Starting phenix.real_space_refine on Thu Sep 26 00:04:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nao_24276/09_2024/7nao_24276.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nao_24276/09_2024/7nao_24276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nao_24276/09_2024/7nao_24276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nao_24276/09_2024/7nao_24276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nao_24276/09_2024/7nao_24276.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nao_24276/09_2024/7nao_24276.cif" } resolution = 2.9 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= 1.000 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 324 5.16 5 C 37185 2.51 5 N 10141 2.21 5 O 10433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 58083 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1696 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1793 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 243} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1703 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 6, 'TRANS': 228} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 86 Chain: "D" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1751 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "E" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1810 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 228} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "F" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1785 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1769 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 74 Chain: "H" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1609 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1564 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 26 Chain: "J" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1544 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 29 Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1525 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "L" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1599 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "M" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "N" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1491 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "O" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1678 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 85 Chain: "P" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1843 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 245} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "Q" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1723 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 6, 'TRANS': 229} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "R" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1693 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 226} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 12, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 76 Chain: "S" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 10, 'TRANS': 226} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 81 Chain: "T" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1784 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 58 Chain: "U" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1789 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 8, 'TRANS': 233} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 67 Chain: "V" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1612 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "W" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1559 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 26 Chain: "X" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1535 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "Y" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1532 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "Z" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1593 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 57 Chain: "a" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1624 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "b" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1478 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 31 Chain: "d" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1686 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "c" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "f" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1648 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "e" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1641 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "h" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1677 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "g" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1626 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "i" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 28.16, per 1000 atoms: 0.48 Number of scatterers: 58083 At special positions: 0 Unit cell: (138.578, 134.932, 249.198, 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 324 16.00 O 10433 8.00 N 10141 7.00 C 37185 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: 10.96 Conformation dependent library (CDL) restraints added in 5.8 seconds 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14386 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 72 sheets defined 48.1% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.84 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 removed outlier: 4.023A pdb=" N PHE A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 31 removed outlier: 3.531A pdb=" N GLY A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.624A pdb=" N VAL A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 101 Processing helix chain 'A' and resid 105 through 123 removed outlier: 3.649A pdb=" N GLN A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.044A pdb=" N HIS A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'B' and resid 18 through 31 removed outlier: 3.517A pdb=" N GLU B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.631A pdb=" N GLN B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 251 removed outlier: 3.828A pdb=" N LYS B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 29 removed outlier: 3.821A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 76 through 99 Processing helix chain 'C' and resid 103 through 121 removed outlier: 4.134A pdb=" N SER C 121 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 179 through 182 Processing helix chain 'C' and resid 183 through 198 removed outlier: 3.764A pdb=" N VAL C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.648A pdb=" N LYS C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 31 removed outlier: 3.761A pdb=" N GLU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 122 removed outlier: 3.571A pdb=" N GLN D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 173 through 185 removed outlier: 6.462A pdb=" N SER D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.732A pdb=" N ALA E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 100 Processing helix chain 'E' and resid 104 through 122 Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 164 through 175 removed outlier: 4.395A pdb=" N ALA E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 removed outlier: 3.929A pdb=" N PHE E 179 " --> pdb=" O HIS E 175 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET E 180 " --> pdb=" O MET E 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 175 through 180' Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.764A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 235 removed outlier: 4.310A pdb=" N GLY E 235 " --> pdb=" O PRO E 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 10 removed outlier: 4.263A pdb=" N ASP F 8 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 9 " --> pdb=" O GLY F 6 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER F 10 " --> pdb=" O TYR F 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 5 through 10' Processing helix chain 'F' and resid 20 through 33 removed outlier: 3.783A pdb=" N GLU F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU F 31 " --> pdb=" O MET F 27 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 103 Processing helix chain 'F' and resid 107 through 125 removed outlier: 3.950A pdb=" N TYR F 122 " --> pdb=" O TYR F 118 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 124 " --> pdb=" O HIS F 120 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 178 Processing helix chain 'F' and resid 185 through 201 removed outlier: 4.294A pdb=" N LYS F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 228 through 244 removed outlier: 3.664A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.890A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 171 through 185 Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 231 through 245 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 91 removed outlier: 3.561A pdb=" N ALA H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 147 through 166 Processing helix chain 'I' and resid 55 through 78 Processing helix chain 'I' and resid 82 through 97 removed outlier: 3.858A pdb=" N LYS I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 153 Processing helix chain 'I' and resid 158 through 176 removed outlier: 3.799A pdb=" N ARG I 176 " --> pdb=" O ASN I 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 72 Processing helix chain 'J' and resid 76 through 94 removed outlier: 3.831A pdb=" N ARG J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 147 removed outlier: 4.034A pdb=" N PHE J 137 " --> pdb=" O GLY J 133 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU J 138 " --> pdb=" O TYR J 134 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER J 141 " --> pdb=" O PHE J 137 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 171 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.829A pdb=" N TYR K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 143 removed outlier: 3.905A pdb=" N GLY K 137 " --> pdb=" O VAL K 133 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 167 Processing helix chain 'K' and resid 192 through 200 Processing helix chain 'L' and resid 57 through 80 Processing helix chain 'L' and resid 84 through 99 removed outlier: 3.965A pdb=" N ARG L 99 " --> pdb=" O ILE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 153 Proline residue: L 147 - end of helix Processing helix chain 'L' and resid 167 through 186 Processing helix chain 'M' and resid 57 through 78 Processing helix chain 'M' and resid 84 through 102 Processing helix chain 'M' and resid 141 through 157 removed outlier: 4.188A pdb=" N GLN M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) Proline residue: M 148 - end of helix Processing helix chain 'M' and resid 161 through 180 Processing helix chain 'M' and resid 210 through 215 removed outlier: 3.862A pdb=" N MET M 214 " --> pdb=" O ASP M 210 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE M 215 " --> pdb=" O ILE M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 210 through 215' Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 Processing helix chain 'N' and resid 131 through 143 removed outlier: 3.788A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 Processing helix chain 'N' and resid 190 through 194 Processing helix chain 'O' and resid 18 through 30 Processing helix chain 'O' and resid 57 through 61 removed outlier: 3.660A pdb=" N VAL O 61 " --> pdb=" O GLU O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 101 Processing helix chain 'O' and resid 105 through 123 Processing helix chain 'O' and resid 165 through 177 Processing helix chain 'O' and resid 182 through 198 removed outlier: 3.669A pdb=" N SER O 197 " --> pdb=" O THR O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 230 Processing helix chain 'P' and resid 19 through 31 removed outlier: 3.617A pdb=" N ALA P 31 " --> pdb=" O ALA P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 102 Processing helix chain 'P' and resid 106 through 124 removed outlier: 3.542A pdb=" N THR P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 179 removed outlier: 3.789A pdb=" N GLN P 177 " --> pdb=" O SER P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 201 Processing helix chain 'P' and resid 229 through 252 Processing helix chain 'Q' and resid 16 through 29 removed outlier: 3.571A pdb=" N GLY Q 29 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 99 Processing helix chain 'Q' and resid 103 through 121 Processing helix chain 'Q' and resid 164 through 176 Processing helix chain 'Q' and resid 177 through 183 removed outlier: 4.132A pdb=" N THR Q 183 " --> pdb=" O GLU Q 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 199 removed outlier: 4.010A pdb=" N VAL Q 198 " --> pdb=" O ALA Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 204 No H-bonds generated for 'chain 'Q' and resid 202 through 204' Processing helix chain 'Q' and resid 221 through 237 removed outlier: 3.651A pdb=" N GLU Q 237 " --> pdb=" O GLU Q 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 32 removed outlier: 3.907A pdb=" N LYS R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 104 removed outlier: 4.145A pdb=" N THR R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU R 88 " --> pdb=" O ASP R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 120 removed outlier: 3.675A pdb=" N LEU R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA R 120 " --> pdb=" O VAL R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 185 Processing helix chain 'R' and resid 190 through 206 Processing helix chain 'R' and resid 230 through 241 Processing helix chain 'S' and resid 19 through 31 removed outlier: 3.657A pdb=" N GLU S 23 " --> pdb=" O ILE S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 100 Processing helix chain 'S' and resid 104 through 121 Proline residue: S 119 - end of helix Processing helix chain 'S' and resid 164 through 175 removed outlier: 4.267A pdb=" N ALA S 168 " --> pdb=" O ARG S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 181 removed outlier: 3.679A pdb=" N PHE S 179 " --> pdb=" O HIS S 175 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET S 180 " --> pdb=" O MET S 176 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU S 181 " --> pdb=" O SER S 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 175 through 181' Processing helix chain 'S' and resid 183 through 199 removed outlier: 3.849A pdb=" N THR S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU S 199 " --> pdb=" O LEU S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 228 through 233 removed outlier: 4.492A pdb=" N PHE S 232 " --> pdb=" O ASP S 228 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 33 removed outlier: 3.614A pdb=" N GLU T 24 " --> pdb=" O VAL T 20 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 103 Processing helix chain 'T' and resid 107 through 125 removed outlier: 4.019A pdb=" N TYR T 122 " --> pdb=" O TYR T 118 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR T 123 " --> pdb=" O VAL T 119 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU T 124 " --> pdb=" O HIS T 120 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR T 125 " --> pdb=" O ALA T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 178 removed outlier: 3.969A pdb=" N LYS T 178 " --> pdb=" O THR T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 201 removed outlier: 4.220A pdb=" N LYS T 191 " --> pdb=" O ARG T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 228 through 244 removed outlier: 3.610A pdb=" N LYS T 244 " --> pdb=" O LYS T 240 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 34 removed outlier: 3.799A pdb=" N GLU U 26 " --> pdb=" O LEU U 22 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 106 Processing helix chain 'U' and resid 110 through 128 removed outlier: 3.512A pdb=" N TYR U 125 " --> pdb=" O ILE U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 186 removed outlier: 3.592A pdb=" N LYS U 186 " --> pdb=" O LYS U 182 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 207 Processing helix chain 'U' and resid 211 through 213 No H-bonds generated for 'chain 'U' and resid 211 through 213' Processing helix chain 'U' and resid 231 through 245 removed outlier: 3.599A pdb=" N ARG U 245 " --> pdb=" O ALA U 241 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 91 removed outlier: 3.641A pdb=" N ALA V 79 " --> pdb=" O ARG V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 Processing helix chain 'V' and resid 147 through 166 Processing helix chain 'W' and resid 2 through 6 removed outlier: 3.952A pdb=" N ASN W 6 " --> pdb=" O MET W 3 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 78 Processing helix chain 'W' and resid 82 through 97 removed outlier: 3.805A pdb=" N LYS W 97 " --> pdb=" O LEU W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 153 Processing helix chain 'W' and resid 158 through 176 removed outlier: 3.682A pdb=" N ARG W 176 " --> pdb=" O ASN W 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 72 Processing helix chain 'X' and resid 76 through 93 removed outlier: 4.302A pdb=" N ARG X 93 " --> pdb=" O ALA X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 147 removed outlier: 4.112A pdb=" N PHE X 137 " --> pdb=" O GLY X 133 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU X 138 " --> pdb=" O TYR X 134 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER X 141 " --> pdb=" O PHE X 137 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE X 142 " --> pdb=" O LEU X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 171 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 3.715A pdb=" N GLN Y 89 " --> pdb=" O ASN Y 85 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 131 through 143 removed outlier: 3.982A pdb=" N GLY Y 137 " --> pdb=" O VAL Y 133 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 167 Processing helix chain 'Y' and resid 192 through 200 Processing helix chain 'Z' and resid 57 through 80 Processing helix chain 'Z' and resid 84 through 99 removed outlier: 3.968A pdb=" N ARG Z 99 " --> pdb=" O ILE Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 141 through 153 Proline residue: Z 147 - end of helix Processing helix chain 'Z' and resid 167 through 186 Processing helix chain 'a' and resid 57 through 78 Processing helix chain 'a' and resid 84 through 102 Processing helix chain 'a' and resid 141 through 157 removed outlier: 4.207A pdb=" N GLN a 147 " --> pdb=" O ALA a 143 " (cutoff:3.500A) Proline residue: a 148 - end of helix Processing helix chain 'a' and resid 161 through 180 Processing helix chain 'a' and resid 209 through 214 removed outlier: 3.622A pdb=" N ALA a 212 " --> pdb=" O TRP a 209 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS a 213 " --> pdb=" O ASP a 210 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 71 Processing helix chain 'b' and resid 75 through 90 Processing helix chain 'b' and resid 129 through 134 removed outlier: 3.715A pdb=" N SER b 133 " --> pdb=" O SER b 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 135 through 143 Processing helix chain 'b' and resid 148 through 167 Processing helix chain 'b' and resid 190 through 194 Processing helix chain 'd' and resid 10 through 34 Processing helix chain 'd' and resid 34 through 49 Processing helix chain 'd' and resid 50 through 53 Processing helix chain 'd' and resid 97 through 129 Proline residue: d 109 - end of helix Processing helix chain 'd' and resid 136 through 181 removed outlier: 4.521A pdb=" N VAL d 140 " --> pdb=" O ASN d 136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE d 168 " --> pdb=" O ILE d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 185 through 223 Processing helix chain 'd' and resid 223 through 229 Processing helix chain 'c' and resid 7 through 31 Processing helix chain 'c' and resid 31 through 46 Processing helix chain 'c' and resid 107 through 138 Proline residue: c 119 - end of helix Processing helix chain 'c' and resid 147 through 191 removed outlier: 4.003A pdb=" N SER c 175 " --> pdb=" O HIS c 171 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 239 removed outlier: 5.658A pdb=" N GLU c 235 " --> pdb=" O LEU c 231 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS c 236 " --> pdb=" O LYS c 232 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 34 Processing helix chain 'f' and resid 34 through 49 removed outlier: 3.577A pdb=" N GLN f 38 " --> pdb=" O ARG f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 50 through 54 removed outlier: 3.855A pdb=" N VAL f 54 " --> pdb=" O SER f 51 " (cutoff:3.500A) Processing helix chain 'f' and resid 97 through 129 Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 137 through 181 removed outlier: 4.152A pdb=" N PHE f 168 " --> pdb=" O ILE f 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER f 169 " --> pdb=" O SER f 165 " (cutoff:3.500A) Processing helix chain 'f' and resid 185 through 223 Processing helix chain 'f' and resid 223 through 229 Processing helix chain 'e' and resid 8 through 31 Processing helix chain 'e' and resid 31 through 46 Processing helix chain 'e' and resid 107 through 138 Proline residue: e 119 - end of helix Processing helix chain 'e' and resid 149 through 191 removed outlier: 3.764A pdb=" N SER e 175 " --> pdb=" O HIS e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 195 through 239 removed outlier: 5.580A pdb=" N GLU e 235 " --> pdb=" O LEU e 231 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS e 236 " --> pdb=" O LYS e 232 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 34 Processing helix chain 'h' and resid 34 through 49 Processing helix chain 'h' and resid 56 through 61 removed outlier: 4.262A pdb=" N LEU h 60 " --> pdb=" O ASP h 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 129 Proline residue: h 109 - end of helix Processing helix chain 'h' and resid 137 through 181 removed outlier: 4.239A pdb=" N PHE h 168 " --> pdb=" O ILE h 164 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER h 169 " --> pdb=" O SER h 165 " (cutoff:3.500A) Processing helix chain 'h' and resid 185 through 223 Processing helix chain 'h' and resid 223 through 229 Processing helix chain 'g' and resid 8 through 31 Processing helix chain 'g' and resid 31 through 46 Processing helix chain 'g' and resid 53 through 58 removed outlier: 3.922A pdb=" N LEU g 57 " --> pdb=" O ASN g 53 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 138 Proline residue: g 119 - end of helix Processing helix chain 'g' and resid 149 through 191 removed outlier: 4.159A pdb=" N PHE g 178 " --> pdb=" O ILE g 174 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER g 179 " --> pdb=" O SER g 175 " (cutoff:3.500A) Processing helix chain 'g' and resid 195 through 239 removed outlier: 3.823A pdb=" N GLN g 199 " --> pdb=" O GLY g 195 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU g 235 " --> pdb=" O LEU g 231 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS g 236 " --> pdb=" O LYS g 232 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 34 Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 56 through 60 Processing helix chain 'i' and resid 97 through 129 Proline residue: i 109 - end of helix Processing helix chain 'i' and resid 137 through 181 removed outlier: 3.895A pdb=" N SER i 165 " --> pdb=" O GLN i 161 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE i 168 " --> pdb=" O ILE i 164 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 223 Processing helix chain 'i' and resid 223 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 69 removed outlier: 6.666A pdb=" N MET B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 134 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 63 through 64 Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 69 Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 65 Processing sheet with id=AB2, first strand: chain 'F' and resid 162 through 165 Processing sheet with id=AB3, first strand: chain 'F' and resid 66 through 70 removed outlier: 6.578A pdb=" N VAL F 73 " --> pdb=" O VAL F 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.888A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 69 through 73 removed outlier: 6.659A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.375A pdb=" N THR H 2 " --> pdb=" O ASP H 17 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE H 173 " --> pdb=" O PRO H 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.281A pdb=" N GLU H 22 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AB9, first strand: chain 'H' and resid 211 through 218 removed outlier: 4.621A pdb=" N VAL I 184 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA I 9 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 27 through 29 removed outlier: 6.876A pdb=" N PHE I 27 " --> pdb=" O VAL I 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 41 through 43 removed outlier: 4.392A pdb=" N ILE I 120 " --> pdb=" O THR I 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 129 through 132 removed outlier: 6.134A pdb=" N PHE J 178 " --> pdb=" O ASN J 193 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN J 193 " --> pdb=" O PHE J 178 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL J 180 " --> pdb=" O LEU J 191 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 35 through 39 removed outlier: 6.825A pdb=" N ILE J 42 " --> pdb=" O MET J 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.592A pdb=" N SER K 188 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS K 178 " --> pdb=" O ARG K 186 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARG K 186 " --> pdb=" O HIS K 178 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.617A pdb=" N ALA K 22 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE K 26 " --> pdb=" O ALA K 22 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 34 through 35 Processing sheet with id=AC8, first strand: chain 'K' and resid 34 through 35 Processing sheet with id=AC9, first strand: chain 'L' and resid 135 through 139 removed outlier: 6.073A pdb=" N THR L 11 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 29 through 31 removed outlier: 6.417A pdb=" N GLU L 31 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 43 through 47 removed outlier: 6.661A pdb=" N THR L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN L 108 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL L 121 " --> pdb=" O ASP L 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 7 through 8 removed outlier: 6.646A pdb=" N THR M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 7 through 8 Processing sheet with id=AD5, first strand: chain 'M' and resid 136 through 138 Processing sheet with id=AD6, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.071A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 20 through 22 removed outlier: 7.311A pdb=" N THR N 20 " --> pdb=" O ALA N 27 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 34 through 36 Processing sheet with id=AD9, first strand: chain 'O' and resid 159 through 162 Processing sheet with id=AE1, first strand: chain 'O' and resid 65 through 66 Processing sheet with id=AE2, first strand: chain 'P' and resid 161 through 164 Processing sheet with id=AE3, first strand: chain 'P' and resid 67 through 69 removed outlier: 5.216A pdb=" N LYS P 67 " --> pdb=" O CYS P 74 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N CYS P 74 " --> pdb=" O LYS P 67 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET P 72 " --> pdb=" O ASN P 69 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU P 134 " --> pdb=" O SER P 150 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 158 through 161 Processing sheet with id=AE5, first strand: chain 'Q' and resid 69 through 75 Processing sheet with id=AE6, first strand: chain 'R' and resid 167 through 170 Processing sheet with id=AE7, first strand: chain 'R' and resid 67 through 69 Processing sheet with id=AE8, first strand: chain 'S' and resid 158 through 161 Processing sheet with id=AE9, first strand: chain 'S' and resid 63 through 65 Processing sheet with id=AF1, first strand: chain 'T' and resid 162 through 165 Processing sheet with id=AF2, first strand: chain 'T' and resid 68 through 70 removed outlier: 5.284A pdb=" N ASN T 68 " --> pdb=" O MET T 75 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET T 75 " --> pdb=" O ASN T 68 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 165 through 169 removed outlier: 6.172A pdb=" N THR U 38 " --> pdb=" O GLN U 53 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 69 through 71 Processing sheet with id=AF5, first strand: chain 'V' and resid 124 through 128 removed outlier: 6.238A pdb=" N THR V 2 " --> pdb=" O ASP V 17 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE V 173 " --> pdb=" O PRO V 188 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.051A pdb=" N GLU V 22 " --> pdb=" O VAL V 26 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL V 26 " --> pdb=" O GLU V 22 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 34 through 36 Processing sheet with id=AF8, first strand: chain 'V' and resid 211 through 218 removed outlier: 3.702A pdb=" N THR V 213 " --> pdb=" O THR W 198 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL W 184 " --> pdb=" O LEU W 199 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA W 9 " --> pdb=" O ASP W 24 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 27 through 28 removed outlier: 7.003A pdb=" N PHE W 27 " --> pdb=" O VAL W 34 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 41 through 43 Processing sheet with id=AG2, first strand: chain 'X' and resid 129 through 132 removed outlier: 6.024A pdb=" N PHE X 178 " --> pdb=" O ASN X 193 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN X 193 " --> pdb=" O PHE X 178 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL X 180 " --> pdb=" O LEU X 191 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 21 through 22 Processing sheet with id=AG4, first strand: chain 'X' and resid 35 through 39 removed outlier: 3.559A pdb=" N MET X 38 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE X 42 " --> pdb=" O MET X 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 125 through 129 removed outlier: 3.603A pdb=" N SER Y 188 " --> pdb=" O LEU Y 176 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS Y 178 " --> pdb=" O ARG Y 186 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG Y 186 " --> pdb=" O HIS Y 178 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG Y 180 " --> pdb=" O TRP Y 184 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TRP Y 184 " --> pdb=" O ARG Y 180 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 20 through 22 removed outlier: 6.474A pdb=" N ALA Y 22 " --> pdb=" O ILE Y 26 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE Y 26 " --> pdb=" O ALA Y 22 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 41 through 42 Processing sheet with id=AG8, first strand: chain 'Y' and resid 41 through 42 Processing sheet with id=AG9, first strand: chain 'Z' and resid 135 through 139 removed outlier: 5.727A pdb=" N THR Z 11 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 29 through 31 removed outlier: 6.793A pdb=" N LEU Z 29 " --> pdb=" O HIS Z 36 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 43 through 47 removed outlier: 6.708A pdb=" N THR Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN Z 108 " --> pdb=" O PHE Z 124 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL Z 121 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 7 through 8 removed outlier: 6.740A pdb=" N THR a 49 " --> pdb=" O VAL a 45 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 7 through 8 Processing sheet with id=AH5, first strand: chain 'a' and resid 136 through 138 Processing sheet with id=AH6, first strand: chain 'a' and resid 28 through 30 removed outlier: 6.705A pdb=" N TYR a 30 " --> pdb=" O ALA a 34 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ALA a 34 " --> pdb=" O TYR a 30 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 125 through 128 Processing sheet with id=AH8, first strand: chain 'b' and resid 20 through 22 removed outlier: 6.957A pdb=" N THR b 20 " --> pdb=" O ALA b 27 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 34 through 38 removed outlier: 6.225A pdb=" N ILE b 41 " --> pdb=" O ILE b 37 " (cutoff:3.500A) 3760 hydrogen bonds defined for protein. 