERT: X 57 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7422 (mtm-85) REVERT: X 58 TRP cc_start: 0.7783 (t-100) cc_final: 0.7158 (t-100) REVERT: X 67 ASP cc_start: 0.9064 (m-30) cc_final: 0.8489 (t70) REVERT: X 68 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8461 (m) REVERT: X 82 TRP cc_start: 0.6540 (p-90) cc_final: 0.6330 (p-90) REVERT: X 89 ILE cc_start: 0.8700 (tp) cc_final: 0.8436 (pt) REVERT: X 104 MET cc_start: 0.4142 (ptt) cc_final: 0.3862 (ttp) REVERT: X 122 SER cc_start: 0.8203 (t) cc_final: 0.7984 (p) REVERT: X 162 GLU cc_start: 0.7135 (tp30) cc_final: 0.6876 (tp30) REVERT: X 166 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: J 4 ARG cc_start: 0.4825 (ttt180) cc_final: 0.4445 (mtp85) outliers start: 129 outliers final: 84 residues processed: 629 average time/residue: 0.4753 time to fit residues: 499.4729 Evaluate side-chains 586 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 493 time to evaluate : 4.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 308 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 207 LYS Chi-restraints excluded: chain 7 residue 10 LEU Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 138 LEU Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 11 ASN Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain X residue 166 TYR Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 222 LEU Chi-restraints excluded: chain X residue 238 THR Chi-restraints excluded: chain J residue 9 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 0.5980 chunk 435 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 483 optimal weight: 20.0000 chunk 401 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 ASN A 48 ASN B 217 GLN B 454 HIS C 6 GLN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 HIS ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 142 GLN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39481 Z= 0.198 Angle : 0.612 11.608 53507 Z= 0.300 Chirality : 0.042 0.224 6349 Planarity : 0.004 0.063 6839 Dihedral : 6.998 161.606 5564 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 2.96 % Allowed : 15.98 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 5060 helix: 0.55 (0.10), residues: 2693 sheet: -0.61 (0.22), residues: 557 loop : -0.89 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP X 234 HIS 0.006 0.001 HIS Z 99 PHE 0.031 0.001 PHE S 64 TYR 0.023 0.001 TYR 7 58 ARG 0.009 0.000 ARG 8 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 533 time to evaluate : 4.557 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 43 ILE cc_start: 0.7435 (tp) cc_final: 0.7207 (tt) REVERT: L 67 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5853 (tmm) REVERT: O 16 THR cc_start: 0.2959 (t) cc_final: 0.2620 (p) REVERT: O 66 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6191 (mt) REVERT: P 53 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7088 (mp) REVERT: R 19 LEU cc_start: 0.5801 (pp) cc_final: 0.5447 (mm) REVERT: S 45 ASP cc_start: 0.8748 (m-30) cc_final: 0.8260 (t0) REVERT: S 70 PHE cc_start: 0.7810 (m-10) cc_final: 0.7609 (m-80) REVERT: T 50 MET cc_start: 0.5278 (ppp) cc_final: 0.4813 (ppp) REVERT: Y 44 GLU cc_start: 0.8774 (tp30) cc_final: 0.8430 (tp30) REVERT: A 40 ILE cc_start: 0.8313 (mt) cc_final: 0.8065 (tp) REVERT: A 69 GLU cc_start: 0.8118 (mp0) cc_final: 0.7695 (mp0) REVERT: A 124 ASP cc_start: 0.8688 (m-30) cc_final: 0.8187 (p0) REVERT: A 260 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8134 (ttp-170) REVERT: A 271 ASP cc_start: 0.8438 (t70) cc_final: 0.8166 (t0) REVERT: A 330 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7352 (tp30) REVERT: A 484 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8643 (mm-30) REVERT: B 84 VAL cc_start: 0.8712 (t) cc_final: 0.8474 (p) REVERT: B 228 MET cc_start: 0.8514 (mmm) cc_final: 0.8119 (mmm) REVERT: B 240 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8092 (mt-10) REVERT: B 281 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7445 (ptt-90) REVERT: B 330 GLU cc_start: 0.8760 (tt0) cc_final: 0.7984 (tm-30) REVERT: B 357 GLU cc_start: 0.8880 (pt0) cc_final: 0.8608 (tp30) REVERT: C 210 GLN cc_start: 0.8034 (mt0) cc_final: 0.7749 (mt0) REVERT: D 38 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8216 (mt-10) REVERT: D 65 ASP cc_start: 0.8437 (t70) cc_final: 0.7636 (m-30) REVERT: D 393 MET cc_start: 0.7190 (mpp) cc_final: 0.6864 (mpp) REVERT: D 459 MET cc_start: 0.8417 (tpp) cc_final: 0.8042 (tpp) REVERT: E 22 ASP cc_start: 0.8280 (m-30) cc_final: 0.8014 (m-30) REVERT: E 57 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7593 (t0) REVERT: E 153 ILE cc_start: 0.9182 (mt) cc_final: 0.8959 (mt) REVERT: E 201 MET cc_start: 0.8862 (mtp) cc_final: 0.8549 (mmt) REVERT: E 288 ASP cc_start: 0.8126 (m-30) cc_final: 0.7889 (m-30) REVERT: E 