Starting phenix.real_space_refine on Fri Dec 27 04:05:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pxa_13695/12_2024/7pxa_13695.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pxa_13695/12_2024/7pxa_13695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pxa_13695/12_2024/7pxa_13695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pxa_13695/12_2024/7pxa_13695.map" model { file = "/net/cci-nas-00/data/ceres_data/7pxa_13695/12_2024/7pxa_13695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pxa_13695/12_2024/7pxa_13695.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 29215 2.51 5 N 8271 2.21 5 O 9016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 131 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 46614 Number of models: 1 Model: "" Number of chains: 35 Chain: "0" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "2" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "4" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "6" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "8" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 50 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'TRANS': 5} Chain: "H" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "J" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1668 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "P" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "R" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "U" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1715 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1715 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "Y" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "a" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "f" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Time building chain proxies: 22.80, per 1000 atoms: 0.49 Number of scatterers: 46614 At special positions: 0 Unit cell: (136.864, 136.864, 174.746, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 9016 8.00 N 8271 7.00 C 29215 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 - 3.00 Amino acid : True - 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: 9.06 Conformation dependent library (CDL) restraints added in 4.4 seconds 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11210 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 70 sheets defined 46.5% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.15 Creating SS restraints... Processing helix chain '0' and resid 8 through 26 Processing helix chain '0' and resid 67 through 89 removed outlier: 3.909A pdb=" N ASN 0 73 " --> pdb=" O ASN 0 69 " (cutoff:3.500A) Processing helix chain '0' and resid 95 through 114 Processing helix chain '0' and resid 159 through 171 removed outlier: 4.530A pdb=" N ILE 0 163 " --> pdb=" O THR 0 159 " (cutoff:3.500A) Processing helix chain '0' and resid 176 through 190 removed outlier: 3.511A pdb=" N ALA 0 190 " --> pdb=" O ALA 0 186 " (cutoff:3.500A) Processing helix chain '0' and resid 227 through 234 Processing helix chain '2' and resid 9 through 26 Processing helix chain '2' and resid 67 through 89 removed outlier: 4.386A pdb=" N ASN 2 73 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) Processing helix chain '2' and resid 90 through 94 Processing helix chain '2' and resid 95 through 114 Processing helix chain '2' and resid 159 through 171 removed outlier: 4.535A pdb=" N ILE 2 163 " --> pdb=" O THR 2 159 " (cutoff:3.500A) Processing helix chain '2' and resid 176 through 190 Processing helix chain '2' and resid 226 through 234 removed outlier: 3.592A pdb=" N LEU 2 230 " --> pdb=" O THR 2 226 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 26 Processing helix chain '4' and resid 67 through 89 removed outlier: 3.753A pdb=" N ASN 4 73 " --> pdb=" O ASN 4 69 " (cutoff:3.500A) Processing helix chain '4' and resid 95 through 114 Processing helix chain '4' and resid 159 through 171 removed outlier: 4.546A pdb=" N ILE 4 163 " --> pdb=" O THR 4 159 " (cutoff:3.500A) Processing helix chain '4' and resid 176 through 190 removed outlier: 3.633A pdb=" N ALA 4 190 " --> pdb=" O ALA 4 186 " (cutoff:3.500A) Processing helix chain '4' and resid 204 through 206 No H-bonds generated for 'chain '4' and resid 204 through 206' Processing helix chain '4' and resid 227 through 234 Processing helix chain '6' and resid 9 through 26 Processing helix chain '6' and resid 67 through 89 removed outlier: 3.764A pdb=" N ASN 6 73 " --> pdb=" O ASN 6 69 " (cutoff:3.500A) Processing helix chain '6' and resid 95 through 114 Processing helix chain '6' and resid 159 through 171 removed outlier: 4.569A pdb=" N ILE 6 163 " --> pdb=" O THR 6 159 " (cutoff:3.500A) Processing helix chain '6' and resid 176 through 190 Processing helix chain '6' and resid 227 through 234 Processing helix chain '8' and resid 9 through 26 Processing helix chain '8' and resid 67 through 89 removed outlier: 3.836A pdb=" N ASN 8 73 " --> pdb=" O ASN 8 69 " (cutoff:3.500A) Processing helix chain '8' and resid 95 through 114 Processing helix chain '8' and resid 159 through 171 removed outlier: 4.452A pdb=" N ILE 8 163 " --> pdb=" O THR 8 159 " (cutoff:3.500A) Processing helix chain '8' and resid 176 through 190 Processing helix chain '8' and resid 227 through 234 Processing helix chain 'H' and resid 348 through 371 Processing helix chain 'H' and resid 375 through 390 Processing helix chain 'H' and resid 390 through 395 Processing helix chain 'H' and resid 413 through 416 Processing helix chain 'H' and resid 442 through 454 removed outlier: 3.692A pdb=" N LYS H 452 " --> pdb=" O SER H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 457 No H-bonds generated for 'chain 'H' and resid 455 through 457' Processing helix chain 'H' and resid 459 through 478 Processing helix chain 'H' and resid 506 through 522 removed outlier: 3.660A pdb=" N ILE H 510 " --> pdb=" O PRO H 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 26 Processing helix chain 'I' and resid 67 through 89 removed outlier: 3.709A pdb=" N ASN I 73 " --> pdb=" O ASN I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 95 through 114 removed outlier: 3.504A pdb=" N LEU I 99 " --> pdb=" O THR I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 4.505A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 removed outlier: 3.590A pdb=" N ALA I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 208 removed outlier: 3.801A pdb=" N LEU I 208 " --> pdb=" O VAL I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 234 Processing helix chain 'J' and resid 348 through 371 Processing helix chain 'J' and resid 375 through 390 Processing helix chain 'J' and resid 390 through 395 Processing helix chain 'J' and resid 413 through 416 Processing helix chain 'J' and resid 442 through 454 removed outlier: 3.539A pdb=" N LYS J 452 " --> pdb=" O SER J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 455 through 457 No H-bonds generated for 'chain 'J' and resid 455 through 457' Processing helix chain 'J' and resid 459 through 478 Processing helix chain 'J' and resid 506 through 522 removed outlier: 3.584A pdb=" N ILE J 510 " --> pdb=" O PRO J 506 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 26 Processing helix chain 'K' and resid 67 through 89 removed outlier: 3.767A pdb=" N ASN K 73 " --> pdb=" O ASN K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'K' and resid 95 through 114 removed outlier: 3.501A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.583A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 192 removed outlier: 3.670A pdb=" N GLY K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 206 No H-bonds generated for 'chain 'K' and resid 204 through 206' Processing helix chain 'K' and resid 227 through 234 Processing helix chain 'L' and resid 348 through 371 Processing helix chain 'L' and resid 375 through 390 Processing helix chain 'L' and resid 390 through 396 removed outlier: 3.500A pdb=" N GLN L 396 " --> pdb=" O ALA L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 416 Processing helix chain 'L' and resid 442 through 454 removed outlier: 3.648A pdb=" N LYS L 452 " --> pdb=" O SER L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 455 through 457 No H-bonds generated for 'chain 'L' and resid 455 through 457' Processing helix chain 'L' and resid 459 through 478 Processing helix chain 'L' and resid 506 through 522 removed outlier: 3.607A pdb=" N ILE L 510 " --> pdb=" O PRO L 506 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 371 Processing helix chain 'M' and resid 375 through 390 Processing helix chain 'M' and resid 390 through 395 Processing helix chain 'M' and resid 413 through 416 Processing helix chain 'M' and resid 442 through 454 removed outlier: 3.547A pdb=" N LYS M 452 " --> pdb=" O SER M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 455 through 457 No H-bonds generated for 'chain 'M' and resid 455 through 457' Processing helix chain 'M' and resid 459 through 478 Processing helix chain 'M' and resid 506 through 522 removed outlier: 3.623A pdb=" N ILE M 510 " --> pdb=" O PRO M 506 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 371 Processing helix chain 'N' and resid 375 through 390 Processing helix chain 'N' and resid 390 through 395 Processing helix chain 'N' and resid 413 through 416 Processing helix chain 'N' and resid 442 through 454 removed outlier: 3.574A pdb=" N LYS N 452 " --> pdb=" O SER N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 455 through 457 No H-bonds generated for 'chain 'N' and resid 455 through 457' Processing helix chain 'N' and resid 459 through 478 Processing helix chain 'N' and resid 506 through 521 removed outlier: 3.588A pdb=" N ILE N 510 " --> pdb=" O PRO N 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 Processing helix chain 'O' and resid 67 through 89 removed outlier: 3.731A pdb=" N ASN O 73 " --> pdb=" O ASN O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 94 Processing helix chain 'O' and resid 95 through 114 Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.315A pdb=" N ILE O 163 " --> pdb=" O THR O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 190 Processing helix chain 'O' and resid 227 through 234 Processing helix chain 'P' and resid 348 through 371 Processing helix chain 'P' and resid 375 through 390 Processing helix chain 'P' and resid 390 through 396 Processing helix chain 'P' and resid 413 through 416 Processing helix chain 'P' and resid 442 through 454 removed outlier: 3.668A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 457 No H-bonds generated for 'chain 'P' and resid 455 through 457' Processing helix chain 'P' and resid 459 through 478 Processing helix chain 'P' and resid 506 through 523 removed outlier: 3.635A pdb=" N ILE P 510 " --> pdb=" O PRO P 506 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY P 523 " --> pdb=" O GLU P 519 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 27 removed outlier: 3.657A pdb=" N ALA Q 27 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 89 removed outlier: 3.714A pdb=" N ASN Q 73 " --> pdb=" O ASN Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 94 Processing helix chain 'Q' and resid 95 through 114 removed outlier: 3.541A pdb=" N LEU Q 99 " --> pdb=" O THR Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 171 removed outlier: 4.402A pdb=" N ILE Q 163 " --> pdb=" O THR Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 Processing helix chain 'Q' and resid 227 through 234 Processing helix chain 'R' and resid 348 through 371 Processing helix chain 'R' and resid 375 through 390 Processing helix chain 'R' and resid 390 through 396 Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 3.673A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 455 through 457 No H-bonds generated for 'chain 'R' and resid 455 through 457' Processing helix chain 'R' and resid 459 through 478 Processing helix chain 'R' and resid 506 through 521 removed outlier: 3.639A pdb=" N ILE R 510 " --> pdb=" O PRO R 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 390 Processing helix chain 'S' and resid 390 through 395 Processing helix chain 'S' and resid 413 through 416 Processing helix chain 'S' and resid 442 through 454 removed outlier: 3.595A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 457 No H-bonds generated for 'chain 'S' and resid 455 through 457' Processing helix chain 'S' and resid 459 through 478 Processing helix chain 'S' and resid 506 through 522 removed outlier: 3.679A pdb=" N ILE S 510 " --> pdb=" O PRO S 506 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 26 Processing helix chain 'T' and resid 67 through 89 removed outlier: 3.864A pdb=" N ASN T 73 " --> pdb=" O ASN T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 94 Processing helix chain 'T' and resid 95 through 114 removed outlier: 3.523A pdb=" N LEU T 99 " --> pdb=" O THR T 95 