10953 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: 26.99 Time building geometry restraints manager: 13.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18771 1.34 - 1.46: 9654 1.46 - 1.58: 30216 1.58 - 1.69: 0 1.69 - 1.81: 535 Bond restraints: 59176 Sorted by residual: bond pdb=" N GLY U 4 " pdb=" CA GLY U 4 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.29e+00 bond pdb=" CA GLY O 79 " pdb=" C GLY O 79 " ideal model delta sigma weight residual 1.511 1.494 0.017 6.90e-03 2.10e+04 5.74e+00 bond pdb=" N GLY T 6 " pdb=" CA GLY T 6 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.60e-02 3.91e+03 5.37e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ARG A 3 " pdb=" CA ARG A 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 ... (remaining 59171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 79319 2.53 - 5.06: 893 5.06 - 7.59: 77 7.59 - 10.12: 3 10.12 - 12.66: 1 Bond angle restraints: 80293 Sorted by residual: angle pdb=" CG1 VAL Q 50 " pdb=" CB VAL Q 50 " pdb=" CG2 VAL Q 50 " ideal model delta sigma weight residual 110.80 123.46 -12.66 2.20e+00 2.07e-01 3.31e+01 angle pdb=" N SER V 171 " pdb=" CA SER V 171 " pdb=" CB SER V 171 " ideal model delta sigma weight residual 114.17 108.35 5.82 1.14e+00 7.69e-01 2.61e+01 angle pdb=" O GLY O 79 " pdb=" C GLY O 79 " pdb=" N PRO O 80 " ideal model delta sigma weight residual 121.07 119.29 1.78 3.60e-01 7.72e+00 2.45e+01 angle pdb=" N SER V 171 " pdb=" CA SER V 171 " pdb=" C SER V 171 " ideal model delta sigma weight residual 113.28 120.03 -6.75 1.57e+00 4.06e-01 1.85e+01 angle pdb=" CA VAL Q 50 " pdb=" CB VAL Q 50 " pdb=" CG2 VAL Q 50 " ideal model delta sigma weight residual 110.40 117.46 -7.06 1.70e+00 3.46e-01 1.72e+01 ... (remaining 80288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 32839 17.95 - 35.90: 2190 35.90 - 53.85: 270 53.85 - 71.80: 93 71.80 - 89.76: 47 Dihedral angle restraints: 35439 sinusoidal: 13005 harmonic: 22434 Sorted by residual: dihedral pdb=" CA ARG H 187 " pdb=" C ARG H 187 " pdb=" N PRO H 188 " pdb=" CA PRO H 188 " ideal model delta harmonic sigma weight residual -180.00 -121.77 -58.23 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA ARG D 5 " pdb=" C ARG D 5 " pdb=" N SER D 6 " pdb=" CA SER D 6 " ideal model delta harmonic sigma weight residual -180.00 -127.11 -52.89 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ILE W 29 " pdb=" C ILE W 29 " pdb=" N GLN W 30 " pdb=" CA GLN W 30 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 35436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.345: 9334 0.345 - 0.689: 0 0.689 - 1.034: 0 1.034 - 1.378: 0 1.378 - 1.723: 1 Chirality restraints: 9335 Sorted by residual: chirality pdb=" CB VAL Q 50 " pdb=" CA VAL Q 50 " pdb=" CG1 VAL Q 50 " pdb=" CG2 VAL Q 50 " both_signs ideal model delta sigma weight residual False -2.63 -0.91 -1.72 2.00e-01 2.50e+01 7.42e+01 chirality pdb=" CG LEU N 202 " pdb=" CB LEU N 202 " pdb=" CD1 LEU N 202 " pdb=" CD2 LEU N 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL L 127 " pdb=" CA VAL L 127 " pdb=" CG1 VAL L 127 " pdb=" CG2 VAL L 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 9332 not shown) Planarity restraints: 10242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 148 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO E 149 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO E 149 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 149 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 158 " -0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO I 159 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO I 159 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 159 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 15 " 0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO F 16 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO F 16 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 16 " 0.044 5.00e-02 4.00e+02 ... (remaining 10239 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 547 2.65 - 3.21: 55332 3.21 - 3.78: 93914 3.78 - 4.34: 130112 4.34 - 4.90: 216914 Nonbonded interactions: 496819 Sorted by model distance: nonbonded pdb=" OG SER N 124 " pdb=" OH TYR N 143 " model vdw 2.090 3.040 nonbonded pdb=" O THR K 44 " pdb=" OG1 THR K 99 " model vdw 2.092 3.040 nonbonded pdb=" OG1 THR H 213 " pdb=" OG1 THR I 198 " model vdw 2.115 3.040 nonbonded pdb=" OG SER T 12 " pdb=" OG SER T 126 " model vdw 2.133 3.040 nonbonded pdb=" O THR G 190 " pdb=" OG1 THR G 194 " model vdw 2.211 3.040 ... (remaining 496814 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 'A' and (resid 3 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 166 or (resid 167 and (name N or na \ me CA or name C or name O or name CB )) or resid 168 through 170 or (resid 171 a \ nd (name N or name CA or name C or name O or name CB )) or resid 172 through 173 \ or (resid 174 through 176 and (name N or name CA or name C or name O or name CB \ )) or resid 177 or (resid 178 through 180 and (name N or name CA or name C or n \ ame O or name CB )) or resid 181 through 184 or (resid 185 through 186 and (name \ N or name CA or name C or name O or name CB )) or resid 187 through 231)) selection = (chain 'O' and (resid 3 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 12 or (resid 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 or (resid 15 and (name N or name \ CA or name C or name O or name CB )) or resid 16 through 21 or (resid 22 and (na \ me N or name CA or name C or name O or name CB )) or resid 23 through 122 or (re \ sid 123 and (name N or name CA or name C or name O or name CB )) or resid 124 th \ rough 138 or (resid 139 through 140 and (name N or name CA or name C or name O o \ r name CB )) or resid 141 through 231)) } ncs_group { reference = (chain 'B' and (resid 3 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 177 or (resid 178 and (name N or na \ me CA or name C or name O or name CB )) or resid 179 through 251)) selection = (chain 'P' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 6 or (resid 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 50 or (resid 51 through 54 and (name \ N or name CA or name C or name O or name CB )) or resid 55 through 56 or (resid \ 57 through 60 and (name N or name CA or name C or name O or name CB )) or resid \ 61 through 70 or (resid 71 and (name N or name CA or name C or name O or name C \ B )) or resid 72 through 184 or (resid 185 and (name N or name CA or name C or n \ ame O or name CB )) or resid 186 or (resid 187 and (name N or name CA or name C \ or name O or name CB )) or resid 188 through 218 or (resid 219 through 220 and ( \ name N or name CA or name C or name O or name CB )) or resid 221 through 231 or \ (resid 232 and (name N or name CA or name C or name O or name CB )) or resid 233 \ through 251)) } ncs_group { reference = (chain 'C' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 45 or (resid 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 99 or (resid 100 and ( \ name N or name CA or name C or name O or name CB )) or resid 101 through 104 or \ (resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 \ through 136 or (resid 137 and (name N or name CA or name C or name O or name CB \ )) or resid 138 through 140 or (resid 141 and (name N or name CA or name C or n \ ame O or name CB )) or resid 142 through 236)) selection = (chain 'Q' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 23 or (resid 24 through 25 and (name N \ or name CA or name C or name O or name CB )) or resid 26 through 37 or (resid 3 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 39 through 4 \ 9 or (resid 50 through 51 and (name N or name CA or name C or name O or name CB \ )) or resid 52 through 120 or (resid 121 and (name N or name CA or name C or nam \ e O or name CB )) or resid 122 through 149 or (resid 150 and (name N or name CA \ or name C or name O or name CB )) or resid 151 through 192 or (resid 193 through \ 194 and (name N or name CA or name C or name O or name CB )) or resid 195 throu \ gh 196 or (resid 197 through 198 and (name N or name CA or name C or name O or n \ ame CB )) or resid 199 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name CB )) or resid 222 through 223 or (resid 224 and (name N or \ name CA or name C or name O or name CB )) or resid 225 through 236)) } ncs_group { reference = (chain 'D' and ((resid 7 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 54 or (resid 55 through 56 and (name N or name C \ A or name C or name O or name CB )) or resid 57 through 156 or (resid 157 and (n \ ame N or name CA or name C or name O or name CB )) or resid 158 through 182 or ( \ resid 183 and (name N or name CA or name C or name O or name CB )) or resid 184 \ through 187 or (resid 188 and (name N or name CA or name C or name O or name CB \ )) or resid 189 through 191 or (resid 192 through 194 and (name N or name CA or \ name C or name O or name CB )) or resid 195 through 212 or (resid 213 and (name \ N or name CA or name C or name O or name CB )) or resid 214 through 240 or (resi \ d 241 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'R' and (resid 7 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 124 or (resid 125 throug \ h 129 and (name N or name CA or name C or name O or name CB )) or resid 130 thro \ ugh 146 or (resid 147 through 148 and (name N or name CA or name C or name O or \ name CB )) or resid 149 through 230 or (resid 231 through 232 and (name N or nam \ e CA or name C or name O or name CB )) or resid 233 through 234 or (resid 235 th \ rough 236 and (name N or name CA or name C or name O or name CB )) or resid 237 \ through 241)) } ncs_group { reference = (chain 'E' and (resid 4 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 41 or (resid 42 and (name N or name C \ A or name C or name O or name CB )) or resid 43 through 54 or (resid 55 and (nam \ e N or name CA or name C or name O or name CB )) or resid 56 through 79 or (resi \ d 80 through 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 through 137 or (resid 138 through 139 and (name N or name CA or name C or n \ ame O or name CB )) or resid 140 through 154 or (resid 155 and (name N or name C \ A or name C or name O or name CB )) or resid 156 through 172 or (resid 173 and ( \ name N or name CA or name C or name O or name CB )) or resid 174 through 177 or \ (resid 178 and (name N or name CA or name C or name O or name CB )) or resid 179 \ or (resid 180 through 181 and (name N or name CA or name C or name O or name CB \ )) or resid 182 through 185 or (resid 186 and (name N or name CA or name C or n \ ame O or name CB )) or resid 187 through 205 or (resid 206 and (name N or name C \ A or name C or name O or name CB )) or resid 207 or (resid 208 and (name N or na \ me CA or name C or name O or name CB )) or resid 209 through 236 or (resid 237 t \ hrough 238 and (name N or name CA or name C or name O or name CB )) or resid 239 \ through 240)) selection = (chain 'S' and (resid 4 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 210 or (resid 211 and (name N or na \ me CA or name C or name O or name CB )) or resid 212 through 240)) } ncs_group { reference = (chain 'F' and (resid 6 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 162 or (resid 163 through 164 and ( \ name N or name CA or name C or name O or name CB )) or resid 165 through 182 or \ (resid 183 and (name N or name CA or name C or name O or name CB )) or resid 184 \ through 228 or (resid 229 through 230 and (name N or name CA or name C or name \ O or name CB )) or resid 231 through 244)) selection = (chain 'T' and (resid 6 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 93 or (resid 94 through 95 and (nam \ e N or name CA or name C or name O or name CB )) or resid 96 through 142 or (res \ id 143 through 144 and (name N or name CA or name C or name O or name CB )) or r \ esid 145 through 220 or (resid 221 and (name N or name CA or name C or name O or \ name CB )) or resid 222 through 244)) } ncs_group { reference = (chain 'G' and (resid 7 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 44 or (resid 45 through 48 and (nam \ e N or name CA or name C or name O or name CB )) or resid 49 through 58 or (resi \ d 59 and (name N or name CA or name C or name O or name CB )) or resid 60 throug \ h 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or re \ sid 65 through 129 or (resid 130 and (name N or name CA or name C or name O or n \ ame CB )) or resid 131 through 143 or (resid 144 through 146 and (name N or name \ CA or name C or name O or name CB )) or resid 147 through 245)) selection = (chain 'U' and (resid 7 through 46 or (resid 47 through 48 and (name N or name C \ A or name C or name O or name CB )) or resid 49 through 96 or (resid 97 through \ 99 and (name N or name CA or name C or name O or name CB )) or resid 100 through \ 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) or r \ esid 181 through 186 or (resid 187 through 188 and (name N or name CA or name C \ or name O or name CB )) or resid 189 through 