308 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: E 311 TYR cc_start: 0.8954 (t80) cc_final: 0.8662 (t80) REVERT: E 341 GLU cc_start: 0.9445 (tt0) cc_final: 0.8918 (tm-30) REVERT: E 349 ASP cc_start: 0.8227 (t70) cc_final: 0.7944 (t0) REVERT: E 465 ASP cc_start: 0.8437 (m-30) cc_final: 0.7867 (t0) REVERT: E 472 LYS cc_start: 0.8576 (mttt) cc_final: 0.8260 (pttt) REVERT: F 201 MET cc_start: 0.9470 (mmp) cc_final: 0.9266 (mmm) REVERT: F 282 GLN cc_start: 0.9420 (pm20) cc_final: 0.8554 (pm20) REVERT: F 316 ASP cc_start: 0.8472 (t0) cc_final: 0.8123 (t0) REVERT: F 341 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8490 (tm-30) REVERT: F 393 MET cc_start: 0.8563 (tpp) cc_final: 0.8234 (tpp) REVERT: F 414 LEU cc_start: 0.8916 (mt) cc_final: 0.8679 (mt) REVERT: F 458 TYR cc_start: 0.8338 (t80) cc_final: 0.8075 (t80) REVERT: F 459 MET cc_start: 0.8412 (tpp) cc_final: 0.7924 (tpp) REVERT: G 53 LYS cc_start: 0.8899 (mmpt) cc_final: 0.8638 (ttpt) REVERT: G 90 GLN cc_start: 0.8265 (tp40) cc_final: 0.7663 (tp-100) REVERT: G 140 PHE cc_start: 0.8167 (t80) cc_final: 0.7873 (t80) REVERT: G 166 TYR cc_start: 0.7274 (p90) cc_final: 0.6455 (p90) REVERT: H 35 LYS cc_start: 0.8662 (tttt) cc_final: 0.7961 (pptt) REVERT: H 44 ASN cc_start: 0.7901 (t0) cc_final: 0.7657 (t0) REVERT: H 66 LYS cc_start: 0.7752 (mttp) cc_final: 0.7457 (mptt) REVERT: I 13 TYR cc_start: 0.8601 (t80) cc_final: 0.8222 (t80) REVERT: I 36 ASN cc_start: 0.8347 (m-40) cc_final: 0.7951 (t0) REVERT: Z 202 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9009 (tm-30) REVERT: 7 96 GLU cc_start: 0.7586 (pp20) cc_final: 0.7252 (pt0) REVERT: 7 163 TYR cc_start: 0.5241 (t80) cc_final: 0.4916 (t80) REVERT: 8 10 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6243 (tmm) REVERT: 8 20 MET cc_start: 0.6762 (mmt) cc_final: 0.6363 (ppp) REVERT: X 43 LEU cc_start: 0.8070 (pp) cc_final: 0.7686 (tt) REVERT: X 46 LEU cc_start: 0.6499 (mm) cc_final: 0.6264 (mt) REVERT: X 47 THR cc_start: 0.5807 (m) cc_final: 0.4475 (m) REVERT: X 57 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7395 (mtm-85) REVERT: X 58 TRP cc_start: 0.7762 (t-100) cc_final: 0.7114 (t-100) REVERT: X 89 ILE cc_start: 0.8697 (tp) cc_final: 0.8485 (pt) REVERT: X 94 MET cc_start: 0.7717 (tpp) cc_final: 0.7256 (mmm) REVERT: X 104 MET cc_start: 0.4251 (ptt) cc_final: 0.4045 (ttp) REVERT: X 122 SER cc_start: 0.8141 (t) cc_final: 0.7922 (p) REVERT: X 166 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: X 220 MET cc_start: 0.7854 (mmm) cc_final: 0.7423 (mmp) REVERT: J 1 MET cc_start: 0.5345 (tmm) cc_final: 0.4980 (tmm) REVERT: J 27 MET cc_start: 0.3109 (tpp) cc_final: 0.2570 (tmm) outliers start: 121 outliers final: 87 residues processed: 610 average time/residue: 0.4595 time to fit residues: 477.0511 Evaluate side-chains 589 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 494 time to evaluate : 4.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 65 CYS Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 65 CYS Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 62 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 308 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 189 PHE Chi-restraints excluded: chain Z residue 207 LYS Chi-restraints excluded: chain 7 residue 10 LEU Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 37 ASP Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain X residue 166 TYR Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 222 LEU Chi-restraints excluded: chain J residue 9 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 466 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 275 optimal weight: 0.7980 chunk 353 optimal weight: 0.1980 chunk 273 optimal weight: 1.9990 chunk 407 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 481 optimal weight: 10.0000 chunk 301 optimal weight: 6.9990 chunk 293 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 203 GLN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39481 Z= 0.170 Angle : 0.603 10.824 53507 Z= 0.293 Chirality : 0.041 0.226 6349 Planarity : 0.004 0.062 6839 Dihedral : 6.788 161.047 5564 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 2.74 % Allowed : 16.81 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.12), residues: 5060 helix: 0.68 (0.10), residues: 2687 sheet: -0.57 (0.22), residues: 569 loop : -0.79 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP X 234 HIS 0.006 0.001 HIS Z 99 PHE 0.031 0.001 PHE 7 95 TYR 0.016 0.001 TYR 7 58 ARG 0.005 0.000 ARG Z 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 527 time to evaluate : 4.389 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 39 ARG cc_start: 0.4835 (ptm-80) cc_final: 0.4593 (ptt90) REVERT: L 52 ILE cc_start: 0.6120 (tp) cc_final: 0.5912 (pt) REVERT: M 30 PHE cc_start: 0.7910 (m-80) cc_final: 0.7512 (m-80) REVERT: N 17 ILE cc_start: 0.7943 (pp) cc_final: 0.7367 (mm) REVERT: O 16 THR cc_start: 0.3230 (t) cc_final: 0.2937 (p) REVERT: P 53 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7085 (mp) REVERT: R 19 LEU cc_start: 0.5762 (pp) cc_final: 0.5427 (mm) REVERT: R 50 MET cc_start: 0.7171 (ttt) cc_final: 0.6829 (ptm) REVERT: S 45 ASP cc_start: 0.8751 (m-30) cc_final: 0.8324 (t0) REVERT: S 70 PHE cc_start: 0.7770 (m-10) cc_final: 0.7529 (m-80) REVERT: Y 44 GLU cc_start: 0.8792 (tp30) cc_final: 0.8426 (tp30) REVERT: A 40 ILE cc_start: 0.8353 (mt) cc_final: 0.8118 (tp) REVERT: A 69 GLU cc_start: 0.8152 (mp0) cc_final: 0.7777 (mp0) REVERT: A 124 ASP cc_start: 0.8670 (m-30) cc_final: 0.8173 (p0) REVERT: A 139 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9077 (mp) REVERT: A 260 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8090 (ttp-170) REVERT: A 271 ASP cc_start: 0.8447 (t70) cc_final: 0.8188 (t0) REVERT: A 330 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7037 (tp30) REVERT: A 484 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8655 (mm-30) REVERT: B 84 VAL cc_start: 0.8677 (t) cc_final: 0.8455 (p) REVERT: B 228 MET cc_start: 0.8415 (mmm) cc_final: 0.8036 (mmm) REVERT: B 240 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8090 (mt-10) REVERT: B 281 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7271 (ptt-90) REVERT: B 330 GLU cc_start: 0.8722 (tt0) cc_final: 0.7978 (tm-30) REVERT: B 357 GLU cc_start: 0.8896 (pt0) cc_final: 0.8380 (tp30) REVERT: C 203 CYS cc_start: 0.8900 (m) cc_final: 0.8359 (p) REVERT: C 210 GLN cc_start: 0.8042 (mt0) cc_final: 0.7763 (mt0) REVERT: D 38 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8208 (mt-10) REVERT: D 65 ASP cc_start: 0.8428 (t70) cc_final: 0.7630 (m-30) REVERT: D 294 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8360 (mm-30) REVERT: D 391 LEU cc_start: 0.6708 (mt) cc_final: 0.6343 (mt) REVERT: D 393 MET cc_start: 0.7386 (mpp) cc_final: 0.6927 (mpp) REVERT: D 459 MET cc_start: 0.8416 (tpp) cc_final: 0.8044 (tpp) REVERT: E 22 ASP cc_start: 0.8266 (m-30) cc_final: 0.7963 (m-30) REVERT: E 153 ILE cc_start: 0.9137 (mt) cc_final: 0.8923 (mt) REVERT: E 172 ASN cc_start: 0.9195 (t0) cc_final: 0.8705 (t0) REVERT: E 201 MET cc_start: 0.8880 (mtp) cc_final: 0.8608 (mmt) REVERT: E 288 ASP cc_start: 0.8065 (m-30) cc_final: 0.7827 (m-30) REVERT: E 308 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: E 311 TYR cc_start: 0.8980 (t80) cc_final: 0.8744 (t80) REVERT: E 341 GLU cc_start: 0.9414 (tt0) cc_final: 0.8876 (tm-30) REVERT: E 349 ASP cc_start: 0.8214 (t70) cc_final: 0.7932 (t0) REVERT: E 465 ASP cc_start: 0.8429 (m-30) cc_final: 0.7849 (t0) REVERT: E 472 LYS cc_start: 0.8575 (mttt) cc_final: 0.8258 (pttt) REVERT: F 282 GLN cc_start: 0.9412 (pm20) cc_final: 0.8520 (pm20) REVERT: F 316 ASP cc_start: 0.8487 (t0) cc_final: 0.8148 (t0) REVERT: F 341 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8479 (tm-30) REVERT: F 393 MET cc_start: 0.8564 (tpp) cc_final: 0.8187 (tpp) REVERT: F 405 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8339 (mm-30) REVERT: F 458 TYR cc_start: 0.8265 (t80) cc_final: 0.8037 (t80) REVERT: F 459 MET cc_start: 0.8442 (tpp) cc_final: 0.7890 (tpp) REVERT: G 23 MET cc_start: 0.8681 (tpp) cc_final: 0.8394 (ttm) REVERT: G 53 LYS cc_start: 0.8899 (mmpt) cc_final: 0.8640 (ttpt) REVERT: G 90 GLN cc_start: 0.8308 (tp40) cc_final: 0.7691 (tp-100) REVERT: G 140 PHE cc_start: 0.8311 (t80) cc_final: 0.8054 (t80) REVERT: G 166 TYR cc_start: 0.7374 (p90) cc_final: 0.6526 (p90) REVERT: G 167 ASN cc_start: 0.7796 (m-40) cc_final: 0.7520 (m-40) REVERT: H 35 LYS cc_start: 0.8584 (tttt) cc_final: 0.7916 (pptt) REVERT: H 44 ASN cc_start: 0.7999 (t0) cc_final: 0.7713 (t0) REVERT: H 66 LYS cc_start: 0.7706 (mttp) cc_final: 0.7397 (mptt) REVERT: I 36 ASN cc_start: 0.8365 (m-40) cc_final: 0.8003 (t0) REVERT: Z 181 GLN cc_start: 0.7119 (mm-40) cc_final: 0.6897 (mp10) REVERT: Z 202 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9010 (tm-30) REVERT: 7 96 GLU cc_start: 0.7563 (pp20) cc_final: 0.7301 (pt0) REVERT: 7 163 TYR cc_start: 0.5132 (t80) cc_final: 0.4804 (t80) REVERT: 7 173 MET cc_start: 0.7018 (mpp) cc_final: 0.6685 (mpp) REVERT: 8 10 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.5955 (tmm) REVERT: 8 20 MET cc_start: 0.6735 (mmt) cc_final: 0.6333 (ppp) REVERT: X 43 LEU cc_start: 0.7973 (pp) cc_final: 0.7645 (tt) REVERT: X 47 THR cc_start: 0.5851 (m) cc_final: 0.4526 (m) REVERT: X 57 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7375 (mtm-85) REVERT: X 58 TRP cc_start: 0.7824 (t-100) cc_final: 0.7252 (t-100) REVERT: X 68 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8265 (m) REVERT: X 88 MET cc_start: 0.7594 (ttp) cc_final: 0.7071 (tpt) REVERT: X 89 ILE cc_start: 0.8695 (tp) cc_final: 0.8454 (pt) REVERT: X 94 MET cc_start: 0.7809 (tpp) cc_final: 0.7528 (mmm) REVERT: X 104 MET cc_start: 0.4250 (ptt) cc_final: 0.3980 (ttp) REVERT: X 122 SER cc_start: 0.8132 (t) cc_final: 0.7912 (p) REVERT: X 166 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: J 27 MET cc_start: 0.3346 (tpp) cc_final: 0.2826 (tmm) outliers start: 112 outliers final: 87 residues processed: 597 average time/residue: 0.4727 time to fit residues: 478.7521 Evaluate side-chains 583 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 489 time to evaluate : 4.