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 171 Processing helix chain 'T' and resid 176 through 190 removed outlier: 3.506A pdb=" N ALA T 190 " --> pdb=" O ALA T 186 " (cutoff:3.500A) Processing helix chain 'T' and resid 204 through 206 No H-bonds generated for 'chain 'T' and resid 204 through 206' Processing helix chain 'T' and resid 227 through 234 Processing helix chain 'U' and resid 348 through 371 Processing helix chain 'U' and resid 375 through 390 Processing helix chain 'U' and resid 390 through 396 Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 3.526A pdb=" N LYS U 452 " --> pdb=" O SER U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 457 No H-bonds generated for 'chain 'U' and resid 455 through 457' Processing helix chain 'U' and resid 459 through 478 Processing helix chain 'U' and resid 506 through 528 removed outlier: 3.680A pdb=" N ILE U 510 " --> pdb=" O PRO U 506 " (cutoff:3.500A) Processing helix chain 'V' and resid 348 through 371 Processing helix chain 'V' and resid 375 through 395 removed outlier: 4.668A pdb=" N ALA V 392 " --> pdb=" O ARG V 388 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA V 393 " --> pdb=" O GLY V 389 " (cutoff:3.500A) Processing helix chain 'V' and resid 413 through 416 Processing helix chain 'V' and resid 442 through 454 removed outlier: 3.646A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 459 through 478 Processing helix chain 'V' and resid 506 through 523 removed outlier: 3.620A pdb=" N ILE V 510 " --> pdb=" O PRO V 506 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY V 523 " --> pdb=" O GLU V 519 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 371 Processing helix chain 'W' and resid 375 through 390 Processing helix chain 'W' and resid 390 through 395 Processing helix chain 'W' and resid 413 through 416 Processing helix chain 'W' and resid 442 through 454 Processing helix chain 'W' and resid 455 through 457 No H-bonds generated for 'chain 'W' and resid 455 through 457' Processing helix chain 'W' and resid 459 through 478 Processing helix chain 'W' and resid 506 through 528 removed outlier: 3.674A pdb=" N ILE W 510 " --> pdb=" O PRO W 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 26 Processing helix chain 'X' and resid 67 through 89 removed outlier: 3.872A pdb=" N ASN X 73 " --> pdb=" O ASN X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 94 Processing helix chain 'X' and resid 95 through 114 removed outlier: 3.523A pdb=" N LEU X 99 " --> pdb=" O THR X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 159 through 171 removed outlier: 4.311A pdb=" N ILE X 163 " --> pdb=" O THR X 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 176 through 190 Processing helix chain 'X' and resid 227 through 234 Processing helix chain 'Y' and resid 348 through 371 Processing helix chain 'Y' and resid 375 through 390 Processing helix chain 'Y' and resid 390 through 397 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 Processing helix chain 'Y' and resid 455 through 457 No H-bonds generated for 'chain 'Y' and resid 455 through 457' Processing helix chain 'Y' and resid 459 through 478 Processing helix chain 'Y' and resid 506 through 523 removed outlier: 3.628A pdb=" N ILE Y 510 " --> pdb=" O PRO Y 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 27 removed outlier: 4.245A pdb=" N MET Z 13 " --> pdb=" O PRO Z 9 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG Z 14 " --> pdb=" O GLU Z 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA Z 27 " --> pdb=" O GLY Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 67 through 89 removed outlier: 3.815A pdb=" N ASN Z 73 " --> pdb=" O ASN Z 69 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 94 Processing helix chain 'Z' and resid 95 through 114 Processing helix chain 'Z' and resid 160 through 171 Processing helix chain 'Z' and resid 176 through 190 Processing helix chain 'Z' and resid 227 through 234 Processing helix chain 'a' and resid 348 through 371 Processing helix chain 'a' and resid 375 through 390 Processing helix chain 'a' and resid 390 through 396 removed outlier: 3.589A pdb=" N GLN a 396 " --> pdb=" O ALA a 392 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 3.522A pdb=" N LYS a 452 " --> pdb=" O SER a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 457 No H-bonds generated for 'chain 'a' and resid 455 through 457' Processing helix chain 'a' and resid 459 through 478 Processing helix chain 'a' and resid 506 through 523 removed outlier: 3.607A pdb=" N ILE a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 390 Processing helix chain 'b' and resid 390 through 396 Processing helix chain 'b' and resid 413 through 416 Processing helix chain 'b' and resid 442 through 454 removed outlier: 3.585A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 457 No H-bonds generated for 'chain 'b' and resid 455 through 457' Processing helix chain 'b' and resid 459 through 478 Processing helix chain 'b' and resid 506 through 523 removed outlier: 3.612A pdb=" N ILE b 510 " --> pdb=" O PRO b 506 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 26 removed outlier: 3.970A pdb=" N ARG d 14 " --> pdb=" O GLU d 10 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG d 16 " --> pdb=" O ALA d 12 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER d 17 " --> pdb=" O MET d 13 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU d 18 " --> pdb=" O ARG d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 89 removed outlier: 4.004A pdb=" N ASN d 73 " --> pdb=" O ASN d 69 " (cutoff:3.500A) Processing helix chain 'd' and resid 95 through 114 Processing helix chain 'd' and resid 159 through 171 removed outlier: 4.675A pdb=" N ILE d 163 " --> pdb=" O THR d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 190 Processing helix chain 'd' and resid 227 through 234 Processing helix chain 'f' and resid 9 through 25 Processing helix chain 'f' and resid 67 through 89 removed outlier: 3.767A pdb=" N ASN f 73 " --> pdb=" O ASN f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 95 through 114 removed outlier: 3.823A pdb=" N THR f 112 " --> pdb=" O GLY f 108 " (cutoff:3.500A) Processing helix chain 'f' and resid 159 through 171 removed outlier: 4.057A pdb=" N ILE f 163 " --> pdb=" O THR f 159 " (cutoff:3.500A) Processing helix chain 'f' and resid 176 through 190 removed outlier: 3.542A pdb=" N ALA f 190 " --> pdb=" O ALA f 186 " (cutoff:3.500A) Processing helix chain 'f' and resid 227 through 234 Processing sheet with id=AA1, first strand: chain '0' and resid 153 through 156 removed outlier: 3.517A pdb=" N VAL 0 39 " --> pdb=" O LEU 0 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 53 through 55 removed outlier: 3.888A pdb=" N ALA 0 125 " --> pdb=" O GLY 0 61 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU 0 138 " --> pdb=" O GLU 0 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 153 through 156 removed outlier: 3.523A pdb=" N VAL 2 39 " --> pdb=" O LEU 2 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 53 through 55 removed outlier: 3.668A pdb=" N ALA 2 125 " --> pdb=" O GLY 2 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU 2 138 " --> pdb=" O GLU 2 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '4' and resid 153 through 156 Processing sheet with id=AA6, first strand: chain '4' and resid 53 through 55 removed outlier: 3.632A pdb=" N ALA 4 125 " --> pdb=" O GLY 4 61 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU 4 138 " --> pdb=" O GLU 4 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '6' and resid 153 through 156 removed outlier: 3.549A pdb=" N VAL 6 39 " --> pdb=" O LEU 6 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '6' and resid 53 through 55 removed outlier: 3.625A pdb=" N ALA 6 125 " --> pdb=" O GLY 6 61 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU 6 138 " --> pdb=" O GLU 6 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '8' and resid 153 through 156 Processing sheet with id=AB1, first strand: chain '8' and resid 53 through 55 removed outlier: 3.678A pdb=" N ALA 8 125 " --> pdb=" O GLY 8 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU 8 138 " --> pdb=" O GLU 8 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 436 through 440 Processing sheet with id=AB3, first strand: chain 'H' and resid 320 through 322 removed outlier: 6.530A pdb=" N SER H 320 " --> pdb=" O SER H 327 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET H 325 " --> pdb=" O GLN H 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 334 through 338 removed outlier: 6.878A pdb=" N THR H 341 " --> pdb=" O THR H 337 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE H 423 " --> pdb=" O PRO H 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 153 through 156 Processing sheet with id=AB6, first strand: chain 'I' and resid 53 through 55 removed outlier: 3.592A pdb=" N ALA I 125 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 436 through 440 Processing sheet with id=AB8, first strand: chain 'J' and resid 320 through 322 removed outlier: 6.625A pdb=" N SER J 320 " --> pdb=" O SER J 327 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 334 through 338 removed outlier: 6.881A pdb=" N THR J 341 " --> pdb=" O THR J 337 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE J 423 " --> pdb=" O PRO J 402 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 153 through 156 Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 55 removed outlier: 3.713A pdb=" N ALA K 125 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 436 through 440 Processing sheet with id=AC4, first strand: chain 'L' and resid 320 through 322 removed outlier: 6.544A pdb=" N SER L 320 " --> pdb=" O SER L 327 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 334 through 336 removed outlier: 4.142A pdb=" N PHE L 423 " --> pdb=" O PRO L 402 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 436 through 440 Processing sheet with id=AC7, first strand: chain 'M' and resid 320 through 322 removed outlier: 6.638A pdb=" N SER M 320 " --> pdb=" O SER M 327 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 334 through 336 removed outlier: 3.963A pdb=" N PHE M 423 " --> pdb=" O PRO M 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 436 through 440 Processing sheet with id=AD1, first strand: chain 'N' and resid 320 through 322 removed outlier: 6.552A pdb=" N SER N 320 " --> pdb=" O SER N 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 334 through 338 removed outlier: 6.860A pdb=" N THR N 341 " --> pdb=" O THR N 337 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE N 423 " --> pdb=" O PRO N 402 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 153 through 156 removed outlier: 3.570A pdb=" N VAL O 39 " --> pdb=" O LEU O 213 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 53 through 55 removed outlier: 3.581A pdb=" N ALA O 125 " --> pdb=" O GLY O 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 436 through 440 Processing sheet with id=AD6, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.571A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.857A pdb=" N THR P 341 " --> pdb=" O THR P 337 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 153 through 156 removed outlier: 3.538A pdb=" N VAL Q 39 " --> pdb=" O LEU Q 213 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 53 through 55 removed outlier: 3.825A pdb=" N LEU Q 138 " --> pdb=" O GLU Q 150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 436 through 440 Processing sheet with id=AE2, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.554A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET R 325 " --> pdb=" O GLN R 322 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 334 through 336 removed outlier: 4.184A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 436 through 440 Processing sheet with id=AE5, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.415A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 334 through 336 removed outlier: 3.984A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 153 through 156 Processing sheet with id=AE8, first strand: chain 'T' and resid 53 through 55 removed outlier: 3.522A pdb=" N ALA T 125 " --> pdb=" O GLY T 61 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU T 138 " --> pdb=" O GLU T 150 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'U' and resid 436 through 440 Processing sheet with id=AF1, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.484A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET U 325 " --> pdb=" O GLN U 322 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.908A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE U 420 " --> pdb=" O GLU U 432 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 436 through 440 Processing sheet with id=AF4, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.524A pdb=" N SER V 320 " --> pdb=" O SER V 327 