210 or (resid 211 and (name N or na \ me CA or name C or name O or name CB )) or resid 212 through 213 or (resid 214 a \ nd (name N or name CA or name C or name O or name CB )) or resid 215 through 220 \ or (resid 221 and (name N or name CA or name C or name O or name CB )) or resid \ 222 through 245)) } ncs_group { reference = (chain 'H' and (resid 1 through 179 or (resid 180 through 181 and (name N or nam \ e CA or name C or name O or name CB )) or resid 182 through 193 or (resid 194 an \ d (name N or name CA or name C or name O or name CB )) or resid 195 through 222) \ ) selection = (chain 'V' and (resid 1 through 8 or (resid 9 through 10 and (name N or name CA \ or name C or name O or name CB )) or resid 11 through 27 or (resid 28 and (name \ N or name CA or name C or name O or name CB )) or resid 29 through 148 or (resid \ 149 and (name N or name CA or name C or name O or name CB )) or resid 150 throu \ gh 183 or (resid 184 and (name N or name CA or name C or name O or name CB )) or \ resid 185 through 222)) } ncs_group { reference = (chain 'I' and (resid 1 through 113 or (resid 114 and (name N or name CA or name \ C or name O or name CB )) or resid 115 through 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 through 157 or (resid 15 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 159 through \ 189 or (resid 190 and (name N or name CA or name C or name O or name CB )) or re \ sid 191 through 204)) selection = (chain 'W' and (resid 1 through 73 or (resid 74 and (name N or name CA or name C \ or name O or name CB )) or resid 75 through 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 through 204)) } ncs_group { reference = (chain 'J' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 196)) selection = (chain 'X' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 38 or (resid 39 through 40 and (nam \ e N or name CA or name C or name O or name CB )) or resid 41 through 93 or (resi \ d 94 through 95 and (name N or name CA or name C or name O or name CB )) or resi \ d 96 through 196)) } ncs_group { reference = (chain 'K' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95 or (resid 96 and (name N or name \ CA or name C or name O or name CB )) or resid 97 through 105 or (resid 106 and \ (name N or name CA or name C or name O or name CB )) or resid 107 through 200)) selection = (chain 'Y' and (resid 1 through 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 149 or (resid 150 and (name N or \ name CA or name C or name O or name CB )) or resid 151 through 189 or (resid 19 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 191 through \ 193 or (resid 194 and (name N or name CA or name C or name O or name CB )) or re \ sid 195 through 200)) } ncs_group { reference = (chain 'L' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 38 or (resid 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 47 or (resid 48 and (n \ ame N or name CA or name C or name O or name CB )) or resid 49 through 124 or (r \ esid 125 and (name N or name CA or name C or name O or name CB )) or resid 126 t \ hrough 183 or (resid 184 and (name N or name CA or name C or name O or name CB ) \ ) or resid 185 through 213)) selection = (chain 'Z' and (resid 1 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 122 or (resid 123 and (name N or na \ me CA or name C or name O or name CB )) or resid 124 through 159 or (resid 160 t \ hrough 162 and (name N or name CA or name C or name O or name CB )) or resid 163 \ through 213)) } ncs_group { reference = (chain 'M' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 73 or (resid 74 throug \ h 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 154 or (resid 155 through 156 and (name N or name CA or name C or name O or na \ me CB )) or resid 157 through 203 or (resid 204 and (name N or name CA or name C \ or name O or name CB )) or resid 205 through 209 or (resid 210 and (name N or n \ ame CA or name C or name O or name CB )) or resid 211 through 215)) selection = (chain 'a' and (resid 1 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 215)) } ncs_group { reference = (chain 'N' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 31 or (resid 32 and (name N or name C \ A or name C or name O or name CB )) or resid 33 through 34 or (resid 35 and (nam \ e N or name CA or name C or name O or name CB )) or resid 36 through 38 or (resi \ d 39 and (name N or name CA or name C or name O or name CB )) or resid 40 throug \ h 71 or (resid 72 and (name N or name CA or name C or name O or name CB )) or re \ sid 73 through 139 or (resid 140 through 141 and (name N or name CA or name C or \ name O or name CB )) or resid 142 through 202)) selection = (chain 'b' and (resid 1 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 184 or (resid 185 and (name N or na \ me CA or name C or name O or name CB )) or resid 186 through 202)) } ncs_group { reference = (chain 'c' and (resid 7 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 249)) selection = (chain 'e' and (resid 7 through 121 or (resid 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 142 or (resid 143 and (name N or \ name CA or name C or name O or name CB )) or resid 144 through 153 or (resid 15 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 155 through \ 157 or (resid 158 and (name N or name CA or name C or name O or name CB )) or re \ sid 159 through 244 or (resid 245 and (name N or name CA or name C or name O or \ name CB )) or resid 246 or (resid 247 and (name N or name CA or name C or name O \ or name CB )) or resid 248 through 249)) selection = (chain 'g' and (resid 7 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 105 or (resid 106 and (name N or na \ me CA or name C or name O or name CB )) or resid 107 through 246 or (resid 247 a \ nd (name N or name CA or name C or name O or name CB )) or resid 248 through 249 \ )) } ncs_group { reference = (chain 'd' and (resid 8 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 58 or (resid 59 and (nam \ e N or name CA or name C or name O or name CB )) or resid 60 through 92 or (resi \ d 93 and (name N or name CA or name C or name O or name CB )) or resid 94 throug \ h 233)) selection = (chain 'f' and (resid 8 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 58 or (resid 59 and (nam \ e N or name CA or name C or name O or name CB )) or resid 60 through 92 or (resi \ d 93 and (name N or name CA or name C or name O or name CB )) or resid 94 throug \ h 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or \ resid 167 through 233)) selection = (chain 'h' and (resid 8 through 58 or (resid 59 and (name N or name CA or name C \ or name O or name CB )) or resid 60 through 147 or (resid 148 and (name N or na \ me CA or name C or name O or name CB )) or resid 149 through 165 or (resid 166 a \ nd (name N or name CA or name C or name O or name CB )) or resid 167 through 233 \ )) selection = (chain 'i' and (resid 8 through 13 or (resid 14 through 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 through 28 or (resid 29 through \ 30 and (name N or name CA or name C or name O or name CB )) or resid 31 through \ 92 or (resid 93 and (name N or name CA or name C or name O or name CB )) or resi \ d 94 through 147 or (resid 148 and (name N or name CA or name C or name O or nam \ e CB )) or resid 149 through 233)) } 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: 1.740 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: 0.060 Extract box with map and model: 1.610 Check model and map are aligned: 0.340 Set scattering table: 0.410 Process input model: 110.330 Find NCS groups from input model: 4.600 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 59176 Z= 0.340 Angle : 0.733 12.656 80293 Z= 0.401 Chirality : 0.049 1.723 9335 Planarity : 0.005 0.087 10242 Dihedral : 12.918 89.756 21053 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.31 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.09), residues: 7657 helix: 1.64 (0.08), residues: 3391 sheet: 0.32 (0.12), residues: 1522 loop : -0.26 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP T 215 HIS 0.009 0.002 HIS R 73 PHE 0.022 0.002 PHE I 68 TYR 0.030 0.002 TYR H 42 ARG 0.007 0.001 ARG X 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1659 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1659 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8833 (pt0) cc_final: 0.8628 (pt0) REVERT: A 187 ILE cc_start: 0.9138 (pt) cc_final: 0.8934 (tt) REVERT: B 26 GLU cc_start: 0.8769 (tp30) cc_final: 0.8463 (mm-30) REVERT: B 49 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7855 (ttm110) REVERT: B 67 LYS cc_start: 0.8353 (ttpt) cc_final: 0.8017 (tttt) REVERT: B 103 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 108 GLU cc_start: 0.8260 (tt0) cc_final: 0.8052 (tt0) REVERT: B 198 ASN cc_start: 0.9292 (t0) cc_final: 0.9060 (t0) REVERT: C 54 GLN cc_start: 0.8630 (tt0) cc_final: 0.8238 (tt0) REVERT: C 67 ASP cc_start: 0.8091 (p0) cc_final: 0.7642 (p0) REVERT: C 105 GLU cc_start: 0.8392 (tt0) cc_final: 0.7991 (tt0) REVERT: C 138 PHE cc_start: 0.8817 (t80) cc_final: 0.8597 (t80) REVERT: C 206 ILE cc_start: 0.9052 (pt) cc_final: 0.8681 (mp) REVERT: D 95 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8036 (mm-30) REVERT: D 137 PHE cc_start: 0.9140 (m-80) cc_final: 0.8764 (m-80) REVERT: D 166 ASP cc_start: 0.8681 (m-30) cc_final: 0.8387 (m-30) REVERT: D 189 MET cc_start: 0.8353 (ptm) cc_final: 0.8134 (ptp) REVERT: E 9 ASP cc_start: 0.7750 (t70) cc_final: 0.7491 (t70) REVERT: E 67 ASP cc_start: 0.8735 (t70) cc_final: 0.8145 (t70) REVERT: E 137 TYR cc_start: 0.8981 (t80) cc_final: 0.8672 (t80) REVERT: E 138 ASP cc_start: 0.7575 (p0) cc_final: 0.7347 (p0) REVERT: F 70 ASP cc_start: 0.8158 (t70) cc_final: 0.7592 (t70) REVERT: F 202 ASP cc_start: 0.8195 (t0) cc_final: 0.7873 (t0) REVERT: G 21 ARG cc_start: 0.8366 (mtp180) cc_final: 0.8129 (mtp180) REVERT: G 50 ILE cc_start: 0.9279 (pt) cc_final: 0.8937 (pp) REVERT: G 80 MET cc_start: 0.8759 (mmm) cc_final: 0.7883 (mmt) REVERT: G 125 TYR cc_start: 0.8446 (m-80) cc_final: 0.7642 (m-10) REVERT: H 30 ASN cc_start: 0.8676 (t0) cc_final: 0.8469 (t0) REVERT: H 53 ASP cc_start: 0.8279 (m-30) cc_final: 0.7996 (m-30) REVERT: H 90 TYR cc_start: 0.9198 (m-80) cc_final: 0.8809 (m-80) REVERT: H 93 TYR cc_start: 0.8969 (m-80) cc_final: 0.8640 (m-10) REVERT: H 153 ASN cc_start: 0.8871 (m-40) cc_final: 0.8560 (m-40) REVERT: I 92 ASN cc_start: 0.8875 (t0) cc_final: 0.8455 (t0) REVERT: I 141 CYS cc_start: 0.8115 (p) cc_final: 0.7808 (p) REVERT: I 143 GLU cc_start: 0.7949 (tp30) cc_final: 0.7715 (mm-30) REVERT: I 150 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8518 (mm-30) REVERT: J 8 GLN cc_start: 0.8479 (tt0) cc_final: 0.8086 (tt0) REVERT: J 37 LYS cc_start: 0.8749 (ptmm) cc_final: 0.8430 (ptmm) REVERT: J 90 ASP cc_start: 0.8672 (m-30) cc_final: 0.8263 (m-30) REVERT: J 108 ASP cc_start: 0.8546 (t0) cc_final: 0.7918 (t0) REVERT: K 36 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8408 (mt-10) REVERT: K 40 TYR cc_start: 0.8301 (p90) cc_final: 0.7854 (p90) REVERT: K 70 ASN cc_start: 0.9280 (m-40) cc_final: 0.8919 (m110) REVERT: K 81 LYS cc_start: 0.9045 (tptt) cc_final: 0.8778 (tmtm) REVERT: K 93 MET cc_start: 0.8617 (mtp) cc_final: 0.8383 (mtm) REVERT: K 154 ASP cc_start: 0.8509 (m-30) cc_final: 0.8218 (m-30) REVERT: L 144 MET cc_start: 0.8760 (mtp) cc_final: 0.8510 (mtt) REVERT: L 177 ASP cc_start: 0.7976 (m-30) cc_final: 0.7539 (m-30) REVERT: M 22 ILE cc_start: 0.9063 (pt) cc_final: 0.8567 (pt) REVERT: M 30 TYR cc_start: 0.8314 (t80) cc_final: 0.7869 (t80) REVERT: M 104 ASN cc_start: 0.8857 (t0) cc_final: 0.8298 (t0) REVERT: M 189 ILE cc_start: 0.9148 (mt) cc_final: 0.8878 (tp) REVERT: M 200 GLU cc_start: 0.7500 (mp0) cc_final: 0.7153 (mp0) REVERT: M 208 ASN cc_start: 0.8935 (t0) cc_final: 0.8070 (t0) REVERT: M 210 ASP cc_start: 0.8338 (p0) cc_final: 0.8095 (p0) REVERT: N 61 TYR cc_start: 0.9127 (t80) cc_final: 0.8737 (t80) REVERT: N 84 LYS cc_start: 0.9173 (ttpt) cc_final: 0.8942 (ttmm) REVERT: O 118 GLN cc_start: 0.9267 (tm-30) cc_final: 0.8817 (tm-30) REVERT: O 211 ILE cc_start: 0.9572 (pt) cc_final: 0.9364 (pp) REVERT: P 48 GLU cc_start: 0.8496 (tt0) cc_final: 0.8151 (tm-30) REVERT: P 108 GLU cc_start: 0.8471 (tt0) cc_final: 0.8125 (tt0) REVERT: P 219 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7859 (mp0) REVERT: Q 4 ASP cc_start: 0.8237 (m-30) cc_final: 0.8035 (m-30) REVERT: Q 55 ASP cc_start: 0.7781 (t0) cc_final: 0.7532 (t0) REVERT: Q 90 GLU cc_start: 0.8477 (tp30) cc_final: 0.7722 (tp30) REVERT: Q 99 GLU cc_start: 0.7305 (mp0) cc_final: 0.6446 (mp0) REVERT: Q 116 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8434 (tp40) REVERT: Q 121 SER cc_start: 0.8982 (t) cc_final: 0.8572 (p) REVERT: Q 148 ASP cc_start: 0.8646 (m-30) cc_final: 0.8133 (m-30) REVERT: Q 153 TYR cc_start: 0.9343 (p90) cc_final: 0.9143 (p90) REVERT: Q 211 MET cc_start: 0.8496 (ttp) cc_final: 0.7100 (ttt) REVERT: Q 215 GLN cc_start: 0.8749 (mt0) cc_final: 0.8542 (mt0) REVERT: R 32 LYS cc_start: 0.9074 (mttt) cc_final: 0.8592 (mtmt) REVERT: R 78 MET cc_start: 0.9025 (ptp) cc_final: 0.8366 (ptp) REVERT: R 86 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8379 (mmmm) REVERT: R 122 GLN cc_start: 0.8519 (mt0) cc_final: 0.8211 (mt0) REVERT: R 166 ASP cc_start: 0.8399 (m-30) cc_final: 0.8016 (m-30) REVERT: S 16 GLN cc_start: 0.8772 (mp-120) cc_final: 0.8333 (mp10) REVERT: S 49 LEU cc_start: 0.9255 (mt) cc_final: 0.9042 (tt) REVERT: S 61 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8723 (mppt) REVERT: S 62 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8388 (mmmt) REVERT: S 86 ASN cc_start: 0.8875 (m-40) cc_final: 0.8586 (m-40) REVERT: S 90 GLN cc_start: 0.8774 (tp-100) cc_final: 0.8574 (tp40) REVERT: S 159 MET cc_start: 0.9139 (tpt) cc_final: 0.8934 (mmm) REVERT: U 83 MET cc_start: 0.8858 (mtt) cc_final: 0.8609 (mtm) REVERT: U 86 ASP cc_start: 0.9049 (m-30) cc_final: 0.8562 (m-30) REVERT: U 214 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8317 (tp30) REVERT: U 234 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8298 (mt-10) REVERT: V 28 ASP cc_start: 0.8466 (t0) cc_final: 0.7751 (t0) REVERT: V 29 LYS cc_start: 0.9443 (mtmm) cc_final: 0.9100 (mtmm) REVERT: V 54 MET cc_start: 0.8721 (mmt) cc_final: 0.8518 (mmp) REVERT: V 82 MET cc_start: 0.9035 (mtt) cc_final: 0.8539 (mtt) REVERT: V 121 LYS cc_start: 0.9325 (ttpt) cc_final: 0.9060 (ttpp) REVERT: V 146 MET cc_start: 0.8838 (mtm) cc_final: 0.8614 (mtp) REVERT: W 11 MET cc_start: 0.8555 (ttp) cc_final: 0.8339 (ttp) REVERT: W 67 LYS cc_start: 0.8721 (tptt) cc_final: 0.8393 (tptp) REVERT: W 71 ASN cc_start: 0.8895 (m-40) cc_final: 0.8626 (m110) REVERT: W 77 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8090 (mm-30) REVERT: W 88 SER cc_start: 0.9054 (m) cc_final: 0.8820 (m) REVERT: W 95 TYR cc_start: 0.9352 (t80) cc_final: 0.9113 (t80) REVERT: W 103 TYR cc_start: 0.9049 (m-80) cc_final: 0.8826 (m-80) REVERT: W 105 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8234 (mm-30) REVERT: W 154 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8324 (mt-10) REVERT: W 157 MET cc_start: 0.8782 (mtm) cc_final: 0.8451 (mtp) REVERT: W 177 ASP cc_start: 