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 55 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 65 CYS Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 62 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 180 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 308 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 207 LYS Chi-restraints excluded: chain 7 residue 10 LEU Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 37 ASP Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 138 LEU Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 38 LEU Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain X residue 166 TYR Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 222 LEU Chi-restraints excluded: chain X residue 238 THR Chi-restraints excluded: chain J residue 9 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 298 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 306 optimal weight: 0.0470 chunk 328 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 378 optimal weight: 7.9990 overall best weight: 2.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 ASN B 217 GLN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 142 GLN ** Z 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 8 ASN ** 6 22 GLN ** 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: 0.7503 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 39481 Z= 0.291 Angle : 0.670 19.888 53507 Z= 0.327 Chirality : 0.043 0.350 6349 Planarity : 0.004 0.066 6839 Dihedral : 6.862 163.581 5564 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 3.13 % Allowed : 16.79 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.12), residues: 5060 helix: 0.68 (0.10), residues: 2643 sheet: -0.60 (0.22), residues: 577 loop : -0.78 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP X 234 HIS 0.007 0.001 HIS Z 99 PHE 0.039 0.002 PHE K 55 TYR 0.028 0.002 TYR 7 74 ARG 0.004 0.001 ARG G 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 502 time to evaluate : 4.761 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: L 39 ARG cc_start: 0.4864 (ptm-80) cc_final: 0.4564 (ptt90) REVERT: N 17 ILE cc_start: 0.7954 (pp) cc_final: 0.7386 (mm) REVERT: P 53 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7089 (mp) REVERT: P 67 MET cc_start: 0.5209 (ppp) cc_final: 0.4599 (mtm) REVERT: R 19 LEU cc_start: 0.5743 (pp) cc_final: 0.5416 (mm) REVERT: R 50 MET cc_start: 0.7366 (ttt) cc_final: 0.7133 (ptm) REVERT: S 45 ASP cc_start: 0.8738 (m-30) cc_final: 0.8348 (t0) REVERT: Y 44 GLU cc_start: 0.8799 (tp30) cc_final: 0.8447 (tp30) REVERT: A 40 ILE cc_start: 0.8478 (mt) cc_final: 0.8177 (tp) REVERT: A 69 GLU cc_start: 0.8235 (mp0) cc_final: 0.7733 (mp0) REVERT: A 124 ASP cc_start: 0.8582 (m-30) cc_final: 0.8110 (p0) REVERT: A 139 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9106 (mp) REVERT: A 271 ASP cc_start: 0.8494 (t70) cc_final: 0.8190 (t0) REVERT: A 484 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8614 (mm-30) REVERT: B 84 VAL cc_start: 0.8732 (t) cc_final: 0.8506 (p) REVERT: B 228 MET cc_start: 0.8583 (mmm) cc_final: 0.8164 (mmm) REVERT: B 281 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7623 (ptt-90) REVERT: B 330 GLU cc_start: 0.8687 (tt0) cc_final: 0.7949 (tm-30) REVERT: B 357 GLU cc_start: 0.8888 (pt0) cc_final: 0.8595 (tp30) REVERT: C 203 CYS cc_start: 0.8928 (m) cc_final: 0.8374 (p) REVERT: C 210 GLN cc_start: 0.8035 (mt0) cc_final: 0.7723 (mt0) REVERT: D 38 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8251 (mt-10) REVERT: D 189 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6144 (mm-30) REVERT: D 393 MET cc_start: 0.7644 (mpp) cc_final: 0.7331 (mpp) REVERT: D 459 MET cc_start: 0.8462 (tpp) cc_final: 0.8068 (tpp) REVERT: E 22 ASP cc_start: 0.8252 (m-30) cc_final: 0.7972 (m-30) REVERT: E 153 ILE cc_start: 0.9128 (mt) cc_final: 0.8892 (mt) REVERT: E 172 ASN cc_start: 0.9243 (t0) cc_final: 0.8792 (t0) REVERT: E 201 MET cc_start: 0.8932 (mtp) cc_final: 0.8669 (mmt) REVERT: E 274 ARG cc_start: 0.9127 (mtt180) cc_final: 0.8897 (mtt180) REVERT: E 288 ASP cc_start: 0.8006 (m-30) cc_final: 0.7746 (m-30) REVERT: E 308 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: E 311 TYR cc_start: 0.8953 (t80) cc_final: 