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.882A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 436 through 440 Processing sheet with id=AF7, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.507A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET W 325 " --> pdb=" O GLN W 322 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 334 through 338 removed outlier: 6.866A pdb=" N THR W 341 " --> pdb=" O THR W 337 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'X' and resid 153 through 156 Processing sheet with id=AG1, first strand: chain 'X' and resid 53 through 55 removed outlier: 3.570A pdb=" N ALA X 125 " --> pdb=" O GLY X 61 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 436 through 440 Processing sheet with id=AG3, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.636A pdb=" N SER Y 320 " --> pdb=" O SER Y 327 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 334 through 336 removed outlier: 4.191A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 153 through 156 removed outlier: 3.517A pdb=" N VAL Z 39 " --> pdb=" O LEU Z 213 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Z' and resid 53 through 55 removed outlier: 3.681A pdb=" N ALA Z 125 " --> pdb=" O GLY Z 61 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU Z 138 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 436 through 440 Processing sheet with id=AG8, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.559A pdb=" N SER a 320 " --> pdb=" O SER a 327 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET a 325 " --> pdb=" O GLN a 322 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.877A pdb=" N THR a 341 " --> pdb=" O THR a 337 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 436 through 440 Processing sheet with id=AH2, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.578A pdb=" N SER b 320 " --> pdb=" O SER b 327 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 334 through 338 removed outlier: 6.862A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'd' and resid 153 through 156 removed outlier: 3.597A pdb=" N VAL d 39 " --> pdb=" O LEU d 213 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 53 through 55 removed outlier: 3.705A pdb=" N ALA d 125 " --> pdb=" O GLY d 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU d 138 " --> pdb=" O GLU d 150 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'f' and resid 153 through 156 Processing sheet with id=AH7, first strand: chain 'f' and resid 53 through 55 removed outlier: 3.792A pdb=" N ALA f 125 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU f 138 " --> pdb=" O GLU f 150 " (cutoff:3.500A) 3003 hydrogen bonds defined for protein. 8631 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: 17.37 Time building geometry restraints manager: 10.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 16087 1.34 - 1.46: 8704 1.46 - 1.58: 22301 1.58 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 47302 Sorted by residual: bond pdb=" C ASN X 45 " pdb=" O ASN X 45 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.70e+00 bond pdb=" CA THR N 301 " pdb=" CB THR N 301 " ideal model delta sigma weight residual 1.540 1.519 0.021 2.70e-02 1.37e+03 5.90e-01 bond pdb=" CA THR a 301 " pdb=" CB THR a 301 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.68e-01 bond pdb=" CA THR R 301 " pdb=" CB THR R 301 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.51e-01 bond pdb=" CA THR M 301 " pdb=" CB THR M 301 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.49e-01 ... (remaining 47297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 62132 1.05 - 2.09: 1562 2.09 - 3.14: 266 3.14 - 4.19: 37 4.19 - 5.23: 16 Bond angle restraints: 64013 Sorted by residual: angle pdb=" C GLU 6 70 " pdb=" N PHE 6 71 " pdb=" CA PHE 6 71 " ideal model delta sigma weight residual 120.72 117.65 3.07 1.67e+00 3.59e-01 3.37e+00 angle pdb=" C GLU f 44 " pdb=" N ASN f 45 " pdb=" CA ASN f 45 " ideal model delta sigma weight residual 122.52 120.41 2.11 1.16e+00 7.43e-01 3.30e+00 angle pdb=" CA GLY N 328 " pdb=" C GLY N 328 " pdb=" N ARG N 329 " ideal model delta sigma weight residual 114.98 117.01 -2.03 1.14e+00 7.69e-01 3.16e+00 angle pdb=" NE ARG f 26 " pdb=" CZ ARG f 26 " pdb=" NH1 ARG f 26 " ideal model delta sigma weight residual 121.50 119.83 1.67 1.00e+00 1.00e+00 2.79e+00 angle pdb=" CA ARG 8 26 " pdb=" C ARG 8 26 " pdb=" N ALA 8 27 " ideal model delta sigma weight residual 114.90 117.14 -2.24 1.37e+00 5.33e-01 2.67e+00 ... (remaining 64008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 27492 17.80 - 35.59: 750 35.59 - 53.39: 171 53.39 - 71.19: 26 71.19 - 88.99: 23 Dihedral angle restraints: 28462 sinusoidal: 10841 harmonic: 17621 Sorted by residual: dihedral pdb=" CB GLU Y 432 " pdb=" CG GLU Y 432 " pdb=" CD GLU Y 432 " pdb=" OE1 GLU Y 432 " ideal model delta sinusoidal sigma weight residual 0.00 -88.99 88.99 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU T 15 " pdb=" CG GLU T 15 " pdb=" CD GLU T 15 " pdb=" OE1 GLU T 15 " ideal model delta sinusoidal sigma weight residual 0.00 -87.48 87.48 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU P 512 " pdb=" CG GLU P 512 " pdb=" CD GLU P 512 " pdb=" OE1 GLU P 512 " ideal model delta sinusoidal sigma weight residual 0.00 85.35 -85.35 1 3.00e+01 1.11e-03 9.80e+00 ... (remaining 28459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 4476 0.026 - 0.053: 1621 0.053 - 0.079: 574 0.079 - 0.106: 338 0.106 - 0.132: 261 Chirality restraints: 7270 Sorted by residual: chirality pdb=" CA ILE 0 53 " pdb=" N ILE 0 53 " pdb=" C ILE 0 53 " pdb=" CB ILE 0 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE 4 53 " pdb=" N ILE 4 53 " pdb=" C ILE 4 53 " pdb=" CB ILE 4 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE d 53 " pdb=" N ILE d 53 " pdb=" C ILE d 53 " pdb=" CB ILE d 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 7267 not shown) Planarity restraints: 8452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 6 71 " 0.011 2.00e-02 2.50e+03 1.00e-02 1.75e+00 pdb=" CG PHE 6 71 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE 6 71 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE 6 71 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 6 71 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 6 71 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE 6 71 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE d 71 " 0.011 2.00e-02 2.50e+03 9.93e-03 1.73e+00 pdb=" CG PHE d 71 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE d 71 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE d 71 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE d 71 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE d 71 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE d 71 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 0 71 " -0.011 2.00e-02 2.50e+03 9.68e-03 1.64e+00 pdb=" CG PHE 0 71 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE 0 71 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE 0 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 0 71 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE 0 71 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE 0 71 " -0.001 2.00e-02 2.50e+03 ... (remaining 8449 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 692 2.70 - 3.25: 42804 3.25 - 3.80: 72499 3.80 - 4.35: 95209 4.35 - 4.90: 162249 Nonbonded interactions: 373453 Sorted by model distance: nonbonded pdb=" OD1 ASP J 338 " pdb=" OG1 THR J 341 " model vdw 2.147 3.040 nonbonded pdb=" OD1 ASP U 338 " pdb=" OG1 THR U 341 " model vdw 2.172 3.040 nonbonded pdb=" OD1 ASP H 338 " pdb=" OG1 THR H 341 " model vdw 2.180 3.040 nonbonded pdb=" OD1 ASP b 338 " pdb=" OG1 THR b 341 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP P 338 " pdb=" OG1 THR P 341 " model vdw 2.191 3.040 ... (remaining 373448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '2' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '4' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '6' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '8' and (resid 8 through 190 or resid 204 through 234)) selection = chain 'I' selection = (chain 'K' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'O' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'Q' and (resid 8 through 190 or resid 204 through 234)) selection = chain 'T' selection = chain 'X' selection = (chain 'Z' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'd' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'f' and (resid 8 through 190 or resid 204 through 234)) } ncs_group { reference = chain '1' selection = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'C' and resid 604 through 609) selection = (chain 'E' and resid 604 through 609) selection = chain 'F' } ncs_group { reference = chain 'H' selection = (chain 'J' and resid 301 through 522) selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = (chain 'P' and resid 301 through 522) selection = chain 'R' selection = chain 'S' selection = (chain 'U' and resid 301 through 522) selection = (chain 'V' and resid 301 through 522) selection = (chain 'W' and resid 301 through 522) selection = (chain 'Y' and resid 301 through 522) selection = (chain 'a' and resid 301 through 522) selection = (chain 'b' and resid 301 through 522) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.510 Check model and map are aligned: 0.270 Set scattering table: 0.310 Process input model: 84.710 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.180 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:13.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.002 0.024 47302 Z= 0.110 Angle : 0.420 5.235 64013 Z= 0.264 Chirality : 0.040 0.132 7270 Planarity : 0.002 0.026 8452 Dihedral : 9.390 88.986 17252 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.14 % Allowed : 2.88 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.11), residues: 6089 helix: 3.20 (0.10), residues: 2542 sheet: 1.19 (0.15), residues: 1483 loop : 0.25 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP V 429 HIS 0.002 0.000 HIS K 152 PHE 0.023 0.001 PHE 6 71 TYR 0.009 0.001 TYR U 359 ARG 0.003 0.000 ARG 4 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 1237 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 44 GLU cc_start: 0.6394 (tt0) cc_final: 0.5789 (tm-30) REVERT: 0 72 ASP cc_start: 0.7871 (t70) cc_final: 0.7624 (t70) REVERT: 0 165 ASN cc_start: 0.7656 (m-40) cc_final: 0.7101 (t0) REVERT: 0 219 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7832 (ttp-110) REVERT: 2 13 MET cc_start: 0.6014 (ttp) cc_final: 0.5700 (tmm) REVERT: 2 45 ASN cc_start: 0.8357 (t0) cc_final: 0.8144 (t0) REVERT: 2 146 SER cc_start: 0.8466 (m) cc_final: 0.8260 (t) REVERT: 4 67 LYS cc_start: 0.7803 (tttm) cc_final: 0.7523 (ttmt) REVERT: 4 183 ILE cc_start: 0.7905 (mt) cc_final: 0.7704 (mp) REVERT: 4 225 ILE cc_start: 0.8504 (mt) cc_final: 0.8212 (mm) REVERT: 6 22 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7409 (mmmm) REVERT: 6 98 GLN cc_start: 0.8453 (mt0) cc_final: 0.8193 (mt0) REVERT: 6 144 ASP cc_start: 0.8281 (p0) cc_final: 0.8052 (p0) REVERT: 6 147 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8179 (pt) REVERT: 6 233 LEU cc_start: 0.7772 (mp) cc_final: 0.7566 (mt) REVERT: 8 163 ILE cc_start: 0.7744 (mt) cc_final: 0.7424 (mt) REVERT: I 69 ASN cc_start: 0.7653 (p0) cc_final: 0.7389 (p0) REVERT: I 134 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7585 (tttt) REVERT: I 182 ARG cc_start: 0.6416 (OUTLIER) cc_final: 0.5981 (mpt90) REVERT: I 228 SER cc_start: 0.6754 (p) cc_final: 0.6294 (m) REVERT: J 330 ASP cc_start: 0.8138 (p0) cc_final: 0.7787 (p0) REVERT: K 26 ARG cc_start: 0.6874 (ttm110) cc_final: 0.6339 (ppt90) REVERT: K 112 THR cc_start: 0.7323 (m) cc_final: 0.6934 (p) REVERT: K 209 GLU cc_start: 0.6094 (tt0) cc_final: 0.5676 (tt0) REVERT: K 214 ASP cc_start: 0.8090 (t0) cc_final: 0.7835 (t0) REVERT: K 216 ASN cc_start: 0.8023 (t0) cc_final: 0.7579 (m-40) REVERT: L 332 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7750 (mtt180) REVERT: O 52 LYS cc_start: 0.7882 (mtpt) cc_final: 0.6776 (mttm) REVERT: O 182 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.5486 (mpt-90) REVERT: P 330 ASP cc_start: 0.7969 (p0) cc_final: 0.7679 (p0) REVERT: Q 49 SER cc_start: 0.7512 (m) cc_final: 0.7242 (p) REVERT: Q 156 MET cc_start: 0.7011 (mtm) cc_final: 0.6711 (mtm) REVERT: Q 207 SER cc_start: 0.5878 (p) cc_final: 0.5590 (p) REVERT: R 507 GLU cc_start: 0.7814 (tt0) cc_final: 0.7401 (tp30) REVERT: T 52 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7941 (mtmm) REVERT: T 98 GLN cc_start: 0.8329 (mt0) cc_final: 0.7948 (mt0) REVERT: T 109 THR cc_start: 0.6370 (m) cc_final: 0.6073 (m) REVERT: T 156 MET cc_start: 0.6698 (mtm) cc_final: 0.6299 (mtm) REVERT: U 330 ASP cc_start: 0.7870 (p0) cc_final: 0.7359 (p0) REVERT: U 401 LEU cc_start: 0.8661 (mt) cc_final: 0.8459 (mt) REVERT: V 