0.8704 (t70) cc_final: 0.8267 (t0) REVERT: X 27 GLN cc_start: 0.8220 (pt0) cc_final: 0.7736 (pp30) REVERT: X 41 LYS cc_start: 0.8993 (mttp) cc_final: 0.8606 (mttt) REVERT: X 71 ASN cc_start: 0.8378 (m-40) cc_final: 0.7942 (m-40) REVERT: X 108 ASP cc_start: 0.8187 (t0) cc_final: 0.7519 (t0) REVERT: X 165 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7933 (mt-10) REVERT: X 166 GLU cc_start: 0.8411 (tp30) cc_final: 0.8149 (tp30) REVERT: Y 62 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8860 (mm110) REVERT: Y 67 GLU cc_start: 0.9003 (tt0) cc_final: 0.8793 (tt0) REVERT: Z 130 TYR cc_start: 0.8982 (p90) cc_final: 0.8608 (p90) REVERT: Z 144 MET cc_start: 0.9043 (mtp) cc_final: 0.8625 (mtt) REVERT: Z 177 ASP cc_start: 0.8118 (m-30) cc_final: 0.7871 (m-30) REVERT: Z 188 TYR cc_start: 0.9273 (m-80) cc_final: 0.8837 (m-80) REVERT: a 59 ASP cc_start: 0.9008 (m-30) cc_final: 0.8724 (m-30) REVERT: a 64 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8535 (ttmt) REVERT: b 85 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8333 (mm-30) REVERT: b 90 TYR cc_start: 0.8901 (m-80) cc_final: 0.8634 (m-80) REVERT: b 110 GLN cc_start: 0.8583 (mt0) cc_final: 0.8288 (mt0) REVERT: b 174 ILE cc_start: 0.9432 (mt) cc_final: 0.9203 (mt) REVERT: d 42 TYR cc_start: 0.9003 (t80) cc_final: 0.8725 (t80) REVERT: d 56 ASP cc_start: 0.8260 (t70) cc_final: 0.7883 (p0) REVERT: d 97 ASN cc_start: 0.8694 (t0) cc_final: 0.8482 (t160) REVERT: d 173 ASP cc_start: 0.8646 (p0) cc_final: 0.8309 (p0) REVERT: d 185 MET cc_start: 0.8792 (mmp) cc_final: 0.8564 (mmp) REVERT: d 210 ARG cc_start: 0.8992 (ttp-170) cc_final: 0.8773 (ttp80) REVERT: d 217 TYR cc_start: 0.8824 (t80) cc_final: 0.8600 (t80) REVERT: c 11 GLN cc_start: 0.8954 (tt0) cc_final: 0.8751 (tm-30) REVERT: c 15 ASP cc_start: 0.8667 (m-30) cc_final: 0.6860 (m-30) REVERT: c 26 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8554 (mt-10) REVERT: c 123 ASP cc_start: 0.8256 (m-30) cc_final: 0.7903 (m-30) REVERT: c 183 ASP cc_start: 0.9051 (m-30) cc_final: 0.8721 (m-30) REVERT: c 187 LYS cc_start: 0.9335 (mttt) cc_final: 0.9132 (mtpm) REVERT: c 208 GLU cc_start: 0.8824 (tp30) cc_final: 0.8335 (tp30) REVERT: f 97 ASN cc_start: 0.9081 (t0) cc_final: 0.8785 (t0) REVERT: f 173 ASP cc_start: 0.9105 (m-30) cc_final: 0.8736 (m-30) REVERT: f 217 TYR cc_start: 0.9143 (t80) cc_final: 0.8898 (t80) REVERT: f 229 ASN cc_start: 0.8846 (t0) cc_final: 0.8584 (t0) REVERT: e 115 GLN cc_start: 0.9097 (mm110) cc_final: 0.8852 (tp40) REVERT: e 173 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8429 (tm-30) REVERT: e 183 ASP cc_start: 0.8684 (m-30) cc_final: 0.8445 (m-30) REVERT: e 227 TYR cc_start: 0.9299 (t80) cc_final: 0.9089 (t80) REVERT: h 34 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.8048 (mtm-85) REVERT: h 61 ARG cc_start: 0.9304 (ttm-80) cc_final: 0.9047 (mtp-110) REVERT: h 205 MET cc_start: 0.8734 (mtm) cc_final: 0.8428 (ttp) REVERT: h 229 ASN cc_start: 0.8846 (t0) cc_final: 0.8500 (t0) REVERT: g 41 ASP cc_start: 0.8791 (p0) cc_final: 0.8472 (p0) REVERT: g 107 ASN cc_start: 0.8794 (t0) cc_final: 0.8323 (t0) REVERT: g 116 ARG cc_start: 0.7966 (ptm160) cc_final: 0.7722 (ptm160) REVERT: g 120 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8412 (mp0) REVERT: g 123 ASP cc_start: 0.8947 (m-30) cc_final: 0.8636 (m-30) REVERT: g 172 THR cc_start: 0.9429 (m) cc_final: 0.9176 (p) REVERT: g 183 ASP cc_start: 0.9288 (m-30) cc_final: 0.9032 (m-30) REVERT: g 199 GLN cc_start: 0.9290 (mm110) cc_final: 0.8770 (mp10) REVERT: g 208 GLU cc_start: 0.8680 (tp30) cc_final: 0.7993 (tp30) REVERT: i 10 SER cc_start: 0.9036 (p) cc_final: 0.8785 (p) REVERT: i 22 GLN cc_start: 0.9078 (pt0) cc_final: 0.8756 (pp30) REVERT: i 23 ASN cc_start: 0.9130 (m110) cc_final: 0.8379 (m-40) REVERT: i 38 GLN cc_start: 0.8869 (mt0) cc_final: 0.8632 (mt0) REVERT: i 42 TYR cc_start: 0.8812 (t80) cc_final: 0.8453 (t80) REVERT: i 44 ASN cc_start: 0.8744 (t0) cc_final: 0.8444 (t0) REVERT: i 48 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8757 (mt0) REVERT: i 112 TRP cc_start: 0.8957 (m100) cc_final: 0.8721 (m100) REVERT: i 145 LYS cc_start: 0.9245 (tttp) cc_final: 0.8988 (tppp) REVERT: i 165 SER cc_start: 0.9556 (m) cc_final: 0.9303 (p) REVERT: i 210 ARG cc_start: 0.9134 (ttp-170) cc_final: 0.8904 (ttp80) REVERT: i 217 TYR cc_start: 0.9255 (t80) cc_final: 0.9002 (t80) REVERT: i 221 SER cc_start: 0.9570 (t) cc_final: 0.9363 (m) outliers start: 0 outliers final: 1 residues processed: 1659 average time/residue: 1.4834 time to fit residues: 3079.0461 Evaluate side-chains 1170 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1169 time to evaluate : 4.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 50 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 640 optimal weight: 6.9990 chunk 575 optimal weight: 8.9990 chunk 319 optimal weight: 1.9990 chunk 196 optimal weight: 0.0670 chunk 388 optimal weight: 9.9990 chunk 307 optimal weight: 0.2980 chunk 594 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 361 optimal weight: 3.9990 chunk 442 optimal weight: 9.9990 chunk 689 optimal weight: 8.9990 overall best weight: 2.0724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 95 GLN A 101 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN F 101 ASN G 24 GLN G 75 ASN G 128 ASN J 55 GLN J 63 ASN J 87 ASN J 101 ASN K 62 GLN L 8 ASN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN M 81 HIS N 123 GLN O 95 GLN ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 HIS P 84 ASN P 100 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 GLN Q 120 GLN Q 175 ASN Q 205 ASN R 204 GLN R 225 ASN S 65 HIS S 68 ASN S 121 GLN ** S 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 110 HIS U 128 ASN V 57 GLN W 6 ASN W 39 GLN X 63 ASN a 3 ASN d 183 HIS c 129 ASN ** c 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 22 GLN f 143 GLN e 11 GLN e 136 GLN e 138 GLN e 147 ASN e 153 GLN h 23 ASN h 38 GLN h 126 GLN h 143 GLN g 136 GLN g 138 GLN g 171 HIS g 193 HIS i 53 ASN i 127 HIS i 151 ASN i 183 HIS i 229 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 59176 Z= 0.276 Angle : 0.627 9.424 80293 Z= 0.338 Chirality : 0.044 0.213 9335 Planarity : 0.005 0.068 10242 Dihedral : 4.895 52.835 8444 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.54 % Favored : 98.45 % Rotamer: Outliers : 2.15 % Allowed : 12.51 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.09), residues: 7657 helix: 2.14 (0.08), residues: 3413 sheet: 0.47 (0.12), residues: 1471 loop : -0.11 (0.11), residues: 2773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP T 215 HIS 0.011 0.001 HIS D 73 PHE 0.024 0.002 PHE b 65 TYR 0.025 0.002 TYR G 160 ARG 0.009 0.001 ARG J 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1240 time to evaluate : 5.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8809 (pt0) cc_final: 0.8585 (pt0) REVERT: A 165 ASN cc_start: 0.8782 (m110) cc_final: 0.7991 (t0) REVERT: B 15 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7884 (mm-30) REVERT: B 26 GLU cc_start: 0.8800 (tp30) cc_final: 0.8423 (mm-30) REVERT: B 49 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.7911 (ttm110) REVERT: B 67 LYS cc_start: 0.8490 (ttpt) cc_final: 0.8173 (tttt) REVERT: B 69 ASN cc_start: 0.8486 (t0) cc_final: 0.8096 (t0) REVERT: B 72 MET cc_start: 0.8346 (ptm) cc_final: 0.8084 (mtp) REVERT: B 103 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7851 (mt-10) REVERT: B 108 GLU cc_start: 0.8566 (tt0) cc_final: 0.8253 (tt0) REVERT: C 13 ASP cc_start: 0.8347 (m-30) cc_final: 0.8146 (m-30) REVERT: C 28 LYS cc_start: 0.9024 (mttm) cc_final: 0.8581 (mttm) REVERT: C 54 GLN cc_start: 0.8625 (tt0) cc_final: 0.8161 (mm110) REVERT: C 55 ASP cc_start: 0.8021 (t0) cc_final: 0.7768 (t0) REVERT: C 67 ASP cc_start: 0.8011 (p0) cc_final: 0.7747 (p0) REVERT: C 93 SER cc_start: 0.9110 (t) cc_final: 0.8888 (t) REVERT: C 105 GLU cc_start: 0.8466 (tt0) cc_final: 0.8147 (tt0) REVERT: C 137 ASP cc_start: 0.7929 (p0) cc_final: 0.7698 (p0) REVERT: C 146 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: C 206 ILE cc_start: 0.9105 (pt) cc_final: 0.8858 (mp) REVERT: D 32 LYS cc_start: 0.9052 (mtpp) cc_final: 0.8753 (mmmm) REVERT: D 95 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8124 (mm-30) REVERT: D 166 ASP cc_start: 0.8730 (m-30) cc_final: 0.8420 (m-30) REVERT: E 9 ASP cc_start: 0.7928 (t70) cc_final: 0.7653 (t0) REVERT: E 137 TYR cc_start: 0.9007 (t80) cc_final: 0.8674 (t80) REVERT: E 138 ASP cc_start: 0.7715 (p0) cc_final: 0.7498 (p0) REVERT: E 178 GLU cc_start: 0.8597 (pm20) cc_final: 0.8313 (pm20) REVERT: G 21 ARG cc_start: 0.8516 (mtp180) cc_final: 0.8295 (mtm110) REVERT: G 26 GLU cc_start: 0.8197 (mp0) cc_final: 0.7955 (mp0) REVERT: G 83 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.7970 (mtm) REVERT: G 113 MET cc_start: 0.9137 (mmm) cc_final: 0.8899 (mmm) REVERT: H 90 TYR cc_start: 0.9179 (m-80) cc_final: 0.8753 (m-80) REVERT: H 93 TYR cc_start: 0.8862 (m-80) cc_final: 0.8655 (m-10) REVERT: H 143 ARG cc_start: 0.8055 (ptt90) cc_final: 0.6922 (ptt90) REVERT: H 157 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8009 (mm-30) REVERT: I 92 ASN cc_start: 0.8974 (t0) cc_final: 0.8566 (t0) REVERT: I 105 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7938 (mm-30) REVERT: I 190 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7483 (mp0) REVERT: J 2 GLU cc_start: 0.8346 (mp0) cc_final: 0.8098 (mt-10) REVERT: J 8 GLN cc_start: 0.8612 (tt0) cc_final: 0.8183 (tt0) REVERT: J 37 LYS cc_start: 0.8891 (ptmm) cc_final: 0.8689 (ptmm) REVERT: J 90 ASP cc_start: 0.8746 (m-30) cc_final: 0.8314 (m-30) REVERT: J 102 LEU cc_start: 0.9235 (mt) cc_final: 0.8846 (mp) REVERT: J 108 ASP cc_start: 0.8460 (t0) cc_final: 0.7589 (t0) REVERT: J 111 GLU cc_start: 0.8395 (mp0) cc_final: 0.7849 (mp0) REVERT: J 161 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7864 (ttp-170) REVERT: J 165 GLU cc_start: 0.7798 (tp30) cc_final: 0.7542 (tp30) REVERT: K 40 TYR cc_start: 0.8274 (p90) cc_final: 0.8011 (p90) REVERT: K 70 ASN cc_start: 0.9338 (m-40) cc_final: 0.8850 (m110) REVERT: K 81 LYS cc_start: 0.9047 (tptt) cc_final: 0.8534 (tmtt) REVERT: L 125 ASP cc_start: 0.8838 (p0) cc_final: 0.8585 (p0) REVERT: M 30 TYR cc_start: 0.8457 (t80) cc_final: 0.8024 (t80) REVERT: M 104 ASN cc_start: 0.9021 (t0) cc_final: 0.8426 (t0) REVERT: M 200 GLU cc_start: 0.7525 (mp0) cc_final: 0.7238 (mp0) REVERT: M 208 ASN cc_start: 0.8944 (t0) cc_final: 0.8020 (t0) REVERT: M 210 ASP cc_start: 0.8344 (p0) cc_final: 0.8080 (p0) REVERT: N 61 TYR cc_start: 0.9217 (t80) cc_final: 0.8748 (t80) REVERT: N 86 MET cc_start: 0.9161 (mtp) cc_final: 0.8923 (ttm) REVERT: N 95 MET cc_start: 0.8109 (tpp) cc_final: 0.7834 (tpp) REVERT: O 48 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: O 118 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8746 (tm-30) REVERT: O 224 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8520 (mp0) REVERT: P 26 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8108 (mp0) REVERT: P 48 GLU cc_start: 0.8358 (tt0) cc_final: 0.8088 (tm-30) REVERT: P 108 GLU cc_start: 0.8461 (tt0) cc_final: 0.8088 (tt0) REVERT: Q 24 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7965 (tm-30) REVERT: Q 55 ASP cc_start: 0.7832 (t0) cc_final: 0.7544 (t0) REVERT: Q 90 GLU cc_start: 0.8666 (tp30) cc_final: 0.8152 (tp30) REVERT: Q 99 GLU cc_start: 0.7404 (mp0) cc_final: 0.6819 (mp0) REVERT: Q 116 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8504 (tp40) REVERT: Q 121 SER cc_start: 0.8914 (t) cc_final: 0.8483 (p) REVERT: Q 122 ASN cc_start: 0.8799 (m-40) cc_final: 0.8416 (m-40) REVERT: Q 153 TYR cc_start: 0.9462 (p90) cc_final: 0.9223 (p90) REVERT: Q 205 ASN cc_start: 0.8261 (t0) cc_final: 0.8033 (t160) REVERT: Q 215 GLN cc_start: 0.8860 (mt0) cc_final: 0.8568 (mt0) REVERT: R 20 ARG cc_start: 0.8115 (pmm-80) cc_final: 0.7751 (mpp80) REVERT: R 78 MET cc_start: 0.9021 (ptp) cc_final: 0.8242 (ptp) REVERT: R 86 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8428 (mmmm) REVERT: R 122 GLN cc_start: 0.8620 (mt0) cc_final: 0.8286 (mt0) REVERT: R 143 PHE cc_start: 0.9459 (m-80) cc_final: 0.9166 (m-10) REVERT: R 166 ASP cc_start: 0.8312 (m-30) cc_final: 0.8021 (m-30) REVERT: S 16 GLN cc_start: 0.8854 (mp-120) cc_final: 0.8413 (mp10) REVERT: S 90 GLN cc_start: 0.8934 (tp-100) cc_final: 0.8704 (tp40) REVERT: U 214 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8348 (tp30) REVERT: V 29 LYS cc_start: 0.9405 (mtmm) cc_final: 0.8873 (mtmm) REVERT: V 82 MET cc_start: 0.9029 (mtt) cc_final: 0.8558 (mtt) REVERT: V 121 LYS cc_start: 0.9286 (ttpt) cc_final: 0.9041 (ttpp) REVERT: V 146 MET cc_start: 0.8783 (mtm) cc_final: 0.8297 (mtp) REVERT: W 11 MET cc_start: 0.8505 (ttp) cc_final: 0.8302 (ttp) REVERT: W 88 SER cc_start: 0.9085 (m) cc_final: 0.8587 (p) REVERT: W 98 ARG cc_start: 0.9262 (tpt90) cc_final: 0.8898 (tpt90) REVERT: W 105 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8180 (mm-30) REVERT: W 154 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8289 (pt0) REVERT: W 157 MET cc_start: 0.8842 (mtm) cc_final: 0.8602 (mtp) REVERT: W 177 ASP cc_start: 0.8727 (t70) cc_final: 0.8301 (t0) REVERT: X 27 GLN cc_start: 0.8503 (pt0) cc_final: 0.7873 (pp30) REVERT: X 37 LYS cc_start: 0.8937 (tttt) cc_final: 0.8675 (tttp) REVERT: X 41 LYS cc_start: 0.8960 (mttp) cc_final: 0.8594 (mttm) REVERT: X 69 MET cc_start: 0.8670 (mmm) cc_final: 0.8406 (mmp) REVERT: X 90 ASP cc_start: 0.8612 (m-30) cc_final: 0.8367 (m-30) REVERT: X 108 ASP cc_start: 0.8086 (t0) cc_final: 0.7651 (t0) REVERT: X 141 SER cc_start: 0.9017 (m) cc_final: 0.8797 (p) REVERT: X 151 ILE cc_start: 0.9312 (tt) cc_final: 0.8758 (pp) REVERT: Y 62 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8957 (mm110) REVERT: Y 81 LYS cc_start: 0.8948 (tptm) cc_final: 0.8464 (tptm) REVERT: Z 130 TYR cc_start: 0.9074 (p90) cc_final: 0.8717 (p90) REVERT: Z 186 ASP cc_start: 0.8289 (t0) cc_final: 0.8021 (t0) REVERT: b 88 TYR cc_start: 0.8975 (t80) cc_final: 0.8704 (t80) REVERT: b 90 TYR cc_start: 0.8925 (m-80) cc_final: 0.8630 (m-80) REVERT: d 36 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9106 (tt) REVERT: d 42 TYR cc_start: 0.9125 (t80) cc_final: 0.8815 (t80) REVERT: d 53 ASN cc_start: 0.9439 (t0) cc_final: 0.9041 (m-40) REVERT: d 56 ASP cc_start: 0.8395 (t70) cc_final: 0.7960 (p0) REVERT: d 173 ASP cc_start: 0.8633 (p0) cc_final: 0.8273 (p0) REVERT: d 185 MET cc_start: 0.8654 (mmp) cc_final: 0.8173 (mmp) REVERT: d 186 ASP cc_start: 0.8658 (p0) cc_final: 0.8151 (p0) REVERT: d 201 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8224 (tp30) REVERT: c 11 GLN cc_start: 0.8886 (tt0) cc_final: 0.8678 (tp40) REVERT: c 15 ASP cc_start: 0.8979 (m-30) cc_final: 0.7720 (m-30) REVERT: c 123 ASP cc_start: 0.8404 (m-30) cc_final: 0.8170 (m-30) REVERT: c 164 HIS cc_start: 0.9002 (t70) cc_final: 0.8799 (t-90) REVERT: c 191 GLN cc_start: 0.8823 (mp-120) cc_final: 0.8315 (mm110) REVERT: c 208 GLU cc_start: 0.8926 (tp30) cc_final: 0.8697 (tp30) REVERT: f 22 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8355 (pp30) REVERT: f 26 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7693 (tp-100) REVERT: f 38 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8629 (mp10) REVERT: f 97 ASN cc_start: 0.9220 (t0) cc_final: 0.8920 (t0) REVERT: f 173 ASP cc_start: 0.9146 (m-30) cc_final: 0.8778 (m-30) REVERT: f 194 ARG cc_start: 0.9006 (mpt90) cc_final: 0.8792 (mpt-90) REVERT: f 201 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8513 (mm-30) REVERT: f 229 ASN cc_start: 0.8854 (t0) cc_final: 0.8527 (t0) REVERT: e 32 TYR cc_start: 0.8928 (t80) cc_final: 0.8454 (t80) REVERT: e 115 GLN cc_start: 0.9187 (mm110) cc_final: 0.8962 (tp40) REVERT: e 123 ASP cc_start: 0.8801 (m-30) cc_final: 0.8332 (t0) REVERT: e 147 ASN cc_start: 0.9134 (m-40) cc_final: 0.8871 (m-40) REVERT: e 173 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8450 (tm-30) REVERT: h 16 GLN cc_start: 0.8624 (mt0) cc_final: 0.8171 (mt0) REVERT: h 22 GLN cc_start: 0.8492 (mm110) cc_final: 0.8286 (mm-40) REVERT: h 23 ASN cc_start: 0.9334 (m-40) cc_final: 0.8984 (m110) REVERT: h 38 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8284 (mp10) REVERT: h 161 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8293 (tm-30) REVERT: h 203 ARG cc_start: 0.9218 (ttt-90) cc_final: 0.8729 (mmm-85) REVERT: h 229 ASN cc_start: 0.8836 (t0) cc_final: 0.8489 (t0) REVERT: g 41 ASP cc_start: 0.8810 (p0) cc_final: 0.8476 (p0) REVERT: g 43 PHE cc_start: 0.9105 (t80) cc_final: 0.8825 (t80) REVERT: g 107 ASN cc_start: 0.8868 (t0) cc_final: 0.8348 (t0) REVERT: g 115 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8772 (mm-40) REVERT: g 116 ARG cc_start: 0.8409 (ptm160) cc_final: 0.7814 (ptm160) REVERT: g 120 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8399 (mp0) REVERT: g 123 ASP cc_start: 0.8957 (m-30) cc_final: 0.8597 (m-30) REVERT: g 160 MET cc_start: 0.8543 (mtt) cc_final: 0.8083 (mpp) REVERT: g 173 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7809 (tm-30) REVERT: g 180 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8286 (mm-30) REVERT: g 183 ASP cc_start: 0.9467 (m-30) cc_final: 0.9109 (m-30) REVERT: g 199 GLN cc_start: 0.9226 (mm110) cc_final: 0.8828 (mp10) REVERT: i 22 GLN cc_start: 0.9075 (pt0) cc_final: 0.8762 (pp30) REVERT: i 23 ASN cc_start: 0.9149 (m110) cc_final: 0.8319 (m-40) REVERT: i 26 GLN cc_start: 0.8339 (pp30) cc_final: 0.8119 (pp30) REVERT: i 38 GLN cc_start: 0.9041 (mt0) cc_final: 0.8702 (mt0) REVERT: i 151 ASN cc_start: 0.8960 (m-40) cc_final: 0.8741 (m110) REVERT: i 205 MET cc_start: 0.9258 (ttp) cc_final: 0.8973 (tpp) REVERT: i 208 ASP cc_start: 0.9206 (m-30) cc_final: 0.8936 (m-30) REVERT: i 217 TYR cc_start: 0.9294 (t80) cc_final: 0.9010 (t80) REVERT: i 221 SER cc_start: 0.9593 (t) cc_final: 0.9384 (m) REVERT: i 238 MET cc_start: 0.8575 (ptt) cc_final: 0.8268 (ptm) outliers start: 123 outliers final: 32 residues processed: 1293 average time/residue: 1.4639 time to fit residues: 2390.4297 Evaluate side-chains 1167 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1128 time to evaluate : 5.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 181 ASN Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain O residue 48 GLU Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain Q residue 221 ASN Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain T residue 144 ASP Chi-restraints excluded: chain V residue 91 GLN Chi-restraints excluded: chain V residue 118 SER Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 62 LYS Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain Y residue 1 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 54 CYS Chi-restraints excluded: chain b residue 106 GLN Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain f residue 21 ARG Chi-restraints excluded: chain f residue 38 GLN Chi-restraints excluded: chain f residue 144 GLU Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain h residue 38 GLN Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain g residue 128 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 383 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 573 optimal weight: 8.9990 chunk 469 optimal weight: 7.9990 chunk 190 optimal weight: 0.7980 chunk 690 optimal weight: 2.9990 chunk 745 optimal weight: 9.9990 chunk 614 optimal weight: 6.9990 chunk 684 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 553 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 147 GLN A 206 ASN B 198 ASN B 240 HIS E 16 GLN F 101 ASN J 55 GLN J 87 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN L 8 ASN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 GLN O 95 GLN P 30 HIS ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 240 HIS ** S 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 HIS S 86 ASN S 121 GLN ** S 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 24 GLN V 57 GLN ** V 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 ASN Z 131 GLN ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 127 HIS c 129 ASN ** c 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 16 GLN ** f 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 11 GLN e 136 GLN h 38 GLN h 143 GLN h 192 HIS g 11 GLN g 136 GLN i 16 GLN ** i 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 53 ASN i 127 HIS i 143 GLN ** i 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 59176 Z= 0.391 Angle : 0.649 8.616 80293 Z= 0.348 Chirality : 0.045 0.229 9335 Planarity : 0.005 0.062 10242 Dihedral : 4.814 51.179 8442 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.01 % Favored : 97.98 % Rotamer: Outliers : 2.79 % Allowed : 15.09 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: 1.47 (0.09), residues: 7657 helix: 2.15 (0.08), residues: 3425 sheet: 0.32 (0.13), residues: 1486 loop : -0.07 (0.12), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 215 HIS 0.008 0.001 HIS D 73 PHE 0.030 0.002 PHE F 135 TYR 0.032 0.002 TYR G 160 ARG 0.010 0.001 ARG h 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1338 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1178 time to evaluate : 5.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8826 (pt0) cc_final: 0.8617 (pt0) REVERT: A 95 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 165 ASN cc_start: 0.8773 (m110) cc_final: 0.8044 (t0) REVERT: A 206 ASN cc_start: 0.8892 (m-40) cc_final: 0.8675 (m-40) REVERT: B 26 GLU cc_start: 0.8798 (tp30) cc_final: 0.8453 (mm-30) REVERT: B 49 ARG cc_start: 0.8299 (mtp-110) cc_final: 0.7914 (ttm110) REVERT: B 67 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8210 (tttt) REVERT: B 69 ASN cc_start: 0.8762 (t0) cc_final: 0.8305 (t0) REVERT: B 72 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8216 (mtp) REVERT: B 103 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7854 (mt-10) REVERT: B 108 GLU cc_start: 0.8653 (tt0) cc_final: 0.8361 (tt0) REVERT: B 174 MET cc_start: 0.8523 (mtp) cc_final: 0.7988 (ttm) REVERT: B 178 ASP cc_start: 0.9055 (m-30) cc_final: 0.8557 (m-30) REVERT: B 184 MET cc_start: 0.8214 (tpp) cc_final: 0.7943 (mpt) REVERT: C 28 LYS cc_start: 0.9053 (mttm) cc_final: 0.8511 (mttp) REVERT: C 54 GLN cc_start: 0.8732 (tt0) cc_final: 0.8156 (mm110) REVERT: C 55 ASP cc_start: 0.8040 (t0) cc_final: 0.7760 (t0) REVERT: C 66 ASP cc_start: 0.8589 (t0) cc_final: 0.8329 (t0) REVERT: C 93 SER cc_start: 0.9166 (t) cc_final: 0.8894 (t) REVERT: C 105 GLU cc_start: 0.8547 (tt0) cc_final: 0.8272 (tt0) REVERT: C 137 ASP cc_start: 0.7940 (p0) cc_final: 0.7632 (p0) REVERT: D 166 ASP cc_start: 0.8756 (m-30) cc_final: 0.8461 (m-30) REVERT: E 9 ASP cc_start: 0.7925 (t0) cc_final: 0.7621 (t0) REVERT: E 60 GLN cc_start: 0.8364 (pt0) cc_final: 0.7524 (pp30) REVERT: E 137 TYR cc_start: 0.8980 (t80) cc_final: 0.8636 (t80) REVERT: E 138 ASP cc_start: 0.7866 (p0) cc_final: 0.7636 (p0) REVERT: E 178 GLU cc_start: 0.8791 (pm20) cc_final: 0.8485 (pm20) REVERT: F 70 ASP cc_start: 0.8612 (t0) cc_final: 0.8019 (t0) REVERT: G 26 GLU cc_start: 0.8297 (mp0) cc_final: 0.7995 (mp0) REVERT: G 80 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7460 (mmt) REVERT: G 83 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8150 (mtm) REVERT: G 88 ARG cc_start: 0.8455 (mmt90) cc_final: 0.8212 (mmt90) REVERT: G 113 MET cc_start: 0.9167 (mmm) cc_final: 0.8894 (mmm) REVERT: G 131 MET cc_start: 0.7806 (ttp) cc_final: 0.7560 (ttp) REVERT: H 93 TYR cc_start: 0.8946 (m-80) cc_final: 0.8729 (m-10) REVERT: H 139 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: H 143 ARG cc_start: 0.8317 (ptt90) cc_final: 0.8030 (ptt90) REVERT: H 150 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: H 157 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7998 (mm-30) REVERT: I 39 GLN cc_start: 0.9106 (tt0) cc_final: 0.8712 (tm-30) REVERT: I 92 ASN cc_start: 0.8996 (t0) cc_final: 0.8599 (t0) REVERT: I 105 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8007 (mm-30) REVERT: I 190 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7717 (mp0) REVERT: J 2 GLU cc_start: 0.8279 (mp0) cc_final: 0.8025 (mt-10) REVERT: J 8 GLN cc_start: 0.8744 (tt0) cc_final: 0.8347 (tt0) REVERT: J 90 ASP cc_start: 0.8759 (m-30) cc_final: 0.8325 (m-30) REVERT: J 108 ASP cc_start: 0.8539 (t0) cc_final: 0.8194 (t0) REVERT: J 161 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7782 (ttp-170) REVERT: J 165 GLU cc_start: 0.7978 (tp30) cc_final: 0.7592 (tp30) REVERT: K 154 ASP cc_start: 0.8689 (m-30) cc_final: 0.8487 (m-30) REVERT: L 198 VAL cc_start: 0.9636 (OUTLIER) cc_final: 0.9419 (m) REVERT: M 30 TYR cc_start: 0.8586 (t80) cc_final: 0.8141 (t80) REVERT: M 104 ASN cc_start: 0.9071 (t0) cc_final: 0.8437 (t0) REVERT: M 110 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8638 (mtm) REVERT: M 200 GLU cc_start: 0.7717 (mp0) cc_final: 0.7382 (mp0) REVERT: M 208 ASN cc_start: 0.9006 (t0) cc_final: 0.8081 (t0) REVERT: M 210 ASP cc_start: 0.8453 (p0) cc_final: 0.8223 (p0) REVERT: N 61 TYR cc_start: 0.9327 (t80) cc_final: 0.8884 (t80) REVERT: N 86 MET cc_start: 0.9171 (mtp) cc_final: 0.8924 (ttm) REVERT: O 48 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: O 118 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8844 (tm-30) REVERT: O 224 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: P 22 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: P 26 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8137 (mp0) REVERT: P 48 GLU cc_start: 0.8413 (tt0) cc_final: 0.8158 (tm-30) REVERT: P 108 GLU cc_start: 0.8573 (tt0) cc_final: 0.8242 (tt0) REVERT: Q 24 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7982 (tm-30) REVERT: Q 52 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8707 (pttp) REVERT: Q 55 ASP cc_start: 0.7792 (t0) cc_final: 0.7468 (t0) REVERT: Q 90 GLU cc_start: 0.8633 (tp30) cc_final: 0.8150 (tp30) REVERT: Q 99 GLU cc_start: 0.7657 (mp0) cc_final: 0.6810 (mp0) REVERT: Q 116 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8452 (tp40) REVERT: Q 122 ASN cc_start: 0.8917 (m-40) cc_final: 0.8642 (m-40) REVERT: Q 148 ASP cc_start: 0.8585 (t0) cc_final: 0.8212 (t0) REVERT: Q 153 TYR cc_start: 0.9502 (p90) cc_final: 0.9264 (p90) REVERT: Q 215 GLN cc_start: 0.8998 (mt0) cc_final: 0.8699 (mt0) REVERT: R 32 LYS cc_start: 0.9133 (mttp) cc_final: 0.8630 (mtmt) REVERT: R 78 MET cc_start: 0.8980 (ptp) cc_final: 0.8331 (ptp) REVERT: R 86 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8459 (mmmm) REVERT: R 166 ASP cc_start: 0.8324 (m-30) cc_final: 0.8048 (m-30) REVERT: S 16 GLN cc_start: 0.8897 (mp-120) cc_final: 0.8388 (mp10) REVERT: S 90 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8751 (tp40) REVERT: S 146 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8731 (tt0) REVERT: U 88 ARG cc_start: 0.8461 (mmm160) cc_final: 0.8159 (mmm160) REVERT: U 180 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8162 (mm-30) REVERT: U 214 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8305 (tp30) REVERT: U 234 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8408 (pt0) REVERT: V 29 LYS cc_start: 0.9392 (mtmm) cc_final: 0.9157 (mtmm) REVERT: V 121 LYS cc_start: 0.9254 (ttpt) cc_final: 0.9045 (ttpp) REVERT: W 88 SER cc_start: 0.9080 (m) cc_final: 0.8655 (p) REVERT: W 98 ARG cc_start: 0.9331 (tpt90) cc_final: 0.8996 (tpt-90) REVERT: W 154 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8257 (pt0) REVERT: W 157 MET cc_start: 0.8847 (mtm) cc_final: 0.8504 (mtp) REVERT: X 27 GLN cc_start: 0.8549 (pt0) cc_final: 0.7879 (pp30) REVERT: X 37 LYS cc_start: 0.8946 (tttt) cc_final: 0.8697 (tttp) REVERT: X 41 LYS cc_start: 0.9059 (mttp) cc_final: 0.8713 (mttt) REVERT: X 69 MET cc_start: 0.8593 (mmm) cc_final: 0.8384 (mmp) REVERT: X 90 ASP cc_start: 0.8659 (m-30) cc_final: 0.8432 (m-30) REVERT: X 108 ASP cc_start: 0.8165 (t0) cc_final: 0.7732 (t0) REVERT: X 141 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8827 (p) REVERT: X 151 ILE cc_start: 0.9354 (tt) cc_final: 0.8764 (pp) REVERT: X 165 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7974 (mt-10) REVERT: Y 62 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8983 (mm110) REVERT: Y 67 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8903 (tt0) REVERT: Y 81 LYS cc_start: 0.9150 (tptm) cc_final: 0.8552 (tptm) REVERT: Z 186 ASP cc_start: 0.8435 (t0) cc_final: 0.8106 (t0) REVERT: a 59 ASP cc_start: 0.8903 (m-30) cc_final: 0.8691 (m-30) REVERT: a 64 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8815 (ttmt) REVERT: b 90 TYR cc_start: 0.8959 (m-80) cc_final: 0.8673 (m-80) REVERT: d 36 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9187 (tt) REVERT: d 42 TYR cc_start: 0.9074 (t80) cc_final: 0.8752 (t80) REVERT: d 50 ASP cc_start: 0.9201 (p0) cc_final: 0.8974 (p0) REVERT: d 53 ASN cc_start: 0.9479 (t0) cc_final: 0.9051 (m-40) REVERT: d 56 ASP cc_start: 0.8390 (t70) cc_final: 0.7969 (p0) REVERT: d 173 ASP cc_start: 0.8631 (p0) cc_final: 0.8258 (p0) REVERT: d 185 MET cc_start: 0.8460 (mmp) cc_final: 0.7977 (mmp) REVERT: d 186 ASP cc_start: 0.8874 (p0) cc_final: 0.8437 (p0) REVERT: d 201 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8276 (tp30) REVERT: c 15 ASP cc_start: 0.8897 (m-30) cc_final: 0.7658 (m-30) REVERT: c 123 ASP cc_start: 0.8420 (m-30) cc_final: 0.8174 (m-30) REVERT: c 164 HIS cc_start: 0.9073 (t70) cc_final: 0.8814 (t-90) REVERT: c 168 GLU cc_start: 0.8479 (tp30) cc_final: 0.7990 (tp30) REVERT: c 173 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8448 (tm-30) REVERT: c 191 GLN cc_start: 0.8866 (mp-120) cc_final: 0.8346 (mm110) REVERT: c 208 GLU cc_start: 0.8933 (tp30) cc_final: 0.8620 (tp30) REVERT: c 228 ASP cc_start: 0.8924 (t70) cc_final: 0.8528 (t70) REVERT: f 22 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8229 (pp30) REVERT: f 23 ASN cc_start: 0.8910 (m-40) cc_final: 0.8321 (m-40) REVERT: f 26 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7762 (tp-100) REVERT: f 38 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8618 (mp10) REVERT: f 173 ASP cc_start: 0.9150 (m-30) cc_final: 0.8826 (m-30) REVERT: f 185 MET cc_start: 0.8680 (mpp) cc_final: 0.8369 (mmp) REVERT: f 194 ARG cc_start: 0.8998 (mpt90) cc_final: 0.8712 (mpt-90) REVERT: f 201 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8525 (mm-30) REVERT: f 208 ASP cc_start: 0.8815 (m-30) cc_final: 0.8566 (m-30) REVERT: f 229 ASN cc_start: 0.8844 (t0) cc_final: 0.8624 (t160) REVERT: e 115 GLN cc_start: 0.9237 (mm110) cc_final: 0.9036 (tp40) REVERT: e 147 ASN cc_start: 0.9135 (m-40) cc_final: 0.8878 (m-40) REVERT: e 173 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8574 (tm-30) REVERT: h 16 GLN cc_start: 0.8570 (mt0) cc_final: 0.8146 (mt0) REVERT: h 22 GLN cc_start: 0.8691 (mm110) cc_final: 0.8348 (mm110) REVERT: h 34 ARG cc_start: 0.8519 (ptp-110) cc_final: 0.8286 (ptp90) REVERT: h 42 TYR cc_start: 0.9183 (t80) cc_final: 0.8800 (t80) REVERT: h 61 ARG cc_start: 0.9157 (mtp-110) cc_final: 0.8945 (ttm110) REVERT: h 151 ASN cc_start: 0.9163 (m-40) cc_final: 0.8928 (m110) REVERT: h 203 ARG cc_start: 0.9149 (ttt-90) cc_final: 0.8725 (mmm-85) REVERT: h 229 ASN cc_start: 0.8821 (t0) cc_final: 0.8378 (t0) REVERT: g 41 ASP cc_start: 0.8788 (p0) cc_final: 0.8497 (p0) REVERT: g 107 ASN cc_start: 0.8946 (t0) cc_final: 0.8411 (t0) REVERT: g 115 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8715 (mm-40) REVERT: g 116 ARG cc_start: 0.8640 (ptm160) cc_final: 0.8106 (ptm160) REVERT: g 120 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8299 (mp0) REVERT: g 123 ASP cc_start: 0.8954 (m-30) cc_final: 0.8601 (m-30) REVERT: g 171 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.8378 (t-170) REVERT: g 173 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8417 (tm-30) REVERT: g 180 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8323 (mm-30) REVERT: g 183 ASP cc_start: 0.9486 (m-30) cc_final: 0.9125 (m-30) REVERT: g 191 GLN cc_start: 0.9104 (mp-120) cc_final: 0.8780 (mp10) REVERT: g 199 GLN cc_start: 0.9244 (mm110) cc_final: 0.8826 (mp10) REVERT: i 22 GLN cc_start: 0.9083 (pt0) cc_final: 0.8727 (pp30) REVERT: i 23 ASN cc_start: 0.9174 (m110) cc_final: 0.8199 (m-40) REVERT: i 26 GLN cc_start: 0.8427 (pp30) cc_final: 0.8139 (pp30) REVERT: i 38 GLN cc_start: 0.9024 (mt0) cc_final: 0.8671 (mt0) REVERT: i 144 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8331 (mp0) REVERT: i 151 ASN cc_start: 0.9055 (m-40) cc_final: 0.8799 (m110) REVERT: i 173 ASP cc_start: 0.9075 (p0) cc_final: 0.8835 (p0) REVERT: i 221 SER cc_start: 0.9634 (t) cc_final: 0.9351 (m) outliers start: 160 outliers final: 53 residues processed: 1257 average time/residue: 1.4533 time to fit residues: 2290.2400 Evaluate side-chains 1156 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1085 time to evaluate : 5.