0.8679 (t80) REVERT: E 341 GLU cc_start: 0.9451 (tt0) cc_final: 0.8942 (tm-30) REVERT: E 349 ASP cc_start: 0.8191 (t70) cc_final: 0.7905 (t0) REVERT: E 393 MET cc_start: 0.8662 (ttt) cc_final: 0.8002 (tmm) REVERT: E 465 ASP cc_start: 0.8424 (m-30) cc_final: 0.7881 (t0) REVERT: E 472 LYS cc_start: 0.8489 (mttt) cc_final: 0.8170 (pttt) REVERT: F 257 ASN cc_start: 0.7146 (OUTLIER) cc_final: 0.6642 (t0) REVERT: F 316 ASP cc_start: 0.8453 (t0) cc_final: 0.8118 (t0) REVERT: F 341 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8522 (tm-30) REVERT: F 393 MET cc_start: 0.8520 (tpp) cc_final: 0.8239 (tpp) REVERT: F 405 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8265 (mm-30) REVERT: G 23 MET cc_start: 0.8705 (tpp) cc_final: 0.8419 (ttm) REVERT: G 53 LYS cc_start: 0.8916 (mmpt) cc_final: 0.8694 (ttpt) REVERT: G 90 GLN cc_start: 0.8324 (tp40) cc_final: 0.7694 (tp-100) REVERT: G 140 PHE cc_start: 0.8313 (t80) cc_final: 0.8108 (t80) REVERT: G 166 TYR cc_start: 0.7305 (p90) cc_final: 0.6522 (p90) REVERT: G 167 ASN cc_start: 0.7828 (m-40) cc_final: 0.7496 (m-40) REVERT: H 35 LYS cc_start: 0.8672 (tttt) cc_final: 0.7959 (pptt) REVERT: H 66 LYS cc_start: 0.7675 (mttp) cc_final: 0.7325 (mptt) REVERT: I 13 TYR cc_start: 0.8781 (t80) cc_final: 0.8339 (t80) REVERT: Z 129 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: Z 181 GLN cc_start: 0.7209 (mm-40) cc_final: 0.7001 (mp10) REVERT: Z 200 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8435 (mp0) REVERT: Z 202 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9031 (tm-30) REVERT: 7 96 GLU cc_start: 0.7509 (pp20) cc_final: 0.7291 (pt0) REVERT: 7 163 TYR cc_start: 0.5173 (t80) cc_final: 0.4799 (t80) REVERT: 7 173 MET cc_start: 0.7035 (mpp) cc_final: 0.6709 (mpp) REVERT: 8 10 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.5675 (tmm) REVERT: 8 20 MET cc_start: 0.6745 (mmt) cc_final: 0.6333 (ppp) REVERT: X 43 LEU cc_start: 0.7896 (pp) cc_final: 0.7615 (tt) REVERT: X 47 THR cc_start: 0.5806 (m) cc_final: 0.4540 (m) REVERT: X 57 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7450 (mtm-85) REVERT: X 58 TRP cc_start: 0.7590 (t-100) cc_final: 0.6913 (t-100) REVERT: X 68 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8344 (m) REVERT: X 89 ILE cc_start: 0.8687 (tp) cc_final: 0.8479 (pt) REVERT: X 94 MET cc_start: 0.7851 (tpp) cc_final: 0.7551 (mmm) REVERT: X 122 SER cc_start: 0.8105 (t) cc_final: 0.7882 (p) REVERT: X 166 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7909 (m-80) REVERT: X 220 MET cc_start: 0.7786 (mmm) cc_final: 0.7309 (mmp) REVERT: X 241 TYR cc_start: 0.8788 (m-10) cc_final: 0.8544 (m-80) REVERT: J 27 MET cc_start: 0.3276 (tpp) cc_final: 0.2895 (tmm) outliers start: 128 outliers final: 104 residues processed: 585 average time/residue: 0.4718 time to fit residues: 465.6580 Evaluate side-chains 581 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 468 time to evaluate : 4.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 55 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 65 CYS Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 65 CYS Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 62 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain Y residue 180 ILE Chi-restraints excluded: chain Y residue 184 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 308 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 189 PHE Chi-restraints excluded: chain Z residue 207 LYS Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 138 LEU Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain 6 residue 59 GLU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain X residue 166 TYR Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 222 LEU Chi-restraints excluded: chain J residue 9 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 438 optimal weight: 5.9990 chunk 461 optimal weight: 10.0000 chunk 421 optimal weight: 0.0970 chunk 449 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 352 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 405 optimal weight: 10.0000 chunk 424 optimal weight: 3.9990 chunk 447 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 ASN A 304 HIS B 217 GLN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39481 Z= 0.201 Angle : 0.624 16.278 53507 Z= 0.304 Chirality : 0.042 0.241 6349 Planarity : 0.004 0.064 6839 Dihedral : 6.753 170.589 5564 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 2.64 % Allowed : 17.52 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.12), residues: 5060 helix: 0.84 (0.11), residues: 2584 sheet: -0.57 (0.22), residues: 569 loop : -0.74 (0.15), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP X 234 HIS 0.007 0.001 HIS Z 99 PHE 0.036 0.002 PHE 7 95 TYR 0.017 0.001 TYR 7 74 ARG 0.006 0.000 ARG Z 