335 TYR cc_start: 0.8784 (m-80) cc_final: 0.8560 (m-80) REVERT: W 314 MET cc_start: 0.9071 (ttm) cc_final: 0.8826 (ttp) REVERT: W 324 ASN cc_start: 0.7755 (m-40) cc_final: 0.7553 (m110) REVERT: X 26 ARG cc_start: 0.7191 (ttm110) cc_final: 0.6777 (ppt170) REVERT: X 216 ASN cc_start: 0.7843 (t0) cc_final: 0.7502 (t0) REVERT: X 233 LEU cc_start: 0.6262 (mp) cc_final: 0.5976 (mm) REVERT: Y 354 GLU cc_start: 0.7455 (tt0) cc_final: 0.7217 (tt0) REVERT: Z 150 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6808 (mp0) REVERT: Z 214 ASP cc_start: 0.8224 (t0) cc_final: 0.8006 (t0) REVERT: Z 228 SER cc_start: 0.6552 (p) cc_final: 0.6332 (t) REVERT: b 324 ASN cc_start: 0.7601 (m-40) cc_final: 0.7386 (m-40) REVERT: b 398 LEU cc_start: 0.8177 (mm) cc_final: 0.7750 (mp) REVERT: b 430 ASN cc_start: 0.8057 (t0) cc_final: 0.7805 (t0) REVERT: d 67 LYS cc_start: 0.8333 (tttp) cc_final: 0.8076 (ttmm) REVERT: d 98 GLN cc_start: 0.8552 (mt0) cc_final: 0.8305 (mt0) REVERT: d 143 TYR cc_start: 0.7203 (p90) cc_final: 0.6999 (p90) REVERT: f 17 SER cc_start: 0.7849 (t) cc_final: 0.7263 (m) REVERT: f 29 SER cc_start: 0.8619 (m) cc_final: 0.8388 (t) REVERT: f 110 ILE cc_start: 0.8538 (mt) cc_final: 0.8201 (mm) outliers start: 53 outliers final: 8 residues processed: 1268 average time/residue: 1.4230 time to fit residues: 2180.3568 Evaluate side-chains 679 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 668 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain X residue 15 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 510 optimal weight: 10.0000 chunk 457 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 308 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 473 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 287 optimal weight: 2.9990 chunk 352 optimal weight: 9.9990 chunk 548 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN ** 1 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 165 ASN 4 45 ASN 6 101 ASN 6 165 ASN C 607 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 396 GLN J 437 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 HIS K 174 ASN L 324 ASN M 437 GLN N 322 GLN O 80 GLN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN P 322 GLN Q 45 ASN Q 114 GLN R 437 GLN T 69 ASN T 152 HIS W 437 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 80 GLN ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 101 ASN Z 129 HIS b 322 GLN b 437 GLN d 80 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 45 ASN f 80 GLN f 101 ASN f 165 ASN f 174 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 47302 Z= 0.230 Angle : 0.539 9.139 64013 Z= 0.286 Chirality : 0.044 0.174 7270 Planarity : 0.004 0.061 8452 Dihedral : 4.081 58.958 6922 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.70 % Allowed : 12.69 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.11), residues: 6089 helix: 3.08 (0.10), residues: 2586 sheet: 1.07 (0.14), residues: 1474 loop : 0.19 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP a 429 HIS 0.005 0.001 HIS P 410 PHE 0.037 0.003 PHE 2 71 TYR 0.017 0.001 TYR L 359 ARG 0.009 0.001 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 677 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6792 (ttm) cc_final: 0.6034 (tmm) REVERT: 0 44 GLU cc_start: 0.6440 (tt0) cc_final: 0.5812 (tm-30) REVERT: 0 54 SER cc_start: 0.8621 (t) cc_final: 0.8358 (m) REVERT: 0 72 ASP cc_start: 0.7799 (t70) cc_final: 0.7529 (t70) REVERT: 0 74 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8760 (mt) REVERT: 0 80 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7629 (tp40) REVERT: 0 149 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: 0 219 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7912 (ttt-90) REVERT: 2 234 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7406 (pt) REVERT: 4 67 LYS cc_start: 0.7623 (tttm) cc_final: 0.7286 (tttp) REVERT: 4 98 GLN cc_start: 0.8743 (mt0) cc_final: 0.8524 (mt0) REVERT: 4 132 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6994 (tt0) REVERT: 4 225 ILE cc_start: 0.8513 (mt) cc_final: 0.8219 (mm) REVERT: 6 22 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7148 (mmpt) REVERT: 6 51 GLN cc_start: 0.7283 (mm-40) cc_final: 0.7065 (mm-40) REVERT: 6 98 GLN cc_start: 0.8531 (mt0) cc_final: 0.8279 (mt0) REVERT: 6 144 ASP cc_start: 0.8127 (p0) cc_final: 0.7924 (p0) REVERT: 6 147 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8103 (pt) REVERT: 6 156 MET cc_start: 0.7867 (mtp) cc_final: 0.7638 (mtm) REVERT: 6 179 ASP cc_start: 0.7239 (m-30) cc_final: 0.6975 (m-30) REVERT: 8 139 TYR cc_start: 0.8182 (m-80) cc_final: 0.7812 (m-80) REVERT: 8 163 ILE cc_start: 0.7613 (mt) cc_final: 0.7375 (mt) REVERT: B 605 LEU cc_start: 0.4964 (OUTLIER) cc_final: 0.4755 (mp) REVERT: F 607 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7395 (tt0) REVERT: I 182 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.6161 (mpt90) REVERT: J 330 ASP cc_start: 0.8230 (p0) cc_final: 0.7953 (p0) REVERT: J 430 ASN cc_start: 0.8097 (t0) cc_final: 0.7890 (t0) REVERT: J 432 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: K 13 MET cc_start: 0.5918 (mmp) cc_final: 0.4816 (ppp) REVERT: K 26 ARG cc_start: 0.6673 (ttm110) cc_final: 0.6072 (ppt90) REVERT: K 112 THR cc_start: 0.7142 (m) cc_final: 0.6878 (p) REVERT: K 146 SER cc_start: 0.7710 (p) cc_final: 0.7497 (t) REVERT: K 214 ASP cc_start: 0.7908 (t0) cc_final: 0.7688 (t0) REVERT: K 216 ASN cc_start: 0.8042 (t0) cc_final: 0.7555 (m-40) REVERT: M 364 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: M 399 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8790 (tt) REVERT: M 434 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7078 (mt-10) REVERT: O 26 ARG cc_start: 0.7408 (ttm110) cc_final: 0.6628 (ppt170) REVERT: O 52 LYS cc_start: 0.7783 (mtpt) cc_final: 0.6958 (mttp) REVERT: O 67 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7403 (tttt) REVERT: O 93 ASP cc_start: 0.8924 (m-30) cc_final: 0.8501 (m-30) REVERT: O 156 MET cc_start: 0.7395 (mtm) cc_final: 0.6700 (mtm) REVERT: O 182 ARG cc_start: 0.5752 (OUTLIER) cc_final: 0.5552 (mtt-85) REVERT: P 432 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: R 434 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6980 (tp30) REVERT: S 401 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8478 (mt) REVERT: T 52 LYS cc_start: 0.8262 (mtpt) cc_final: 0.8010 (mtmm) REVERT: W 364 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7087 (pt0) REVERT: X 48 ARG cc_start: 0.6231 (mmm160) cc_final: 0.5940 (mmp-170) REVERT: X 219 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7623 (ttt-90) REVERT: Y 324 ASN cc_start: 0.7853 (m-40) cc_final: 0.7483 (t0) REVERT: Z 28 LYS cc_start: 0.7177 (mptm) cc_final: 0.5632 (mptt) REVERT: Z 150 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6835 (tm-30) REVERT: b 324 ASN cc_start: 0.8030 (m-40) cc_final: 0.7717 (m-40) REVERT: b 325 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7249 (mtt) REVERT: b 401 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8532 (mp) REVERT: d 13 MET cc_start: 0.4127 (tmm) cc_final: 0.3352 (mmm) REVERT: d 22 LYS cc_start: 0.7693 (mtpt) cc_final: 0.7429 (mtpt) REVERT: d 143 TYR cc_start: 0.7368 (p90) cc_final: 0.7162 (p90) REVERT: d 167 LEU cc_start: 0.7775 (mt) cc_final: 0.7461 (mt) REVERT: d 168 LYS cc_start: 0.7941 (ttpp) cc_final: 0.7732 (tttm) outliers start: 172 outliers final: 61 residues processed: 787 average time/residue: 1.3202 time to fit residues: 1274.6380 Evaluate side-chains 690 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 607 time to evaluate : 3.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 0 residue 149 ASP Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 51 GLN Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 388 ARG Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 399 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 434 GLU Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 146 SER Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 219 ARG Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 106 THR Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 49 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 304 optimal weight: 0.0000 chunk 170 optimal weight: 30.0000 chunk 456 optimal weight: 2.9990 chunk 373 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 549 optimal weight: 3.9990 chunk 593 optimal weight: 9.9990 chunk 489 optimal weight: 3.9990 chunk 544 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 440 optimal weight: 9.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 4 45 ASN 8 174 ASN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 396 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN N 322 GLN O 80 GLN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN T 69 ASN U 322 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 216 ASN Z 80 GLN ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 101 ASN b 322 GLN d 80 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 80 GLN f 129 HIS f 174 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 47302 Z= 0.256 Angle : 0.538 9.738 64013 Z= 0.285 Chirality : 0.044 0.177 7270 Planarity : 0.004 0.058 8452 Dihedral : 4.082 57.044 6914 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.11 % Allowed : 13.72 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.11), residues: 6089 helix: 3.01 (0.10), residues: 2586 sheet: 0.94 (0.14), residues: 1474 loop : 0.04 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP a 429 HIS 0.005 0.001 HIS P 410 PHE 0.034 0.003 PHE 6 71 TYR 0.022 0.002 TYR 4 118 ARG 0.010 0.001 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 628 time to evaluate : 4.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6881 (ttm) cc_final: 0.6156 (tmm) REVERT: 0 44 GLU cc_start: 0.6451 (tt0) cc_final: 0.5776 (tm-30) REVERT: 0 54 SER cc_start: 0.8647 (t) cc_final: 0.8367 (m) REVERT: 0 74 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8742 (mt) REVERT: 0 80 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7643 (tp40) REVERT: 0 219 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7979 (ttt-90) REVERT: 2 98 GLN cc_start: 0.8246 (mt0) cc_final: 0.8042 (mt0) REVERT: 4 28 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6776 (mptp) REVERT: 4 67 LYS cc_start: 0.7830 (tttm) cc_final: 0.7419 (tttp) REVERT: 4 74 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8455 (mp) REVERT: 4 98 GLN cc_start: 0.8743 (mt0) cc_final: 0.8522 (mt0) REVERT: 4 132 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: 4 214 ASP cc_start: 0.8249 (t0) cc_final: 0.7982 (t0) REVERT: 4 225 ILE cc_start: 0.8526 (mt) cc_final: 0.8259 (mm) REVERT: 6 22 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7200 (mmpt) REVERT: 6 98 GLN cc_start: 0.8568 (mt0) cc_final: 0.8324 (mt0) REVERT: 6 144 ASP cc_start: 0.8175 (p0) cc_final: 0.7954 (p0) REVERT: 6 147 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7996 (pt) REVERT: 6 179 ASP cc_start: 0.7319 (m-30) cc_final: 0.7075 (m-30) REVERT: 8 139 TYR cc_start: 0.8181 (m-80) cc_final: 0.7806 (m-80) REVERT: 8 216 ASN cc_start: 0.8091 (m-40) cc_final: 0.7810 (t0) REVERT: B 605 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4871 (mp) REVERT: F 607 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: I 111 PHE cc_start: 0.7552 (t80) cc_final: 0.7089 (t80) REVERT: I 233 LEU cc_start: 0.7804 (tt) cc_final: 0.7575 (tp) REVERT: J 330 ASP cc_start: 0.8132 (p0) cc_final: 0.7931 (p0) REVERT: J 395 MET cc_start: 0.7762 (mmm) cc_final: 0.7503 (mmm) REVERT: J 430 ASN cc_start: 0.8046 (t0) cc_final: 0.7723 (t0) REVERT: J 432 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: K 13 MET cc_start: 0.6259 (mmp) cc_final: 0.4860 (ttp) REVERT: K 14 ARG cc_start: 0.5753 (tpm170) cc_final: 0.5270 (tpm170) REVERT: K 26 ARG cc_start: 0.6689 (ttm110) cc_final: 0.6248 (ppt90) REVERT: K 156 MET cc_start: 0.7110 (mtm) cc_final: 0.6738 (mtm) REVERT: K 214 ASP cc_start: 0.7893 (t0) cc_final: 0.7666 (t0) REVERT: K 216 ASN cc_start: 0.8067 (t0) cc_final: 0.7561 (m-40) REVERT: M 364 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: M 399 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8845 (tt) REVERT: M 401 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8379 (mp) REVERT: M 434 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6891 (mt-10) REVERT: N 395 MET cc_start: 0.7195 (mmm) cc_final: 0.6989 (mmm) REVERT: O 26 ARG cc_start: 0.7345 (ttm110) cc_final: 0.6634 (ppt170) REVERT: O 52 LYS cc_start: 0.7839 (mtpt) cc_final: 0.6936 (mttp) REVERT: O 67 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7464 (tttt) REVERT: O 116 LYS cc_start: 0.6824 (tttm) cc_final: 0.6619 (tttm) REVERT: O 156 MET cc_start: 0.7283 (mtm) cc_final: 0.6466 (mtm) REVERT: P 432 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: R 324 ASN cc_start: 0.7899 (m-40) cc_final: 0.7694 (m110) REVERT: R 434 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6929 (tp30) REVERT: R 509 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7662 (ttm170) REVERT: T 52 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7733 (mtmm) REVERT: V 345 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8856 (mm) REVERT: W 401 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8477 (mp) REVERT: X 48 ARG cc_start: 0.6388 (mmm160) cc_final: 0.6163 (mmp-170) REVERT: Y 324 ASN cc_start: 0.7941 (m-40) cc_final: 0.7622 (t0) REVERT: Z 28 LYS cc_start: 0.7224 (mptm) cc_final: 0.5684 (mptt) REVERT: Z 150 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6937 (mm-30) REVERT: b 324 ASN cc_start: 0.8084 (m-40) cc_final: 0.7794 (m-40) REVERT: b 325 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7204 (mtt) REVERT: b 339 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7343 (m-30) REVERT: b 401 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8518 (mp) REVERT: d 98 GLN cc_start: 0.8497 (mt0) cc_final: 0.8293 (mt0) REVERT: d 143 TYR cc_start: 0.7417 (p90) cc_final: 0.7168 (p90) REVERT: d 167 LEU cc_start: 0.7808 (mt) cc_final: 0.7489 (mt) REVERT: d 168 LYS cc_start: 0.7986 (ttpp) cc_final: 0.7744 (tttm) REVERT: f 14 ARG cc_start: 0.6328 (ttm110) cc_final: 0.6099 (ptp-110) REVERT: f 85 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.7224 (tpp80) outliers start: 191 outliers final: 82 residues processed: 759 average time/residue: 1.2922 time to fit residues: 1206.5156 Evaluate side-chains 694 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 589 time to evaluate : 3.