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain O residue 48 GLU Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain O residue 212 CYS Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain Q residue 221 ASN Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain S residue 146 GLN Chi-restraints excluded: chain S residue 148 CYS Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain U residue 180 GLU Chi-restraints excluded: chain V residue 91 GLN Chi-restraints excluded: chain V residue 118 SER Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 167 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 62 LYS Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain Y residue 1 THR Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 54 CYS Chi-restraints excluded: chain a residue 65 GLN Chi-restraints excluded: chain b residue 135 ILE Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain f residue 38 GLN Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 144 GLU Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain g residue 50 ASN Chi-restraints excluded: chain g residue 162 SER Chi-restraints excluded: chain g residue 171 HIS Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 126 GLN Chi-restraints excluded: chain i residue 140 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 682 optimal weight: 2.9990 chunk 519 optimal weight: 0.9980 chunk 358 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 329 optimal weight: 5.9990 chunk 463 optimal weight: 4.9990 chunk 692 optimal weight: 2.9990 chunk 733 optimal weight: 0.9990 chunk 362 optimal weight: 2.9990 chunk 656 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 146 GLN B 198 ASN D 122 GLN E 16 GLN F 101 ASN G 128 ASN I 161 HIS J 55 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN K 62 GLN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 HIS ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 HIS S 60 GLN S 65 HIS S 86 ASN S 121 GLN S 146 GLN V 57 GLN W 80 GLN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 3 ASN a 47 ASN c 127 GLN c 129 ASN ** c 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 161 GLN e 11 GLN e 136 GLN h 23 ASN h 38 GLN h 143 GLN g 11 GLN g 171 HIS ** g 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 127 HIS i 143 GLN ** i 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 59176 Z= 0.220 Angle : 0.588 8.047 80293 Z= 0.316 Chirality : 0.042 0.173 9335 Planarity : 0.004 0.061 10242 Dihedral : 4.614 49.166 8442 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.83 % Favored : 98.16 % Rotamer: Outliers : 2.53 % Allowed : 16.77 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: 1.54 (0.09), residues: 7657 helix: 2.28 (0.08), residues: 3430 sheet: 0.28 (0.13), residues: 1479 loop : -0.11 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 215 HIS 0.006 0.001 HIS D 73 PHE 0.023 0.001 PHE R 143 TYR 0.030 0.001 TYR G 160 ARG 0.011 0.001 ARG J 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1221 time to evaluate : 5.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 142 ARG cc_start: 0.8238 (ptm-80) cc_final: 0.7990 (ptm-80) REVERT: A 165 ASN cc_start: 0.8736 (m110) cc_final: 0.8070 (t0) REVERT: B 26 GLU cc_start: 0.8773 (tp30) cc_final: 0.8049 (tp30) REVERT: B 49 ARG cc_start: 0.8315 (mtp-110) cc_final: 0.7881 (ttm110) REVERT: B 67 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8201 (tttt) REVERT: B 69 ASN cc_start: 0.8686 (t0) cc_final: 0.8321 (t0) REVERT: B 72 MET cc_start: 0.8446 (ptm) cc_final: 0.8138 (mtp) REVERT: B 103 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7845 (mt-10) REVERT: B 108 GLU cc_start: 0.8593 (tt0) cc_final: 0.8298 (tt0) REVERT: B 117 ILE cc_start: 0.9312 (mm) cc_final: 0.9096 (mp) REVERT: B 174 MET cc_start: 0.8492 (mtp) cc_final: 0.8185 (ttm) REVERT: B 178 ASP cc_start: 0.9148 (m-30) cc_final: 0.8829 (m-30) REVERT: B 184 MET cc_start: 0.8246 (tpp) cc_final: 0.7939 (mpp) REVERT: C 28 LYS cc_start: 0.9084 (mttm) cc_final: 0.8753 (mttm) REVERT: C 47 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7814 (mtmm) REVERT: C 54 GLN cc_start: 0.8743 (tt0) cc_final: 0.8246 (mm110) REVERT: C 55 ASP cc_start: 0.7987 (t0) cc_final: 0.7723 (t0) REVERT: C 66 ASP cc_start: 0.8511 (t0) cc_final: 0.8200 (t0) REVERT: C 67 ASP cc_start: 0.8281 (p0) cc_final: 0.8076 (p0) REVERT: C 93 SER cc_start: 0.9228 (t) cc_final: 0.8954 (t) REVERT: C 137 ASP cc_start: 0.7965 (p0) cc_final: 0.7648 (p0) REVERT: C 146 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: D 5 ARG cc_start: 0.7795 (tmm160) cc_final: 0.7304 (tpt170) REVERT: D 78 MET cc_start: 0.7765 (ppp) cc_final: 0.7527 (ppp) REVERT: D 166 ASP cc_start: 0.8733 (m-30) cc_final: 0.8442 (m-30) REVERT: D 196 LYS cc_start: 0.9280 (mtpp) cc_final: 0.8928 (mppt) REVERT: E 60 GLN cc_start: 0.8434 (pt0) cc_final: 0.7608 (pp30) REVERT: E 137 TYR cc_start: 0.8982 (t80) cc_final: 0.8623 (t80) REVERT: E 138 ASP cc_start: 0.7884 (p0) cc_final: 0.7636 (p0) REVERT: E 178 GLU cc_start: 0.8771 (pm20) cc_final: 0.8504 (pm20) REVERT: F 31 GLU cc_start: 0.8284 (mp0) cc_final: 0.7980 (mp0) REVERT: F 70 ASP cc_start: 0.8587 (t0) cc_final: 0.7958 (t0) REVERT: F 93 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7407 (tm-30) REVERT: F 225 GLU cc_start: 0.8561 (pt0) cc_final: 0.8119 (pm20) REVERT: G 21 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8028 (mtm110) REVERT: G 26 GLU cc_start: 0.8297 (mp0) cc_final: 0.8012 (mp0) REVERT: G 80 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7544 (mmt) REVERT: G 113 MET cc_start: 0.9124 (mmm) cc_final: 0.8916 (mmm) REVERT: G 131 MET cc_start: 0.7707 (ttp) cc_final: 0.7453 (ttp) REVERT: H 139 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: H 143 ARG cc_start: 0.8396 (ptt90) cc_final: 0.7760 (ptt90) REVERT: H 153 ASN cc_start: 0.8985 (m-40) cc_final: 0.8330 (m110) REVERT: H 157 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7959 (mm-30) REVERT: H 202 TYR cc_start: 0.7964 (m-80) cc_final: 0.7714 (m-80) REVERT: I 11 MET cc_start: 0.8810 (ttp) cc_final: 0.8578 (tpp) REVERT: I 39 GLN cc_start: 0.9107 (tt0) cc_final: 0.8798 (tm-30) REVERT: I 92 ASN cc_start: 0.8982 (t0) cc_final: 0.8592 (t0) REVERT: I 105 GLU cc_start: 0.8520 (mm-30) cc_final: 0.7980 (mm-30) REVERT: I 123 LEU cc_start: 0.9625 (mp) cc_final: 0.9367 (mt) REVERT: I 190 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7594 (mp0) REVERT: J 8 GLN cc_start: 0.8682 (tt0) cc_final: 0.8186 (tt0) REVERT: J 18 ASP cc_start: 0.8815 (p0) cc_final: 0.8515 (p0) REVERT: J 90 ASP cc_start: 0.8745 (m-30) cc_final: 0.8281 (m-30) REVERT: J 165 GLU cc_start: 0.8027 (tp30) cc_final: 0.7633 (tp30) REVERT: K 71 LYS cc_start: 0.9243 (mmmm) cc_final: 0.9004 (mppt) REVERT: L 146 GLN cc_start: 0.9019 (tp40) cc_final: 0.8430 (tm-30) REVERT: M 30 TYR cc_start: 0.8515 (t80) cc_final: 0.8152 (t80) REVERT: M 104 ASN cc_start: 0.9055 (t0) cc_final: 0.8432 (t0) REVERT: M 200 GLU cc_start: 0.7681 (mp0) cc_final: 0.7350 (mp0) REVERT: M 208 ASN cc_start: 0.8964 (t0) cc_final: 0.7989 (t0) REVERT: M 210 ASP cc_start: 0.8338 (p0) cc_final: 0.8135 (p0) REVERT: M 213 HIS cc_start: 0.8736 (m-70) cc_final: 0.8498 (m-70) REVERT: N 61 TYR cc_start: 0.9258 (t80) cc_final: 0.8767 (t80) REVERT: N 86 MET cc_start: 0.9161 (mtp) cc_final: 0.8938 (ttm) REVERT: O 118 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8781 (tm-30) REVERT: O 224 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8478 (mp0) REVERT: P 22 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: P 26 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8076 (mp0) REVERT: P 48 GLU cc_start: 0.8369 (tt0) cc_final: 0.8113 (tm-30) REVERT: P 108 GLU cc_start: 0.8482 (tt0) cc_final: 0.8121 (tt0) REVERT: Q 24 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7943 (tm-30) REVERT: Q 55 ASP cc_start: 0.7740 (t0) cc_final: 0.7426 (t0) REVERT: Q 90 GLU cc_start: 0.8580 (tp30) cc_final: 0.8115 (tp30) REVERT: Q 99 GLU cc_start: 0.7681 (mp0) cc_final: 0.6860 (mp0) REVERT: Q 116 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8451 (tp40) REVERT: Q 121 SER cc_start: 0.8611 (t) cc_final: 0.8218 (p) REVERT: Q 122 ASN cc_start: 0.8856 (m-40) cc_final: 0.8571 (m-40) REVERT: Q 153 TYR cc_start: 0.9510 (p90) cc_final: 0.9267 (p90) REVERT: Q 193 LYS cc_start: 0.9258 (mttm) cc_final: 0.9024 (mttp) REVERT: R 32 LYS cc_start: 0.9126 (mttp) cc_final: 0.8705 (mtmm) REVERT: R 78 MET cc_start: 0.8954 (ptp) cc_final: 0.8356 (ptp) REVERT: R 86 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8513 (mmmm) REVERT: R 143 PHE cc_start: 0.9461 (m-80) cc_final: 0.9219 (m-10) REVERT: R 166 ASP cc_start: 0.8328 (m-30) cc_final: 0.8066 (m-30) REVERT: S 16 GLN cc_start: 0.8888 (mp-120) cc_final: 0.8383 (mp10) REVERT: U 88 ARG cc_start: 0.8430 (mmm160) cc_final: 0.8162 (mmm160) REVERT: U 180 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.7985 (mm-30) REVERT: U 214 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8310 (tp30) REVERT: V 29 LYS cc_start: 0.9379 (mtmm) cc_final: 0.9127 (mtmm) REVERT: V 51 ASP cc_start: 0.8973 (m-30) cc_final: 0.8572 (m-30) REVERT: W 77 GLU cc_start: 0.8217 (mt-10) cc_final: 0.8002 (mt-10) REVERT: W 154 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8316 (pt0) REVERT: W 157 MET cc_start: 0.8887 (mtm) cc_final: 0.8515 (mtp) REVERT: W 164 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8238 (mm-30) REVERT: W 177 ASP cc_start: 0.8607 (t0) cc_final: 0.8089 (t0) REVERT: X 27 GLN cc_start: 0.8503 (pt0) cc_final: 0.7877 (pp30) REVERT: X 35 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7844 (mtt) REVERT: X 37 LYS cc_start: 0.8940 (tttt) cc_final: 0.8698 (tttp) REVERT: X 41 LYS cc_start: 0.9002 (mttp) cc_final: 0.8713 (mttm) REVERT: X 69 MET cc_start: 0.8548 (mmm) cc_final: 0.8285 (mmp) REVERT: X 90 ASP cc_start: 0.8675 (m-30) cc_final: 0.8396 (m-30) REVERT: X 102 LEU cc_start: 0.9165 (mp) cc_final: 0.8960 (mm) REVERT: X 108 ASP cc_start: 0.8157 (t0) cc_final: 0.7721 (t0) REVERT: X 141 SER cc_start: 0.8999 (m) cc_final: 0.8798 (p) REVERT: X 151 ILE cc_start: 0.9324 (tt) cc_final: 0.8711 (pp) REVERT: X 165 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7974 (mt-10) REVERT: Y 44 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.9072 (p) REVERT: Y 62 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8986 (mm110) REVERT: Y 67 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8888 (tt0) REVERT: Y 81 LYS cc_start: 0.9158 (tptm) cc_final: 0.8456 (tptm) REVERT: Z 130 TYR cc_start: 0.9175 (p90) cc_final: 0.8736 (p90) REVERT: Z 186 ASP cc_start: 0.8194 (t0) cc_final: 0.7884 (t0) REVERT: b 85 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8156 (mm-30) REVERT: b 90 TYR cc_start: 0.8880 (m-80) cc_final: 0.8640 (m-80) REVERT: d 34 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8503 (mtm-85) REVERT: d 36 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9150 (tt) REVERT: d 42 TYR cc_start: 0.8989 (t80) cc_final: 0.8691 (t80) REVERT: d 53 ASN cc_start: 0.9420 (t0) cc_final: 0.9169 (m-40) REVERT: d 56 ASP cc_start: 0.8387 (t70) cc_final: 0.7954 (p0) REVERT: d 173 ASP cc_start: 0.8569 (p0) cc_final: 0.8183 (p0) REVERT: d 185 MET cc_start: 0.8345 (mmp) cc_final: 0.7908 (mmp) REVERT: d 186 ASP cc_start: 0.8773 (p0) cc_final: 0.8402 (p0) REVERT: d 201 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8204 (tp30) REVERT: c 11 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8215 (tp-100) REVERT: c 27 ASN cc_start: 0.9058 (p0) cc_final: 0.8670 (p0) REVERT: c 123 ASP cc_start: 0.8429 (m-30) cc_final: 0.8225 (m-30) REVERT: c 164 HIS cc_start: 0.9070 (t70) cc_final: 0.8809 (t-90) REVERT: c 168 GLU cc_start: 0.8515 (tp30) cc_final: 0.8092 (tp30) REVERT: c 187 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9081 (mtpm) REVERT: c 191 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8331 (mm110) REVERT: c 208 GLU cc_start: 0.8882 (tp30) cc_final: 0.8574 (tp30) REVERT: c 228 ASP cc_start: 0.8865 (t70) cc_final: 0.8550 (t70) REVERT: c 249 TYR cc_start: 0.8650 (m-80) cc_final: 0.8373 (m-80) REVERT: f 22 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8372 (pp30) REVERT: f 26 GLN cc_start: 0.8151 (tp-100) cc_final: 0.7748 (tp-100) REVERT: f 38 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8670 (mp10) REVERT: f 52 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9330 (tt) REVERT: f 65 ASP cc_start: 0.8859 (t70) cc_final: 0.8633 (t70) REVERT: f 173 ASP cc_start: 0.9122 (m-30) cc_final: 0.8788 (m-30) REVERT: f 194 ARG cc_start: 0.8981 (mpt90) cc_final: 0.8642 (mpt-90) REVERT: f 201 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8597 (mm-30) REVERT: f 208 ASP cc_start: 0.8806 (m-30) cc_final: 0.8516 (m-30) REVERT: f 229 ASN cc_start: 0.8836 (t0) cc_final: 0.8613 (t160) REVERT: e 115 GLN cc_start: 0.9230 (mm110) cc_final: 0.9029 (tp40) REVERT: e 123 ASP cc_start: 0.8824 (m-30) cc_final: 0.8283 (t0) REVERT: e 147 ASN cc_start: 0.9035 (m-40) cc_final: 0.8792 (m-40) REVERT: e 173 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8596 (tm-30) REVERT: h 16 GLN cc_start: 0.8470 (mt0) cc_final: 0.8071 (mt0) REVERT: h 22 GLN cc_start: 0.8740 (mm110) cc_final: 0.8350 (mm110) REVERT: h 23 ASN cc_start: 0.9248 (m-40) cc_final: 0.9045 (m110) REVERT: h 34 ARG cc_start: 0.8618 (ptp-110) cc_final: 0.8254 (ptp90) REVERT: h 61 ARG cc_start: 0.9143 (mtp-110) cc_final: 0.8829 (ttm110) REVERT: h 151 ASN cc_start: 0.9204 (m-40) cc_final: 0.8985 (m110) REVERT: h 161 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8369 (tm-30) REVERT: h 203 ARG cc_start: 0.9073 (ttt-90) cc_final: 0.8768 (mmm-85) REVERT: h 229 ASN cc_start: 0.8789 (t0) cc_final: 0.8406 (t0) REVERT: g 41 ASP cc_start: 0.8819 (p0) cc_final: 0.8535 (p0) REVERT: g 107 ASN cc_start: 0.8895 (t0) cc_final: 0.8614 (t0) REVERT: g 115 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8723 (mm-40) REVERT: g 116 ARG cc_start: 0.8640 (ptm160) cc_final: 0.8219 (ptm160) REVERT: g 120 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8324 (mp0) REVERT: g 123 ASP cc_start: 0.8954 (m-30) cc_final: 0.8610 (m-30) REVERT: g 180 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8262 (mm-30) REVERT: g 183 ASP cc_start: 0.9482 (m-30) cc_final: 0.9204 (m-30) REVERT: g 199 GLN cc_start: 0.9228 (mm110) cc_final: 0.8888 (mp10) REVERT: i 22 GLN cc_start: 0.9097 (pt0) cc_final: 0.8848 (pp30) REVERT: i 23 ASN cc_start: 0.9147 (m110) cc_final: 0.8142 (m-40) REVERT: i 26 GLN cc_start: 0.8398 (pp30) cc_final: 0.8052 (pp30) REVERT: i 38 GLN cc_start: 0.8932 (mt0) cc_final: 0.8581 (mt0) REVERT: i 151 ASN cc_start: 0.9108 (m-40) cc_final: 0.8854 (m110) REVERT: i 173 ASP cc_start: 0.9098 (p0) cc_final: 0.8786 (p0) REVERT: i 221 SER cc_start: 0.9628 (t) cc_final: 0.9335 (m) outliers start: 145 outliers final: 51 residues processed: 1292 average time/residue: 1.4971 time to fit residues: 2430.6461 Evaluate side-chains 1183 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1117 time to evaluate : 5.