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 509 time to evaluate : 4.556 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: N 17 ILE cc_start: 0.7943 (pp) cc_final: 0.7352 (mm) REVERT: N 63 LEU cc_start: 0.7458 (mt) cc_final: 0.7015 (mm) REVERT: P 53 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7034 (mp) REVERT: R 19 LEU cc_start: 0.5749 (pp) cc_final: 0.5466 (mm) REVERT: S 30 PHE cc_start: 0.8451 (m-80) cc_final: 0.8191 (t80) REVERT: S 45 ASP cc_start: 0.8824 (m-30) cc_final: 0.8403 (t0) REVERT: S 70 PHE cc_start: 0.7902 (m-80) cc_final: 0.7586 (m-80) REVERT: T 50 MET cc_start: 0.5103 (ppp) cc_final: 0.4440 (ppp) REVERT: Y 44 GLU cc_start: 0.8791 (tp30) cc_final: 0.8426 (tp30) REVERT: A 40 ILE cc_start: 0.8438 (mt) cc_final: 0.8186 (tp) REVERT: A 69 GLU cc_start: 0.8255 (mp0) cc_final: 0.7823 (mp0) REVERT: A 124 ASP cc_start: 0.8598 (m-30) cc_final: 0.8113 (p0) REVERT: A 139 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9096 (mp) REVERT: A 271 ASP cc_start: 0.8496 (t70) cc_final: 0.8195 (t0) REVERT: A 484 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8604 (mm-30) REVERT: B 84 VAL cc_start: 0.8730 (t) cc_final: 0.8517 (p) REVERT: B 240 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8011 (mt-10) REVERT: B 281 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7485 (ptt-90) REVERT: B 330 GLU cc_start: 0.8666 (tt0) cc_final: 0.7778 (tm-30) REVERT: B 357 GLU cc_start: 0.8877 (pt0) cc_final: 0.8573 (tp30) REVERT: C 203 CYS cc_start: 0.8944 (m) cc_final: 0.8392 (p) REVERT: C 210 GLN cc_start: 0.8030 (mt0) cc_final: 0.7732 (mt0) REVERT: D 38 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8275 (mt-10) REVERT: D 294 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8294 (mm-30) REVERT: D 393 MET cc_start: 0.7420 (mpp) cc_final: 0.6971 (mpp) REVERT: D 459 MET cc_start: 0.8498 (tpp) cc_final: 0.8116 (tpp) REVERT: E 22 ASP cc_start: 0.8277 (m-30) cc_final: 0.8047 (m-30) REVERT: E 153 ILE cc_start: 0.9100 (mt) cc_final: 0.8872 (mt) REVERT: E 172 ASN cc_start: 0.9207 (t0) cc_final: 0.8797 (t0) REVERT: E 201 MET cc_start: 0.8895 (mtp) cc_final: 0.8641 (mmt) REVERT: E 288 ASP cc_start: 0.7987 (m-30) cc_final: 0.7730 (m-30) REVERT: E 308 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: E 311 TYR cc_start: 0.8941 (t80) cc_final: 0.8676 (t80) REVERT: E 341 GLU cc_start: 0.9419 (tt0) cc_final: 0.8883 (tm-30) REVERT: E 349 ASP cc_start: 0.8189 (t70) cc_final: 0.7902 (t0) REVERT: E 393 MET cc_start: 0.8566 (ttt) cc_final: 0.7884 (tmm) REVERT: E 465 ASP cc_start: 0.8383 (m-30) cc_final: 0.7762 (t0) REVERT: E 472 LYS cc_start: 0.8460 (mttt) cc_final: 0.8140 (pttt) REVERT: F 257 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6675 (t0) REVERT: F 282 GLN cc_start: 0.9457 (pm20) cc_final: 0.8602 (pm20) REVERT: F 316 ASP cc_start: 0.8473 (t0) cc_final: 0.8137 (t0) REVERT: F 341 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8486 (tm-30) REVERT: F 393 MET cc_start: 0.8489 (tpp) cc_final: 0.8206 (tpp) REVERT: F 405 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8244 (mm-30) REVERT: G 23 MET cc_start: 0.8691 (tpp) cc_final: 0.8398 (ttm) REVERT: G 53 LYS cc_start: 0.8916 (mmpt) cc_final: 0.8700 (ttpt) REVERT: G 90 GLN cc_start: 0.8274 (tp40) cc_final: 0.7636 (tp-100) REVERT: G 140 PHE cc_start: 0.8301 (t80) cc_final: 0.8080 (t80) REVERT: G 166 TYR cc_start: 0.7408 (p90) cc_final: 0.6668 (p90) REVERT: G 167 ASN cc_start: 0.7796 (m-40) cc_final: 0.7454 (m-40) REVERT: G 249 ASN cc_start: 0.8175 (m-40) cc_final: 0.7825 (t0) REVERT: H 35 LYS cc_start: 0.8600 (tttt) cc_final: 0.7918 (pptt) REVERT: H 66 LYS cc_start: 0.7735 (mttp) cc_final: 0.7394 (mptt) REVERT: I 13 TYR cc_start: 0.8745 (t80) cc_final: 0.8279 (t80) REVERT: I 36 ASN cc_start: 0.8369 (m-40) cc_final: 0.7989 (t0) REVERT: Z 129 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: Z 202 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9039 (tm-30) REVERT: Z 203 GLN cc_start: 0.8353 (tp40) cc_final: 0.7701 (tp-100) REVERT: 7 163 TYR cc_start: 0.5203 (t80) cc_final: 0.4832 (t80) REVERT: 7 173 MET cc_start: 0.7036 (mpp) cc_final: 0.6715 (mpp) REVERT: 8 10 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.5666 (tmm) REVERT: 8 20 MET cc_start: 0.6719 (mmt) cc_final: 0.6297 (ppp) REVERT: X 43 LEU cc_start: 0.7981 (pp) cc_final: 0.7669 (tt) REVERT: X 46 LEU cc_start: 0.6581 (mm) cc_final: 0.6344 (mt) REVERT: X 47 THR cc_start: 0.5772 (m) cc_final: 0.4477 (m) REVERT: X 58 TRP cc_start: 0.7607 (t-100) cc_final: 0.6913 (t-100) REVERT: X 68 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8332 (m) REVERT: X 72 MET cc_start: 0.8686 (tmm) cc_final: 0.8399 (tmm) REVERT: X 88 MET cc_start: 0.7528 (ttp) cc_final: 0.7067 (tpt) REVERT: X 89 ILE cc_start: 0.8644 (tp) cc_final: 0.8361 (pt) REVERT: X 94 MET cc_start: 0.7768 (tpp) cc_final: 