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 74 LEU Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 28 LYS Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 388 ARG Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 396 GLN Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 434 GLU Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain S residue 341 THR Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 207 SER Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 106 THR Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 49 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 85 ARG Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 542 optimal weight: 6.9990 chunk 413 optimal weight: 3.9990 chunk 285 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 551 optimal weight: 4.9990 chunk 583 optimal weight: 0.1980 chunk 288 optimal weight: 6.9990 chunk 522 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 4 45 ASN 4 51 GLN E 607 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 HIS J 396 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 80 GLN Z 98 GLN Z 101 ASN Z 152 HIS a 437 GLN b 322 GLN d 80 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN f 80 GLN f 174 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 47302 Z= 0.421 Angle : 0.634 15.239 64013 Z= 0.335 Chirality : 0.048 0.195 7270 Planarity : 0.005 0.066 8452 Dihedral : 4.393 36.613 6906 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.75 % Allowed : 13.87 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.11), residues: 6089 helix: 2.62 (0.10), residues: 2585 sheet: 0.77 (0.14), residues: 1404 loop : -0.28 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 429 HIS 0.007 0.002 HIS T 129 PHE 0.039 0.003 PHE 2 71 TYR 0.022 0.002 TYR I 143 ARG 0.011 0.001 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 605 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6840 (ttm) cc_final: 0.6107 (tmm) REVERT: 0 21 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6926 (mtp85) REVERT: 0 44 GLU cc_start: 0.6702 (tt0) cc_final: 0.5961 (tm-30) REVERT: 0 54 SER cc_start: 0.8658 (t) cc_final: 0.8374 (m) REVERT: 0 74 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8706 (mt) REVERT: 0 80 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7658 (tp40) REVERT: 4 28 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6698 (mptp) REVERT: 4 45 ASN cc_start: 0.8326 (t0) cc_final: 0.7851 (t0) REVERT: 4 98 GLN cc_start: 0.8801 (mt0) cc_final: 0.8571 (mt0) REVERT: 4 132 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: 4 214 ASP cc_start: 0.8344 (t0) cc_final: 0.8112 (t0) REVERT: 4 225 ILE cc_start: 0.8585 (mt) cc_final: 0.8282 (mm) REVERT: 6 22 LYS cc_start: 0.7798 (mtpt) cc_final: 0.7038 (mmtt) REVERT: 6 98 GLN cc_start: 0.8661 (mt0) cc_final: 0.8454 (mt0) REVERT: 6 144 ASP cc_start: 0.8395 (p0) cc_final: 0.8066 (p0) REVERT: 6 147 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7989 (pt) REVERT: 6 179 ASP cc_start: 0.7220 (m-30) cc_final: 0.6952 (m-30) REVERT: 8 139 TYR cc_start: 0.8175 (m-80) cc_final: 0.7810 (m-80) REVERT: 8 171 TYR cc_start: 0.7076 (t80) cc_final: 0.6541 (t80) REVERT: 8 203 LEU cc_start: 0.5882 (mt) cc_final: 0.5652 (mp) REVERT: 8 205 VAL cc_start: 0.7641 (m) cc_final: 0.7336 (p) REVERT: 8 216 ASN cc_start: 0.8179 (m-40) cc_final: 0.7933 (t0) REVERT: B 605 LEU cc_start: 0.5048 (OUTLIER) cc_final: 0.4797 (mp) REVERT: F 605 LEU cc_start: 0.5082 (OUTLIER) cc_final: 0.4775 (mm) REVERT: F 607 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: I 53 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8364 (mt) REVERT: I 80 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: I 111 PHE cc_start: 0.7708 (t80) cc_final: 0.7353 (t80) REVERT: I 169 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6393 (pp20) REVERT: J 330 ASP cc_start: 0.8197 (p0) cc_final: 0.7978 (p0) REVERT: J 395 MET cc_start: 0.7785 (mmm) cc_final: 0.7543 (mmm) REVERT: J 430 ASN cc_start: 0.8019 (t0) cc_final: 0.7687 (t0) REVERT: J 432 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: K 13 MET cc_start: 0.6377 (mmp) cc_final: 0.5036 (tmm) REVERT: K 14 ARG cc_start: 0.5687 (tpm170) cc_final: 0.5173 (tpm170) REVERT: K 26 ARG cc_start: 0.6773 (ttm110) cc_final: 0.6287 (ppt90) REVERT: K 73 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.8065 (m-40) REVERT: K 85 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8061 (ttt90) REVERT: K 146 SER cc_start: 0.7735 (p) cc_final: 0.7528 (p) REVERT: K 156 MET cc_start: 0.6904 (mtm) cc_final: 0.6311 (mtm) REVERT: K 216 ASN cc_start: 0.8089 (t0) cc_final: 0.7550 (m-40) REVERT: L 432 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: M 363 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8725 (mp) REVERT: M 364 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: M 399 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8865 (tt) REVERT: M 401 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8406 (mp) REVERT: M 434 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: N 395 MET cc_start: 0.7220 (mmm) cc_final: 0.7010 (mmm) REVERT: O 26 ARG cc_start: 0.7447 (ttm110) cc_final: 0.6623 (ppt170) REVERT: O 93 ASP cc_start: 0.8912 (m-30) cc_final: 0.8476 (m-30) REVERT: O 99 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8400 (mt) REVERT: O 156 MET cc_start: 0.7189 (mtm) cc_final: 0.6323 (mtm) REVERT: P 330 ASP cc_start: 0.8426 (p0) cc_final: 0.8105 (p0) REVERT: P 432 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: R 434 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6914 (tp30) REVERT: R 509 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7687 (ttm170) REVERT: S 444 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8465 (mp) REVERT: T 52 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7724 (mtmm) REVERT: T 113 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: V 345 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8890 (mm) REVERT: W 364 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7187 (pt0) REVERT: W 401 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8482 (mp) REVERT: Y 324 ASN cc_start: 0.7976 (m-40) cc_final: 0.7665 (t0) REVERT: Y 433 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: Z 70 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: Z 143 TYR cc_start: 0.6793 (p90) cc_final: 0.5957 (p90) REVERT: Z 150 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7028 (mm-30) REVERT: b 325 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7241 (mtt) REVERT: b 339 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7399 (m-30) REVERT: b 355 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8372 (t80) REVERT: b 401 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8534 (mp) REVERT: d 167 LEU cc_start: 0.7805 (mt) cc_final: 0.7504 (mt) REVERT: d 168 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7800 (tttm) REVERT: f 85 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7233 (tpp80) outliers start: 221 outliers final: 102 residues processed: 750 average time/residue: 1.3008 time to fit residues: 1205.2238 Evaluate side-chains 707 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 569 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 67 LYS Chi-restraints excluded: chain 2 residue 74 LEU Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 28 LYS Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 112 THR Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 183 ILE Chi-restraints excluded: chain 6 residue 67 LYS Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 168 LYS Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 388 ARG Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 434 GLU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 409 ILE Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain S residue 444 LEU Chi-restraints excluded: chain T residue 26 ARG Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 433 GLU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 70 GLU Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 106 THR Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 317 ASP Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 49 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 85 ARG Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 486 optimal weight: 6.9990 chunk 331 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 434 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 498 optimal weight: 3.9990 chunk 403 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 298 optimal weight: 0.5980 chunk 524 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 4 80 GLN E 607 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 396 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN O 101 ASN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN U 396 GLN V 322 GLN X 69 ASN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 80 GLN Z 101 ASN a 322 GLN b 322 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN f 80 GLN f 174 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 47302 Z= 0.158 Angle : 0.496 9.893 64013 Z= 0.263 Chirality : 0.043 0.164 7270 Planarity : 0.004 0.048 8452 Dihedral : 3.954 41.041 6906 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.23 % Allowed : 15.91 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.11), residues: 6089 helix: 3.13 (0.10), residues: 2579 sheet: 0.89 (0.14), residues: 1408 loop : -0.16 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 429 HIS 0.003 0.001 HIS S 365 PHE 0.033 0.002 PHE 6 71 TYR 0.019 0.001 TYR 4 118 ARG 0.010 0.000 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 597 time to evaluate : 3.