0.7496 (mmm) REVERT: X 122 SER cc_start: 0.8178 (t) cc_final: 0.7946 (p) REVERT: X 166 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: X 220 MET cc_start: 0.7784 (mmm) cc_final: 0.7398 (mmp) REVERT: J 27 MET cc_start: 0.3170 (tpp) cc_final: 0.2793 (tmm) outliers start: 108 outliers final: 84 residues processed: 580 average time/residue: 0.4571 time to fit residues: 448.5996 Evaluate side-chains 579 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 486 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 55 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 65 CYS Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 62 LEU Chi-restraints excluded: chain Y residue 74 ILE Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain Y residue 180 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 308 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain X residue 61 SER Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain X residue 166 TYR Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain X residue 222 LEU Chi-restraints excluded: chain J residue 9 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 294 optimal weight: 0.9990 chunk 474 optimal weight: 10.0000 chunk 289 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 330 optimal weight: 4.9990 chunk 498 optimal weight: 0.9990 chunk 458 optimal weight: 9.9990 chunk 396 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 ASN B 217 GLN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39481 Z= 0.179 Angle : 0.628 17.190 53507 Z= 0.306 Chirality : 0.042 0.249 6349 Planarity : 0.004 0.066 6839 Dihedral : 6.651 172.731 5564 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 2.35 % Allowed : 17.82 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.12), residues: 5060 helix: 0.91 (0.11), residues: 2581 sheet: -0.49 (0.22), residues: 562 loop : -0.65 (0.15), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP X 234 HIS 0.007 0.001 HIS Z 99 PHE 0.028 0.002 PHE 7 95 TYR 0.023 0.001 TYR E 458 ARG 0.014 0.000 ARG Z 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 521 time to evaluate : 4.755 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: N 17 ILE cc_start: 0.7921 (pp) cc_final: 0.7364 (mm) REVERT: P 53 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7048 (mp) REVERT: P 67 MET cc_start: 0.5989 (ppp) cc_final: 0.5323 (mtm) REVERT: R 50 MET cc_start: 0.6819 (ptm) cc_final: 0.6546 (ptt) REVERT: R 63 LEU cc_start: 0.4754 (tt) cc_final: 0.4425 (tp) REVERT: R 73 LEU cc_start: 0.7057 (tp) cc_final: 0.6830 (mt) REVERT: S 45 ASP cc_start: 0.8819 (m-30) cc_final: 0.8393 (t0) REVERT: S 70 PHE cc_start: 0.7843 (m-80) cc_final: 0.7607 (m-80) REVERT: T 50 MET cc_start: 0.4979 (ppp) cc_final: 0.4185 (ppp) REVERT: Y 44 GLU cc_start: 0.8776 (tp30) cc_final: 0.8398 (tp30) REVERT: Y 60 PRO cc_start: 0.8112 (Cg_endo) cc_final: 0.7881 (Cg_exo) REVERT: A 40 ILE cc_start: 0.8424 (mt) cc_final: 0.8195 (tp) REVERT: A 52 GLU cc_start: 0.8484 (tp30) cc_final: 0.8039 (tp30) REVERT: A 69 GLU cc_start: 0.8253 (mp0) cc_final: 0.7849 (mp0) REVERT: A 81 ASP cc_start: 0.9081 (p0) cc_final: 0.8648 (p0) REVERT: A 124 ASP cc_start: 0.8629 (m-30) cc_final: 0.8139 (p0) REVERT: A 271 ASP cc_start: 0.8475 (t70) cc_final: 0.8184 (t0) REVERT: A 484 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8595 (mm-30) REVERT: B 240 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 281 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7444 (ptt-90) REVERT: B 330 GLU cc_start: 0.8647 (tt0) cc_final: 0.7769 (tm-30) REVERT: B 357 GLU cc_start: 0.8870 (pt0) cc_final: 0.8408 (tp30) REVERT: C 203 CYS cc_start: 0.8964 (m) cc_final: 0.8403 (p) REVERT: C 210 GLN cc_start: 0.8034 (mt0) cc_final: 0.7738 (mt0) REVERT: D 38 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8228 (mt-10) REVERT: D 294 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8291 (mm-30) REVERT: D 393 MET cc_start: 0.7401 (mpp) cc_final: 0.6956 (mpp) REVERT: D 459 MET cc_start: 0.8499 (tpp) cc_final: 0.8122 (tpp) REVERT: E 22 ASP cc_start: 0.8269 (m-30) cc_final: 0.8035 (m-30) REVERT: E 101 GLU cc_start: 0.8372 (mp0) cc_final: 0.8167 (mp0) REVERT: E 153 ILE cc_start: 0.9074 (mt) cc_final: 0.8826 (mt) REVERT: E 172 ASN cc_start: 0.9202 (t0) cc_final: 0.8804 (t0) REVERT: E 201 MET cc_start: 0.8899 (mtp) cc_final: 0.8639 (mmt) REVERT: E 288 ASP cc_start: 0.8137 (m-30) cc_final: 0.7860 (m-30) REVERT: E 289 MET cc_start: 0.8452 (tpp) cc_final: 0.8122 (tpp) REVERT: E 308 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: E 311 TYR cc_start: 0.8930 (t80) cc_final: 0.8692 (t80) REVERT: E 341 GLU cc_start: 0.9412 (tt0) cc_final: 0.8861 (tm-30) REVERT: E 349 ASP cc_start: 0.8198 (t70) cc_final: 0.7907 (t0) REVERT: E 393 MET cc_start: 0.8722 (ttt) cc_final: 0.8025 (tmm) REVERT: E 465 ASP cc_start: 0.8396 (m-30) cc_final: 0.7805 (t0) REVERT: E 472 LYS cc_start: 0.8463 (mttt) cc_final: 0.8144 (pttt) REVERT: F 282 GLN cc_start: 0.9493 (pm20) cc_final: 0.8587 (pm20) REVERT: F 316 ASP cc_start: 0.8542 (t0) cc_final: 0.8192 (t0) REVERT: F 341 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8483 (tm-30) REVERT: F 393 MET cc_start: 0.8431 (tpp) cc_final: 0.8148 (tpp) REVERT: F 405 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8251 (mm-30) REVERT: G 23 MET cc_start: 0.8752 (tpp) cc_final: 0.8447 (ttm) REVERT: G 53 LYS cc_start: 0.8929 (mmpt) cc_final: 0.8728 (ttpt) REVERT: G 90 GLN cc_start: 0.8242 (tp40) cc_final: 0.7597 (tp-100) REVERT: G 140 PHE cc_start: 0.8403 (t80) cc_final: 0.8085 (t80) REVERT: G 166 TYR cc_start: 0.7330 (p90) cc_final: 0.6528 (p90) REVERT: G 167 ASN cc_start: 0.7785 (m-40) cc_final: 0.7440 (m-40) REVERT: G 246 ASP cc_start: 0.8689 (t0) cc_final: 0.8328 (m-30) REVERT: G 249 ASN cc_start: 0.8173 (m-40) cc_final: 0.7836 (t0) REVERT: H 35 LYS cc_start: 0.8600 (tttt) cc_final: 0.7907 (pptt) REVERT: H 66 LYS cc_start: 0.7779 (mttp) cc_final: 0.7429 (mptt) REVERT: I 13 TYR cc_start: 0.8775 (t80) cc_final: 0.8330 (t80) REVERT: I 36 ASN cc_start: 0.8409 (m-40) cc_final: 0.8031 (t0) REVERT: Z 202 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9060 (tm-30) REVERT: Z 203 GLN cc_start: 0.8355 (tp40) cc_final: 0.7711 (tp-100) REVERT: 7 163 TYR cc_start: 0.5192 (t80) cc_final: 0.4820 (t80) REVERT: 7 173 MET cc_start: 0.7060 (mpp) cc_final: 0.6700 (mpp) REVERT: 8 20 MET cc_start: 0.6695 (mmt) cc_final: 0.6273 (ppp) REVERT: X 43 LEU cc_start: 0.8072 (pp) cc_final: 0.7868 (tt) REVERT: X 47 THR cc_start: 0.5788 (m) cc_final: 0.4375 (m) REVERT: X 58 TRP cc_start: 0.7685 (t-100) cc_final: 0.6930 (t-100) REVERT: X 68 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8365 (m) REVERT: X 72 MET cc_start: 0.8706 (tmm) cc_final: 0.8468 (tmm) REVERT: X 82 TRP cc_start: 0.6335 (p-90) cc_final: 0.6083 (p-90) REVERT: X 88 MET cc_start: 0.7516 (ttp) cc_final: 0.7051 (tpt) REVERT: X 89 ILE cc_start: 0.8640 (tp) cc_final: 0.8370 (pt) REVERT: X 94 MET cc_start: 0.7811 (tpp) cc_final: 0.7518 (mmm) REVERT: X 122 SER cc_start: 0.8169 (t) cc_final: 0.7942 (p) REVERT: X 166 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: X 220 MET cc_start: 0.7738 (mmm) cc_final: 0.7371 (mmp) outliers start: 96 outliers final: 82 residues processed: 585 average time/residue: 0.4857 time to fit residues: 481.2409 Evaluate side-chains 571 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 484 time to evaluate : 4.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 55 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 65 CYS Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 62 LEU Chi-restraints excluded: chain Y residue 74 ILE Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 180 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 308 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 189 PHE Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 37 ASP Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain X residue 61 SER Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain X residue 166 TYR Chi-restraints excluded: chain X residue 222 LEU Chi-restraints excluded: chain J residue 9 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 315 optimal weight: 0.1980 chunk 422 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 365 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 397 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 407 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 96 ASN Y 112 ASN A 145 HIS A 304 HIS B 217 GLN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 98 HIS ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.117756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083601 restraints weight = 116914.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085642 restraints weight = 68834.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086215 restraints weight = 41252.256| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39481 Z= 0.290 Angle : 0.676 17.224 53507 Z= 0.333 Chirality : 0.043 0.289 6349 Planarity : 0.004 0.068 6839 Dihedral : 6.539 133.211 5564 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 2.52 % Allowed : 17.79 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.12), residues: 5060 helix: 0.76 (0.10), residues: 2620 sheet: -0.47 (0.23), residues: 550 loop : -0.70 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP X 234 HIS 0.007 0.001 HIS 6 92 PHE 0.035 0.002 PHE 7 95 TYR 0.014 0.002 TYR 7 74 ARG 0.009 0.001 ARG G 207 =============================================================================== Job complete usr+sys time: 9665.03 seconds wall clock time: 176 minutes 44.14 seconds (10604.14 seconds total)