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6925 (ttm) cc_final: 0.6234 (tmm) REVERT: 0 54 SER cc_start: 0.8665 (t) cc_final: 0.8379 (m) REVERT: 0 74 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8728 (mt) REVERT: 0 80 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7606 (tp40) REVERT: 4 74 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8362 (mp) REVERT: 4 163 ILE cc_start: 0.7610 (mt) cc_final: 0.7327 (mp) REVERT: 4 214 ASP cc_start: 0.8208 (t0) cc_final: 0.7983 (t0) REVERT: 4 225 ILE cc_start: 0.8466 (mt) cc_final: 0.8199 (mm) REVERT: 6 22 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7047 (mmtt) REVERT: 6 98 GLN cc_start: 0.8545 (mt0) cc_final: 0.8337 (mt0) REVERT: 6 144 ASP cc_start: 0.8198 (p0) cc_final: 0.7960 (p0) REVERT: 6 147 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7993 (pt) REVERT: 6 179 ASP cc_start: 0.7294 (m-30) cc_final: 0.7081 (m-30) REVERT: 8 33 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8622 (pp) REVERT: 8 205 VAL cc_start: 0.7681 (m) cc_final: 0.7310 (p) REVERT: 8 216 ASN cc_start: 0.8159 (m-40) cc_final: 0.7908 (t0) REVERT: F 605 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.5153 (mm) REVERT: F 607 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: H 395 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6803 (mpm) REVERT: J 364 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.7011 (pt0) REVERT: J 395 MET cc_start: 0.7736 (mmm) cc_final: 0.7495 (mmm) REVERT: J 430 ASN cc_start: 0.7952 (t0) cc_final: 0.7623 (t0) REVERT: J 432 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: K 13 MET cc_start: 0.6359 (mmp) cc_final: 0.5012 (tmm) REVERT: K 14 ARG cc_start: 0.5888 (tpm170) cc_final: 0.5447 (tpm170) REVERT: K 18 GLU cc_start: 0.6550 (tp30) cc_final: 0.5915 (tp30) REVERT: K 26 ARG cc_start: 0.6752 (ttm110) cc_final: 0.6257 (ppt90) REVERT: K 146 SER cc_start: 0.7882 (p) cc_final: 0.7557 (p) REVERT: K 156 MET cc_start: 0.6982 (mtm) cc_final: 0.6662 (mtm) REVERT: K 216 ASN cc_start: 0.7992 (t0) cc_final: 0.7560 (m-40) REVERT: L 432 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: M 364 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: M 399 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8805 (tt) REVERT: M 401 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8398 (mp) REVERT: M 434 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6957 (mt-10) REVERT: N 395 MET cc_start: 0.7228 (mmm) cc_final: 0.6935 (mmm) REVERT: O 26 ARG cc_start: 0.7413 (ttm110) cc_final: 0.6552 (ppt170) REVERT: O 67 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7425 (tttt) REVERT: O 93 ASP cc_start: 0.8890 (m-30) cc_final: 0.8471 (m-30) REVERT: O 105 GLN cc_start: 0.6888 (tp40) cc_final: 0.6640 (tp-100) REVERT: O 156 MET cc_start: 0.7159 (mtm) cc_final: 0.6215 (mtm) REVERT: P 330 ASP cc_start: 0.8438 (p0) cc_final: 0.8221 (p0) REVERT: P 424 ASP cc_start: 0.8013 (p0) cc_final: 0.7662 (p0) REVERT: P 432 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: Q 13 MET cc_start: 0.5681 (tmm) cc_final: 0.5418 (tmm) REVERT: R 434 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6870 (tp30) REVERT: R 509 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7493 (ttm170) REVERT: T 52 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7686 (mtmm) REVERT: V 345 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8822 (mm) REVERT: W 364 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7081 (pt0) REVERT: W 401 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8441 (mp) REVERT: X 48 ARG cc_start: 0.6558 (mmm160) cc_final: 0.6305 (mmp-170) REVERT: Y 324 ASN cc_start: 0.7825 (m-40) cc_final: 0.7568 (t0) REVERT: Y 433 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: Z 111 PHE cc_start: 0.7602 (t80) cc_final: 0.7333 (t80) REVERT: Z 150 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6841 (mp0) REVERT: b 324 ASN cc_start: 0.8013 (m-40) cc_final: 0.7710 (m-40) REVERT: b 339 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: b 401 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8513 (mp) REVERT: d 167 LEU cc_start: 0.7838 (mt) cc_final: 0.7557 (mt) REVERT: f 14 ARG cc_start: 0.6283 (ttm110) cc_final: 0.6022 (ptp-110) REVERT: f 214 ASP cc_start: 0.8171 (t0) cc_final: 0.7935 (t0) outliers start: 150 outliers final: 59 residues processed: 689 average time/residue: 1.3111 time to fit residues: 1115.6749 Evaluate side-chains 657 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 573 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 395 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 364 GLU Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 434 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 113 GLU Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 203 LEU Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 433 GLU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 196 optimal weight: 0.9990 chunk 525 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 342 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 584 optimal weight: 7.9990 chunk 485 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 73 ASN 0 174 ASN 1 607 GLN 4 45 ASN 4 80 GLN 4 98 GLN 6 174 ASN E 607 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 396 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 410 HIS O 80 GLN O 114 GLN O 174 ASN ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN U 396 GLN V 322 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 80 GLN Z 101 ASN a 322 GLN b 322 GLN d 216 ASN f 69 ASN f 80 GLN f 165 ASN f 174 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 47302 Z= 0.240 Angle : 0.526 9.761 64013 Z= 0.278 Chirality : 0.044 0.175 7270 Planarity : 0.004 0.048 8452 Dihedral : 4.025 39.361 6906 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.53 % Allowed : 16.32 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.11), residues: 6089 helix: 3.09 (0.10), residues: 2585 sheet: 0.86 (0.14), residues: 1418 loop : -0.18 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 429 HIS 0.003 0.001 HIS S 365 PHE 0.033 0.002 PHE 6 71 TYR 0.015 0.001 TYR 4 118 ARG 0.013 0.000 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 586 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6924 (ttm) cc_final: 0.6237 (tmm) REVERT: 0 44 GLU cc_start: 0.6363 (tt0) cc_final: 0.6159 (tm-30) REVERT: 0 54 SER cc_start: 0.8703 (t) cc_final: 0.8409 (m) REVERT: 0 74 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8698 (mt) REVERT: 0 80 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7618 (tp40) REVERT: 2 14 ARG cc_start: 0.6126 (OUTLIER) cc_final: 0.5749 (mtt90) REVERT: 4 74 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8387 (mp) REVERT: 4 132 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: 4 163 ILE cc_start: 0.7639 (mt) cc_final: 0.7351 (mp) REVERT: 4 214 ASP cc_start: 0.8267 (t0) cc_final: 0.8023 (t0) REVERT: 4 225 ILE cc_start: 0.8497 (mt) cc_final: 0.8219 (mm) REVERT: 6 22 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7008 (mmtt) REVERT: 6 144 ASP cc_start: 0.8192 (p0) cc_final: 0.7943 (p0) REVERT: 6 147 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8001 (pt) REVERT: 8 33 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8651 (pp) REVERT: 8 98 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7891 (mt0) REVERT: 8 205 VAL cc_start: 0.7703 (m) cc_final: 0.7364 (p) REVERT: 8 216 ASN cc_start: 0.8171 (m-40) cc_final: 0.7922 (t0) REVERT: F 605 LEU cc_start: 0.5590 (OUTLIER) cc_final: 0.5224 (mm) REVERT: F 607 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: J 395 MET cc_start: 0.7731 (mmm) cc_final: 0.7504 (mmm) REVERT: J 430 ASN cc_start: 0.7993 (t0) cc_final: 0.7650 (t0) REVERT: J 432 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: K 13 MET cc_start: 0.6310 (mmp) cc_final: 0.4975 (tmm) REVERT: K 14 ARG cc_start: 0.5807 (tpm170) cc_final: 0.5388 (tpm170) REVERT: K 18 GLU cc_start: 0.6619 (tp30) cc_final: 0.5979 (tp30) REVERT: K 26 ARG cc_start: 0.6749 (ttm110) cc_final: 0.6264 (ppt90) REVERT: K 146 SER cc_start: 0.7883 (p) cc_final: 0.7552 (p) REVERT: K 156 MET cc_start: 0.6981 (mtm) cc_final: 0.6662 (mtm) REVERT: K 216 ASN cc_start: 0.7995 (t0) cc_final: 0.7557 (m-40) REVERT: K 234 LEU cc_start: 0.5934 (mt) cc_final: 0.5726 (mt) REVERT: L 432 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: M 364 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: M 399 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8858 (tt) REVERT: M 401 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8417 (mp) REVERT: M 434 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: N 395 MET cc_start: 0.7214 (mmm) cc_final: 0.6920 (mmm) REVERT: N 432 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: O 26 ARG cc_start: 0.7438 (ttm110) cc_final: 0.6554 (ppt170) REVERT: O 67 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7516 (tttt) REVERT: O 105 GLN cc_start: 0.6988 (tp40) cc_final: 0.6543 (tp-100) REVERT: O 156 MET cc_start: 0.7150 (mtm) cc_final: 0.6128 (mtm) REVERT: P 424 ASP cc_start: 0.8018 (p0) cc_final: 0.7588 (p0) REVERT: P 430 ASN cc_start: 0.7670 (t0) cc_final: 0.7291 (t0) REVERT: P 432 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: Q 13 MET cc_start: 0.5705 (tmm) cc_final: 0.5467 (tmm) REVERT: R 434 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6796 (tp30) REVERT: R 509 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7559 (ttm170) REVERT: S 401 LEU cc_start: 0.8896 (mt) cc_final: 0.8469 (mt) REVERT: S 444 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8445 (mp) REVERT: T 52 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7670 (mtmm) REVERT: V 345 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8857 (mm) REVERT: W 364 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7094 (pt0) REVERT: W 401 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8456 (mp) REVERT: X 48 ARG cc_start: 0.6575 (mmm160) cc_final: 0.6244 (mmp-170) REVERT: X 179 ASP cc_start: 0.5688 (t0) cc_final: 0.5399 (t0) REVERT: Y 324 ASN cc_start: 0.7894 (m-40) cc_final: 0.7577 (t0) REVERT: Y 433 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: Z 143 TYR cc_start: 0.6539 (p90) cc_final: 0.5733 (p90) REVERT: Z 150 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6870 (mp0) REVERT: b 339 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: b 401 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8528 (mp) REVERT: d 167 LEU cc_start: 0.7849 (mt) cc_final: 0.7560 (mt) REVERT: f 14 ARG cc_start: 0.6303 (ttm110) cc_final: 0.6047 (ptp-110) REVERT: f 22 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7543 (tmtt) REVERT: f 85 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7114 (tpp80) REVERT: f 214 ASP cc_start: 0.8157 (t0) cc_final: 0.7945 (t0) outliers start: 164 outliers final: 90 residues processed: 692 average time/residue: 1.2488 time to fit residues: 1071.3194 Evaluate side-chains 690 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 571 time to evaluate : 3.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 51 GLN Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 176 SER Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain 8 residue 80 GLN Chi-restraints excluded: chain 8 residue 98 GLN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 434 GLU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 432 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 325 MET Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain S residue 444 LEU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 433 GLU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 307 LYS Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 85 ARG Chi-restraints excluded: chain f residue 133 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 563 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 332 optimal weight: 0.3980 chunk 426 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 491 optimal weight: 0.9980 chunk 326 optimal weight: 1.9990 chunk 582 optimal weight: 0.2980 chunk 364 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 268 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 73 ASN 0 174 ASN 1 607 GLN 4 45 ASN 4 80 GLN 6 174 ASN E 607 GLN I 114 GLN J 396 GLN K 114 GLN O 80 GLN ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN U 396 GLN V 322 GLN W 430 ASN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 80 GLN Z 98 GLN Z 101 ASN a 322 GLN b 322 GLN d 216 ASN f 69 ASN f 80 GLN f 165 ASN f 174 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 47302 Z= 0.164 Angle : 0.488 9.114 64013 Z= 0.258 Chirality : 0.042 0.164 7270 Planarity : 0.004 0.042 8452 Dihedral : 3.849 41.119 6906 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.03 % Allowed : 16.99 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.11), residues: 6089 helix: 3.30 (0.10), residues: 2582 sheet: 0.88 (0.14), residues: 1424 loop : -0.13 (0.14), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 429 HIS 0.005 0.001 HIS Z 152 PHE 0.035 0.002 PHE Z 111 TYR 0.017 0.001 TYR I 143 ARG 0.013 0.000 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 601 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6887 (ttm) cc_final: 0.6209 (tmm) REVERT: 0 44 GLU cc_start: 0.6280 (tt0) cc_final: 0.6048 (tm-30) REVERT: 0 54 SER cc_start: 0.8699 (t) cc_final: 0.8405 (m) REVERT: 0 74 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8746 (mt) REVERT: 0 80 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7610 (tp40) REVERT: 1 605 LEU cc_start: 0.4071 (OUTLIER) cc_final: 0.3864 (tp) REVERT: 2 14 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.5849 (mtt90) REVERT: 4 28 LYS cc_start: 0.7565 (mptp) cc_final: 0.6997 (mmtp) REVERT: 4 74 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8381 (mp) REVERT: 4 132 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: 4 163 ILE cc_start: 0.7630 (mt) cc_final: 0.7347 (mp) REVERT: 4 214 ASP cc_start: 0.8113 (t0) cc_final: 0.7906 (t0) REVERT: 4 225 ILE cc_start: 0.8466 (mt) cc_final: 0.8193 (mm) REVERT: 6 22 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7068 (mmtt) REVERT: 6 144 ASP cc_start: 0.8110 (p0) cc_final: 0.7893 (p0) REVERT: 6 147 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7996 (pt) REVERT: 8 22 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7325 (pttm) REVERT: 8 33 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8545 (pp) REVERT: 8 205 VAL cc_start: 0.7720 (m) cc_final: 0.7390 (p) REVERT: 8 216 ASN cc_start: 0.8157 (m-40) cc_final: 0.7911 (t0) REVERT: F 605 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5446 (mm) REVERT: F 607 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: I 45 ASN cc_start: 0.7753 (t0) cc_final: 0.7169 (t0) REVERT: I 111 PHE cc_start: 0.7629 (t80) cc_final: 0.7326 (t80) REVERT: J 395 MET cc_start: 0.7714 (mmm) cc_final: 0.7501 (mmm) REVERT: J 430 ASN cc_start: 0.7962 (t0) cc_final: 0.7611 (t0) REVERT: J 432 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: K 13 MET cc_start: 0.6333 (mmp) cc_final: 0.4977 (tmm) REVERT: K 14 ARG cc_start: 0.5784 (tpm170) cc_final: 0.5424 (tpm170) REVERT: K 18 GLU cc_start: 0.6554 (tp30) cc_final: 0.5948 (tp30) REVERT: K 26 ARG cc_start: 0.6739 (ttm110) cc_final: 0.6223 (ppt90) REVERT: K 146 SER cc_start: 0.7910 (p) cc_final: 0.7569 (p) REVERT: K 156 MET cc_start: 0.6950 (mtm) cc_final: 0.6670 (mtm) REVERT: K 216 ASN cc_start: 0.7975 (t0) cc_final: 0.7557 (m-40) REVERT: M 363 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8644 (mp) REVERT: M 364 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: M 399 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8772 (tt) REVERT: M 401 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8404 (mp) REVERT: N 395 MET cc_start: 0.7133 (mmm) cc_final: 0.6877 (mmm) REVERT: N 432 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: O 26 ARG cc_start: 0.7350 (ttm110) cc_final: 0.6482 (ppt170) REVERT: O 67 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7494 (tttt) REVERT: O 105 GLN cc_start: 0.6970 (tp40) cc_final: 0.6526 (tp-100) REVERT: P 424 ASP cc_start: 0.7959 (p0) cc_final: 0.7584 (p0) REVERT: P 430 ASN cc_start: 0.7629 (t0) cc_final: 0.7267 (t0) REVERT: P 432 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: Q 13 MET cc_start: 0.5601 (tmm) cc_final: 0.5342 (tmm) REVERT: Q 21 ARG cc_start: 0.6322 (ptm-80) cc_final: 0.5973 (mtm180) REVERT: R 434 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6811 (tp30) REVERT: R 509 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7336 (ttm170) REVERT: S 401 LEU cc_start: 0.8875 (mt) cc_final: 0.8471 (mt) REVERT: T 52 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7634 (mtmm) REVERT: V 345 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8822 (mm) REVERT: V 509 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7226 (ttp-170) REVERT: W 364 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7086 (pt0) REVERT: W 401 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8468 (mp) REVERT: X 21 ARG cc_start: 0.6549 (ttp-110) cc_final: 0.5988 (ttp80) REVERT: X 179 ASP cc_start: 0.5749 (t0) cc_final: 0.5400 (t0) REVERT: Y 324 ASN cc_start: 0.7801 (m-40) cc_final: 0.7556 (t0) REVERT: Y 433 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: b 324 ASN cc_start: 0.8002 (m-40) cc_final: 0.7725 (m-40) REVERT: b 339 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7302 (m-30) REVERT: b 401 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8508 (mp) REVERT: d 167 LEU cc_start: 0.7830 (mt) cc_final: 0.7553 (mt) REVERT: f 22 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7540 (tmtt) REVERT: f 214 ASP cc_start: 0.8072 (t0) cc_final: 0.7869 (t0) outliers start: 141 outliers final: 77 residues processed: 690 average time/residue: 1.2131 time to fit residues: 1041.8826 Evaluate side-chains 685 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 581 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 135 ARG Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 1 residue 605 LEU Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 51 GLN Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 176 SER Chi-restraints excluded: chain 6 residue 13 MET Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 432 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 433 GLU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 307 LYS Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 360 optimal weight: 5.9990 chunk 232 optimal weight: 0.6980 chunk 347 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 370 optimal weight: 10.0000 chunk 396 optimal weight: 9.9990 chunk 287 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 457 optimal weight: 0.9980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 4 45 ASN 4 80 GLN 6 73 ASN 6 174 ASN E 607 GLN J 396 GLN L 410 HIS O 80 GLN O 174 ASN U 322 GLN U 396 GLN V 322 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 80 GLN Z 101 ASN a 322 GLN b 322 GLN d 216 ASN f 69 ASN f 80 GLN f 165 ASN f 174 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 47302 Z= 0.247 Angle : 0.528 8.985 64013 Z= 0.280 Chirality : 0.044 0.177 7270 Planarity : 0.004 0.047 8452 Dihedral : 4.016 37.829 6906 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.40 % Allowed : 16.96 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.11), residues: 6089 helix: 3.15 (0.10), residues: 2594 sheet: 0.89 (0.14), residues: 1468 loop : -0.27 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 429 HIS 0.004 0.001 HIS K 152 PHE 0.032 0.002 PHE 6 71 TYR 0.015 0.002 TYR 6 118 ARG 0.010 0.000 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 581 time to evaluate : 4.049 Fit side-chains revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6908 (ttm) cc_final: 0.6228 (tmm) REVERT: 0 54 SER cc_start: 0.8701 (t) cc_final: 0.8405 (m) REVERT: 0 74 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8720 (mt) REVERT: 0 80 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7639 (tp40) REVERT: 4 74 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8377 (mp) REVERT: 4 132 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7145 (tt0) REVERT: 4 163 ILE cc_start: 0.7648 (mt) cc_final: 0.7358 (mp) REVERT: 4 214 ASP cc_start: 0.8240 (t0) cc_final: 0.8013 (t0) REVERT: 4 225 ILE cc_start: 0.8489 (mt) cc_final: 0.8213 (mm) REVERT: 6 22 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7068 (mmtt) REVERT: 6 144 ASP cc_start: 0.8178 (p0) cc_final: 0.7932 (p0) REVERT: 6 147 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7999 (pt) REVERT: 8 33 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8590 (pp) REVERT: 8 174 ASN cc_start: 0.7985 (m110) cc_final: 0.7736 (m110) REVERT: 8 205 VAL cc_start: 0.7819 (m) cc_final: 0.7481 (p) REVERT: 8 216 ASN cc_start: 0.8177 (m-40) cc_final: 0.7938 (t0) REVERT: F 605 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5397 (mm) REVERT: F 607 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: I 45 ASN cc_start: 0.7746 (t0) cc_final: 0.7162 (t0) REVERT: J 395 MET cc_start: 0.7722 (mmm) cc_final: 0.7489 (mmm) REVERT: J 430 ASN cc_start: 0.8008 (t0) cc_final: 0.7704 (t0) REVERT: J 432 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: K 13 MET cc_start: 0.6344 (mmp) cc_final: 0.4976 (tmm) REVERT: K 14 ARG cc_start: 0.5790 (tpm170) cc_final: 0.5468 (tpm170) REVERT: K 18 GLU cc_start: 0.6793 (tp30) cc_final: 0.5924 (tp30) REVERT: K 26 ARG cc_start: 0.6753 (ttm110) cc_final: 0.6228 (ppt90) REVERT: K 146 SER cc_start: 0.7879 (p) cc_final: 0.7529 (p) REVERT: K 156 MET cc_start: 0.6899 (mtm) cc_final: 0.6485 (mtm) REVERT: K 216 ASN cc_start: 0.7979 (t0) cc_final: 0.7573 (m-40) REVERT: L 432 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.6466 (mp0) REVERT: M 363 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8704 (mp) REVERT: M 364 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: M 399 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8853 (tt) REVERT: M 401 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8367 (mp) REVERT: M 434 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: N 395 MET cc_start: 0.7130 (mmm) cc_final: 0.6864 (mmm) REVERT: N 432 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: O 26 ARG cc_start: 0.7405 (ttm110) cc_final: 0.6539 (ppt170) REVERT: O 67 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7558 (tttt) REVERT: O 99 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8387 (mt) REVERT: O 105 GLN cc_start: 0.7002 (tp40) cc_final: 0.6547 (tp-100) REVERT: P 424 ASP cc_start: 0.8067 (p0) cc_final: 0.7620 (p0) REVERT: P 430 ASN cc_start: 0.7652 (t0) cc_final: 0.7299 (t0) REVERT: P 432 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: Q 13 MET cc_start: 0.5580 (tmm) cc_final: 0.5324 (tmm) REVERT: R 434 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6826 (tp30) REVERT: R 509 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7441 (ttm170) REVERT: S 401 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8491 (mt) REVERT: S 444 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8446 (mp) REVERT: T 52 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7632 (mtmm) REVERT: V 345 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8867 (mm) REVERT: V 509 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7314 (ttp-170) REVERT: W 364 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7068 (pt0) REVERT: W 401 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8466 (mp) REVERT: X 179 ASP cc_start: 0.5794 (t0) cc_final: 0.5467 (t0) REVERT: Y 324 ASN cc_start: 0.7895 (m-40) cc_final: 0.7598 (t0) REVERT: Y 433 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: Z 143 TYR cc_start: 0.6510 (p90) cc_final: 0.5719 (p90) REVERT: b 339 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: b 401 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8534 (mp) REVERT: d 167 LEU cc_start: 0.7817 (mt) cc_final: 0.7529 (mt) REVERT: f 22 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7537 (tmtt) REVERT: f 85 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7044 (tpp80) outliers start: 158 outliers final: 88 residues processed: 684 average time/residue: 1.2359 time to fit residues: 1049.4587 Evaluate side-chains 683 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 564 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 135 ARG Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 67 LYS Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 51 GLN Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 176 SER Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 80 GLN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 434 GLU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 434 GLU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 432 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 444 LEU Chi-restraints excluded: chain T residue 26 ARG Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 433 GLU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 85 ARG Chi-restraints excluded: chain f residue 133 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 529 optimal weight: 0.4980 chunk 557 optimal weight: 8.9990 chunk 508 optimal weight: 10.0000 chunk 542 optimal weight: 5.9990 chunk 326 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 425 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 490 optimal weight: 3.9990 chunk 513 optimal weight: 9.9990 chunk 540 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 4 45 ASN 4 80 GLN 6 73 ASN 6 174 ASN E 607 GLN J 396 GLN L 410 HIS O 80 GLN U 396 GLN V 322 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 80 GLN Z 101 ASN a 322 GLN b 322 GLN d 216 ASN f 69 ASN f 80 GLN f 165 ASN f 174 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 47302 Z= 0.202 Angle : 0.509 8.902 64013 Z= 0.270 Chirality : 0.043 0.168 7270 Planarity : 0.004 0.057 8452 Dihedral : 3.932 38.162 6906 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.07 % Allowed : 17.27 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.11), residues: 6089 helix: 3.20 (0.10), residues: 2594 sheet: 0.89 (0.14), residues: 1474 loop : -0.25 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 429 HIS 0.004 0.001 HIS S 365 PHE 0.032 0.002 PHE K 111 TYR 0.017 0.001 TYR 6 118 ARG 0.015 0.000 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 576 time to evaluate : 3.900 Fit side-chains revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6893 (ttm) cc_final: 0.6217 (tmm) REVERT: 0 21 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6773 (mtm-85) REVERT: 0 54 SER cc_start: 0.8700 (t) cc_final: 0.8404 (m) REVERT: 0 74 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8744 (mt) REVERT: 0 80 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7628 (tp40) REVERT: 2 14 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5856 (mtt90) REVERT: 4 74 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8368 (mp) REVERT: 4 132 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: 4 163 ILE cc_start: 0.7654 (mt) cc_final: 0.7360 (mp) REVERT: 4 214 ASP cc_start: 0.8215 (t0) cc_final: 0.7993 (t0) REVERT: 4 225 ILE cc_start: 0.8468 (mt) cc_final: 0.8192 (mm) REVERT: 6 22 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7065 (mmtt) REVERT: 6 144 ASP cc_start: 0.8344 (p0) cc_final: 0.8103 (p0) REVERT: 6 147 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7969 (pt) REVERT: 6 156 MET cc_start: 0.7903 (mtm) cc_final: 0.7588 (mmm) REVERT: 8 22 LYS cc_start: 0.7382 (mtmm) cc_final: 0.7113 (pttm) REVERT: 8 33 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8536 (pp) REVERT: 8 174 ASN cc_start: 0.8013 (m110) cc_final: 0.7768 (m110) REVERT: 8 205 VAL cc_start: 0.7898 (m) cc_final: 0.7567 (p) REVERT: 8 216 ASN cc_start: 0.8141 (m-40) cc_final: 0.7900 (t0) REVERT: F 607 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: I 45 ASN cc_start: 0.7724 (t0) cc_final: 0.7107 (t0) REVERT: I 168 LYS cc_start: 0.7091 (mtpt) cc_final: 0.6639 (mttt) REVERT: J 395 MET cc_start: 0.7671 (mmm) cc_final: 0.7459 (mmm) REVERT: J 430 ASN cc_start: 0.7996 (t0) cc_final: 0.7696 (t0) REVERT: J 432 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: K 13 MET cc_start: 0.6315 (mmp) cc_final: 0.4984 (tmm) REVERT: K 14 ARG cc_start: 0.5780 (tpm170) cc_final: 0.5465 (tpm170) REVERT: K 18 GLU cc_start: 0.6848 (tp30) cc_final: 0.5953 (tp30) REVERT: K 26 ARG cc_start: 0.6779 (ttm110) cc_final: 0.6237 (ppt90) REVERT: K 146 SER cc_start: 0.7916 (p) cc_final: 0.7549 (p) REVERT: K 154 VAL cc_start: 0.7062 (t) cc_final: 0.6735 (m) REVERT: K 156 MET cc_start: 0.6861 (mtm) cc_final: 0.6593 (mtm) REVERT: K 216 ASN cc_start: 0.7949 (t0) cc_final: 0.7555 (m-40) REVERT: K 234 LEU cc_start: 0.5883 (mt) cc_final: 0.5656 (mt) REVERT: L 432 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.6482 (mp0) REVERT: M 363 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8659 (mp) REVERT: M 364 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: M 399 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8811 (tt) REVERT: M 401 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8363 (mp) REVERT: N 395 MET cc_start: 0.7212 (mmm) cc_final: 0.6960 (mmm) REVERT: N 432 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: O 26 ARG cc_start: 0.7451 (ttm110) cc_final: 0.6462 (ppt170) REVERT: O 67 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7423 (tttt) REVERT: O 99 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8389 (mt) REVERT: O 105 GLN cc_start: 0.6998 (tp40) cc_final: 0.6571 (tp-100) REVERT: P 424 ASP cc_start: 0.8072 (p0) cc_final: 0.7670 (p0) REVERT: P 430 ASN cc_start: 0.7637 (t0) cc_final: 0.7294 (t0) REVERT: P 432 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: Q 13 MET cc_start: 0.5541 (tmm) cc_final: 0.5299 (tmm) REVERT: Q 21 ARG cc_start: 0.6393 (ptm-80) cc_final: 0.5986 (mtm180) REVERT: R 434 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6837 (tp30) REVERT: R 509 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7416 (ttm170) REVERT: S 401 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8480 (mt) REVERT: S 444 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8447 (mp) REVERT: T 52 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7642 (mtmm) REVERT: V 345 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8830 (mm) REVERT: V 509 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7250 (ttp-170) REVERT: W 364 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7087 (pt0) REVERT: W 401 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8461 (mp) REVERT: X 21 ARG cc_start: 0.6468 (ttp-110) cc_final: 0.5928 (ttp80) REVERT: X 179 ASP cc_start: 0.5827 (t0) cc_final: 0.5497 (t0) REVERT: Y 324 ASN cc_start: 0.7866 (m-40) cc_final: 0.7579 (t0) REVERT: Y 433 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: Z 21 ARG cc_start: 0.6385 (ptm160) cc_final: 0.6119 (ttp-110) REVERT: b 339 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: b 401 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8518 (mp) REVERT: d 167 LEU cc_start: 0.7852 (mt) cc_final: 0.7563 (mt) REVERT: f 22 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7535 (tmtt) outliers start: 143 outliers final: 93 residues processed: 668 average time/residue: 1.2348 time to fit residues: 1024.5653 Evaluate side-chains 692 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 569 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 ARG Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 135 ARG Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 22 LYS Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 67 LYS Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 51 GLN Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 176 SER Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 395 MET Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 434 GLU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 432 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 203 LEU Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 325 MET Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 444 LEU Chi-restraints excluded: chain T residue 26 ARG Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 433 GLU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 307 LYS Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 133 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 356 optimal weight: 7.9990 chunk 573 optimal weight: 9.9990 chunk 350 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 398 optimal weight: 5.9990 chunk 601 optimal weight: 10.0000 chunk 553 optimal weight: 2.9990 chunk 479 optimal weight: 0.0170 chunk 49 optimal weight: 0.7980 chunk 370 optimal weight: 9.9990 chunk 293 optimal weight: 0.7980 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 4 45 ASN 4 80 GLN 6 73 ASN 6 174 ASN J 396 GLN O 45 ASN O 80 GLN U 396 GLN V 322 GLN X 114 GLN Z 80 GLN Z 101 ASN a 322 GLN d 216 ASN f 69 ASN f 80 GLN f 174 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 47302 Z= 0.151 Angle : 0.486 8.752 64013 Z= 0.257 Chirality : 0.042 0.162 7270 Planarity : 0.003 0.060 8452 Dihedral : 3.776 38.781 6906 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.58 % Allowed : 18.02 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.11), residues: 6089 helix: 3.34 (0.10), residues: 2591 sheet: 0.93 (0.14), residues: 1474 loop : -0.19 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 429 HIS 0.003 0.001 HIS S 365 PHE 0.031 0.002 PHE O 111 TYR 0.020 0.001 TYR I 143 ARG 0.013 0.000 ARG X 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 611 time to evaluate : 3.936 Fit side-chains revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6875 (ttm) cc_final: 0.6213 (tmm) REVERT: 0 21 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6831 (mtm-85) REVERT: 0 54 SER cc_start: 0.8693 (t) cc_final: 0.8386 (m) REVERT: 0 74 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8741 (mt) REVERT: 0 80 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7595 (tp40) REVERT: 2 14 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.5843 (mtt90) REVERT: 4 28 LYS cc_start: 0.7581 (mptp) cc_final: 0.7219 (mmtp) REVERT: 4 74 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8388 (mp) REVERT: 4 163 ILE cc_start: 0.7641 (mt) cc_final: 0.7346 (mp) REVERT: 4 225 ILE cc_start: 0.8455 (mt) cc_final: 0.8183 (mm) REVERT: 6 22 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7067 (mmtt) REVERT: 6 144 ASP cc_start: 0.8273 (p0) cc_final: 0.8060 (p0) REVERT: 6 147 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8079 (pt) REVERT: 6 156 MET cc_start: 0.7965 (mtm) cc_final: 0.7665 (mmm) REVERT: 8 22 LYS cc_start: 0.7440 (mtmm) cc_final: 0.7169 (pttm) REVERT: 8 33 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8558 (pp) REVERT: 8 98 GLN cc_start: 0.8244 (mt0) cc_final: 0.8032 (mt0) REVERT: 8 174 ASN cc_start: 0.7947 (m110) cc_final: 0.7676 (m110) REVERT: 8 205 VAL cc_start: 0.7912 (m) cc_final: 0.7584 (p) REVERT: 8 216 ASN cc_start: 0.8166 (m-40) cc_final: 0.7927 (t0) REVERT: I 45 ASN cc_start: 0.7761 (t0) cc_final: 0.7153 (t0) REVERT: I 111 PHE cc_start: 0.7655 (t80) cc_final: 0.7249 (t80) REVERT: J 395 MET cc_start: 0.7628 (mmm) cc_final: 0.7414 (mmm) REVERT: J 430 ASN cc_start: 0.7971 (t0) cc_final: 0.7682 (t0) REVERT: J 432 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: K 13 MET cc_start: 0.6299 (mmp) cc_final: 0.5019 (tmm) REVERT: K 14 ARG cc_start: 0.5874 (tpm170) cc_final: 0.5558 (tpm170) REVERT: K 18 GLU cc_start: 0.6871 (tp30) cc_final: 0.5969 (tp30) REVERT: K 26 ARG cc_start: 0.6854 (ttm110) cc_final: 0.6379 (ppt90) REVERT: K 111 PHE cc_start: 0.7049 (t80) cc_final: 0.6666 (t80) REVERT: K 146 SER cc_start: 0.7865 (p) cc_final: 0.7492 (p) REVERT: K 156 MET cc_start: 0.6891 (mtm) cc_final: 0.6687 (mtm) REVERT: K 216 ASN cc_start: 0.7976 (t0) cc_final: 0.7546 (m-40) REVERT: K 234 LEU cc_start: 0.5887 (mt) cc_final: 0.5636 (mt) REVERT: L 432 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: M 363 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8614 (mp) REVERT: M 364 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: M 399 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8726 (tt) REVERT: M 401 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8352 (mp) REVERT: N 395 MET cc_start: 0.7222 (mmm) cc_final: 0.6948 (mmm) REVERT: N 432 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: O 26 ARG cc_start: 0.7414 (ttm110) cc_final: 0.6426 (ppt170) REVERT: O 67 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7233 (tttt) REVERT: O 99 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8453 (mt) REVERT: P 424 ASP cc_start: 0.7947 (p0) cc_final: 0.7572 (p0) REVERT: P 430 ASN cc_start: 0.7607 (t0) cc_final: 0.7378 (t0) REVERT: P 432 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7267 (mm-30) REVERT: Q 13 MET cc_start: 0.5597 (tmm) cc_final: 0.5366 (tmm) REVERT: Q 21 ARG cc_start: 0.6401 (ptm-80) cc_final: 0.5636 (tmm-80) REVERT: Q 234 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6154 (tp) REVERT: R 509 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7389 (ttm170) REVERT: S 401 LEU cc_start: 0.8873 (mt) cc_final: 0.8497 (mt) REVERT: T 21 ARG cc_start: 0.6456 (ttp-110) cc_final: 0.6066 (ttp80) REVERT: T 52 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7642 (mtmm) REVERT: V 345 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8808 (mm) REVERT: V 509 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7226 (ttp-170) REVERT: W 364 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7155 (pt0) REVERT: W 401 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8461 (mp) REVERT: X 21 ARG cc_start: 0.6482 (ttp-110) cc_final: 0.5938 (ttp80) REVERT: X 179 ASP cc_start: 0.5825 (t0) cc_final: 0.5497 (t0) REVERT: Y 324 ASN cc_start: 0.7787 (m-40) cc_final: 0.7552 (t0) REVERT: Y 433 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: Z 143 TYR cc_start: 0.6378 (p90) cc_final: 0.5681 (p90) REVERT: b 324 ASN cc_start: 0.7964 (m-40) cc_final: 0.7684 (m-40) REVERT: b 339 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: b 401 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8504 (mp) REVERT: d 167 LEU cc_start: 0.7840 (mt) cc_final: 0.7557 (mt) REVERT: f 22 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7520 (tmtt) outliers start: 120 outliers final: 66 residues processed: 684 average time/residue: 1.2210 time to fit residues: 1041.7277 Evaluate side-chains 681 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 589 time to evaluate : 3.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 ARG Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 135 ARG Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain H residue 395 MET Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 432 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 325 MET Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 433 GLU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 133 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 380 optimal weight: 0.7980 chunk 510 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 441 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 479 optimal weight: 0.0970 chunk 200 optimal weight: 3.9990 chunk 492 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 4 45 ASN 6 73 ASN 6 174 ASN B 607 GLN J 396 GLN O 80 GLN O 174 ASN U 324 ASN U 396 GLN V 322 GLN Z 80 GLN Z 101 ASN a 322 GLN d 216 ASN f 69 ASN f 80 GLN f 174 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.094536 restraints weight = 59569.033| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.78 r_work: 0.2933 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 47302 Z= 0.183 Angle : 0.501 8.938 64013 Z= 0.265 Chirality : 0.043 0.166 7270 Planarity : 0.004 0.057 8452 Dihedral : 3.818 37.374 6904 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.32 % Allowed : 18.56 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.11), residues: 6089 helix: 3.30 (0.10), residues: 2591 sheet: 0.92 (0.14), residues: 1474 loop : -0.21 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 429 HIS 0.004 0.001 HIS S 365 PHE 0.030 0.002 PHE O 111 TYR 0.025 0.001 TYR T 118 ARG 0.013 0.000 ARG X 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16431.84 seconds wall clock time: 283 minutes 17.06 seconds (16997.06 seconds total)