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 181 ASN Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 221 ASN Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain U residue 180 GLU Chi-restraints excluded: chain V residue 118 SER Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 167 SER Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain X residue 35 MET Chi-restraints excluded: chain Y residue 1 THR Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 54 CYS Chi-restraints excluded: chain Z residue 166 LEU Chi-restraints excluded: chain b residue 135 ILE Chi-restraints excluded: chain d residue 34 ARG Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain c residue 187 LYS Chi-restraints excluded: chain c residue 191 GLN Chi-restraints excluded: chain f residue 38 GLN Chi-restraints excluded: chain f residue 52 LEU Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 144 GLU Chi-restraints excluded: chain f residue 201 GLU Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 126 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 611 optimal weight: 5.9990 chunk 416 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 546 optimal weight: 0.0370 chunk 302 optimal weight: 9.9990 chunk 626 optimal weight: 7.9990 chunk 507 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 374 optimal weight: 0.4980 chunk 658 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 overall best weight: 1.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN E 16 GLN J 55 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN L 8 ASN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 HIS ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 HIS S 121 GLN V 57 GLN ** V 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 6 ASN W 80 GLN ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 ASN a 108 ASN b 193 GLN ** c 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 136 GLN ** e 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 GLN h 143 GLN g 136 GLN i 23 ASN i 127 HIS i 143 GLN ** i 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 59176 Z= 0.236 Angle : 0.592 8.460 80293 Z= 0.318 Chirality : 0.042 0.186 9335 Planarity : 0.004 0.062 10242 Dihedral : 4.517 47.564 8442 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.72 % Allowed : 18.24 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: 1.53 (0.09), residues: 7657 helix: 2.29 (0.08), residues: 3441 sheet: 0.26 (0.13), residues: 1471 loop : -0.14 (0.12), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 215 HIS 0.005 0.001 HIS D 73 PHE 0.032 0.001 PHE F 135 TYR 0.031 0.001 TYR G 160 ARG 0.010 0.001 ARG W 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1348 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1192 time to evaluate : 5.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 165 ASN cc_start: 0.8729 (m110) cc_final: 0.8078 (t0) REVERT: A 206 ASN cc_start: 0.8913 (m-40) cc_final: 0.8223 (t160) REVERT: B 26 GLU cc_start: 0.8747 (tp30) cc_final: 0.8052 (tp30) REVERT: B 49 ARG cc_start: 0.8317 (mtp-110) cc_final: 0.7879 (ttm110) REVERT: B 50 ARG cc_start: 0.8589 (tpp80) cc_final: 0.7633 (tpp80) REVERT: B 67 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8198 (tttt) REVERT: B 69 ASN cc_start: 0.8545 (t0) cc_final: 0.8195 (t0) REVERT: B 72 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8179 (mtp) REVERT: B 103 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7892 (mt-10) REVERT: B 108 GLU cc_start: 0.8543 (tt0) cc_final: 0.8297 (tt0) REVERT: B 117 ILE cc_start: 0.9311 (mm) cc_final: 0.9109 (mp) REVERT: B 174 MET cc_start: 0.8524 (mtp) cc_final: 0.8239 (ttm) REVERT: B 178 ASP cc_start: 0.9140 (m-30) cc_final: 0.8830 (m-30) REVERT: B 184 MET cc_start: 0.8271 (tpp) cc_final: 0.7994 (mpp) REVERT: C 28 LYS cc_start: 0.9088 (mttm) cc_final: 0.8805 (mttm) REVERT: C 47 LYS cc_start: 0.8312 (mtmm) cc_final: 0.7948 (mtmm) REVERT: C 54 GLN cc_start: 0.8714 (tt0) cc_final: 0.8393 (mm110) REVERT: C 55 ASP cc_start: 0.8012 (t0) cc_final: 0.7749 (t0) REVERT: C 66 ASP cc_start: 0.8510 (t0) cc_final: 0.8193 (m-30) REVERT: C 93 SER cc_start: 0.9230 (t) cc_final: 0.8956 (t) REVERT: C 105 GLU cc_start: 0.8621 (tp30) cc_final: 0.8386 (tp30) REVERT: C 137 ASP cc_start: 0.7878 (p0) cc_final: 0.7486 (p0) REVERT: C 206 ILE cc_start: 0.9105 (pt) cc_final: 0.8820 (mp) REVERT: D 5 ARG cc_start: 0.7769 (tmm160) cc_final: 0.7308 (tpt170) REVERT: D 78 MET cc_start: 0.7763 (ppp) cc_final: 0.7528 (ppp) REVERT: D 166 ASP cc_start: 0.8726 (m-30) cc_final: 0.8432 (m-30) REVERT: D 196 LYS cc_start: 0.9275 (mtpp) cc_final: 0.8932 (mppt) REVERT: D 206 MET cc_start: 0.8002 (mtm) cc_final: 0.7763 (mtm) REVERT: E 60 GLN cc_start: 0.8429 (pt0) cc_final: 0.7591 (pp30) REVERT: E 137 TYR cc_start: 0.8979 (t80) cc_final: 0.8617 (t80) REVERT: E 138 ASP cc_start: 0.7936 (p0) cc_final: 0.7684 (p0) REVERT: E 178 GLU cc_start: 0.8777 (pm20) cc_final: 0.8495 (pm20) REVERT: F 31 GLU cc_start: 0.8286 (mp0) cc_final: 0.8066 (mp0) REVERT: F 70 ASP cc_start: 0.8571 (t0) cc_final: 0.7940 (t0) REVERT: F 93 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7365 (tm-30) REVERT: F 225 GLU cc_start: 0.8555 (pt0) cc_final: 0.8134 (pp20) REVERT: G 21 ARG cc_start: 0.8539 (mtp180) cc_final: 0.7956 (mtm110) REVERT: G 26 GLU cc_start: 0.8286 (mp0) cc_final: 0.8001 (mp0) REVERT: G 80 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7995 (mmt) REVERT: G 113 MET cc_start: 0.9116 (mmm) cc_final: 0.8869 (mmm) REVERT: G 131 MET cc_start: 0.7707 (ttp) cc_final: 0.7464 (ttp) REVERT: H 139 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: H 143 ARG cc_start: 0.8452 (ptt90) cc_final: 0.8031 (ptt90) REVERT: H 153 ASN cc_start: 0.8968 (m-40) cc_final: 0.8134 (m-40) REVERT: H 157 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8073 (mm-30) REVERT: I 11 MET cc_start: 0.8756 (ttp) cc_final: 0.8553 (tpp) REVERT: I 39 GLN cc_start: 0.9096 (tt0) cc_final: 0.8803 (tm-30) REVERT: I 92 ASN cc_start: 0.8986 (t0) cc_final: 0.8612 (t0) REVERT: I 105 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8029 (mm-30) REVERT: I 123 LEU cc_start: 0.9635 (mp) cc_final: 0.9372 (mt) REVERT: I 190 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7619 (mp0) REVERT: J 8 GLN cc_start: 0.8710 (tt0) cc_final: 0.8236 (tt0) REVERT: J 18 ASP cc_start: 0.8829 (p0) cc_final: 0.8527 (p0) REVERT: J 90 ASP cc_start: 0.8758 (m-30) cc_final: 0.8298 (m-30) REVERT: J 108 ASP cc_start: 0.8359 (t0) cc_final: 0.6942 (t0) REVERT: J 165 GLU cc_start: 0.8105 (tp30) cc_final: 0.7701 (tp30) REVERT: K 71 LYS cc_start: 0.9263 (mmmm) cc_final: 0.9045 (mppt) REVERT: K 72 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: K 140 ASP cc_start: 0.8768 (m-30) cc_final: 0.8513 (m-30) REVERT: L 146 GLN cc_start: 0.8983 (tp40) cc_final: 0.8497 (mm-40) REVERT: L 198 VAL cc_start: 0.9621 (OUTLIER) cc_final: 0.9415 (m) REVERT: M 30 TYR cc_start: 0.8518 (t80) cc_final: 0.8146 (t80) REVERT: M 104 ASN cc_start: 0.9046 (t0) cc_final: 0.8458 (t0) REVERT: M 110 MET cc_start: 0.8766 (mtm) cc_final: 0.8550 (mtm) REVERT: M 200 GLU cc_start: 0.7741 (mp0) cc_final: 0.7318 (mp0) REVERT: M 213 HIS cc_start: 0.8783 (m-70) cc_final: 0.8532 (m-70) REVERT: N 61 TYR cc_start: 0.9266 (t80) cc_final: 0.8709 (t80) REVERT: N 167 ASP cc_start: 0.8495 (t0) cc_final: 0.8211 (t0) REVERT: O 118 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8776 (tm-30) REVERT: O 224 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: P 22 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: P 26 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8074 (mp0) REVERT: P 48 GLU cc_start: 0.8379 (tt0) cc_final: 0.8121 (tm-30) REVERT: P 108 GLU cc_start: 0.8475 (tt0) cc_final: 0.8145 (tt0) REVERT: Q 24 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8028 (tm-30) REVERT: Q 52 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8690 (pttp) REVERT: Q 55 ASP cc_start: 0.7676 (t0) cc_final: 0.7340 (t0) REVERT: Q 90 GLU cc_start: 0.8586 (tp30) cc_final: 0.8137 (tp30) REVERT: Q 99 GLU cc_start: 0.7727 (mp0) cc_final: 0.6978 (mp0) REVERT: Q 116 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8431 (tp40) REVERT: Q 121 SER cc_start: 0.8695 (t) cc_final: 0.8306 (p) REVERT: Q 122 ASN cc_start: 0.8840 (m-40) cc_final: 0.8551 (m-40) REVERT: Q 153 TYR cc_start: 0.9517 (p90) cc_final: 0.9265 (p90) REVERT: Q 193 LYS cc_start: 0.9211 (mttm) cc_final: 0.8996 (mttp) REVERT: R 20 ARG cc_start: 0.8312 (pmm-80) cc_final: 0.7776 (mpp80) REVERT: R 32 LYS cc_start: 0.9130 (mttp) cc_final: 0.8813 (mtmt) REVERT: R 78 MET cc_start: 0.8963 (ptp) cc_final: 0.8401 (ptp) REVERT: R 86 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8507 (mmmm) REVERT: R 166 ASP cc_start: 0.8317 (m-30) cc_final: 0.8065 (m-30) REVERT: S 16 GLN cc_start: 0.8899 (mp-120) cc_final: 0.8420 (mp10) REVERT: S 189 LYS cc_start: 0.9153 (mtmm) cc_final: 0.8852 (ptpp) REVERT: U 88 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8167 (mmm160) REVERT: U 180 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8096 (mm-30) REVERT: U 214 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8310 (tp30) REVERT: V 91 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8616 (mt0) REVERT: W 105 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: W 150 GLU cc_start: 0.8555 (tp30) cc_final: 0.8122 (tt0) REVERT: W 154 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8314 (pt0) REVERT: W 157 MET cc_start: 0.8965 (mtm) cc_final: 0.8639 (mtp) REVERT: W 170 MET cc_start: 0.9133 (tpt) cc_final: 0.8927 (tpp) REVERT: W 177 ASP cc_start: 0.8642 (t0) cc_final: 0.8124 (t0) REVERT: X 27 GLN cc_start: 0.8551 (pt0) cc_final: 0.7843 (pp30) REVERT: X 37 LYS cc_start: 0.8952 (tttt) cc_final: 0.8730 (tttp) REVERT: X 41 LYS cc_start: 0.8990 (mttp) cc_final: 0.8693 (mttt) REVERT: X 90 ASP cc_start: 0.8684 (m-30) cc_final: 0.8412 (m-30) REVERT: X 108 ASP cc_start: 0.8169 (t0) cc_final: 0.7769 (t0) REVERT: X 141 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8788 (p) REVERT: X 144 ASP cc_start: 0.8669 (m-30) cc_final: 0.8405 (m-30) REVERT: X 151 ILE cc_start: 0.9357 (tt) cc_final: 0.8829 (pp) REVERT: X 165 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7934 (mt-10) REVERT: Y 44 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9038 (p) REVERT: Y 62 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8983 (mm110) REVERT: Y 81 LYS cc_start: 0.9198 (tptm) cc_final: 0.8487 (tptm) REVERT: Z 146 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8425 (tm-30) REVERT: Z 186 ASP cc_start: 0.8201 (t0) cc_final: 0.7876 (t0) REVERT: a 26 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8282 (mtp) REVERT: b 90 TYR cc_start: 0.8853 (m-80) cc_final: 0.8649 (m-80) REVERT: d 36 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9158 (tt) REVERT: d 42 TYR cc_start: 0.8963 (t80) cc_final: 0.8760 (t80) REVERT: d 53 ASN cc_start: 0.9420 (t0) cc_final: 0.9189 (m-40) REVERT: d 56 ASP cc_start: 0.8386 (t70) cc_final: 0.7763 (p0) REVERT: d 173 ASP cc_start: 0.8545 (p0) cc_final: 0.8155 (p0) REVERT: d 185 MET cc_start: 0.8282 (mmp) cc_final: 0.7842 (mmp) REVERT: d 186 ASP cc_start: 0.8690 (p0) cc_final: 0.8278 (p0) REVERT: d 201 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8113 (tp30) REVERT: c 11 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8063 (tp-100) REVERT: c 27 ASN cc_start: 0.9033 (p0) cc_final: 0.8672 (p0) REVERT: c 123 ASP cc_start: 0.8433 (m-30) cc_final: 0.8205 (m-30) REVERT: c 164 HIS cc_start: 0.9091 (t70) cc_final: 0.8857 (t-90) REVERT: c 168 GLU cc_start: 0.8647 (tp30) cc_final: 0.8107 (tp30) REVERT: c 179 SER cc_start: 0.9137 (t) cc_final: 0.8849 (p) REVERT: c 191 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8350 (mm110) REVERT: c 208 GLU cc_start: 0.8891 (tp30) cc_final: 0.8620 (tp30) REVERT: c 228 ASP cc_start: 0.8875 (t70) cc_final: 0.8574 (t70) REVERT: c 249 TYR cc_start: 0.8600 (m-80) cc_final: 0.8295 (m-80) REVERT: f 22 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8402 (pp30) REVERT: f 26 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7744 (tp-100) REVERT: f 38 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8693 (mp10) REVERT: f 65 ASP cc_start: 0.8881 (t70) cc_final: 0.8634 (t70) REVERT: f 194 ARG cc_start: 0.8974 (mpt90) cc_final: 0.8761 (mpt-90) REVERT: f 201 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8603 (mm-30) REVERT: f 208 ASP cc_start: 0.8836 (m-30) cc_final: 0.8482 (m-30) REVERT: f 229 ASN cc_start: 0.8837 (t0) cc_final: 0.8605 (t160) REVERT: e 11 GLN cc_start: 0.8857 (tp40) cc_final: 0.8517 (tp40) REVERT: e 115 GLN cc_start: 0.9216 (mm110) cc_final: 0.8979 (tp40) REVERT: e 132 THR cc_start: 0.9495 (m) cc_final: 0.9102 (p) REVERT: e 147 ASN cc_start: 0.8994 (m-40) cc_final: 0.8765 (m-40) REVERT: e 173 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8708 (tm-30) REVERT: h 16 GLN cc_start: 0.8439 (mt0) cc_final: 0.7881 (mt0) REVERT: h 22 GLN cc_start: 0.8819 (mm110) cc_final: 0.8483 (mm110) REVERT: h 34 ARG cc_start: 0.8650 (ptp-110) cc_final: 0.8230 (ptp90) REVERT: h 61 ARG cc_start: 0.9119 (mtp-110) cc_final: 0.8796 (ttm110) REVERT: h 185 MET cc_start: 0.8560 (mmm) cc_final: 0.7568 (mmm) REVERT: h 203 ARG cc_start: 0.9044 (ttt-90) cc_final: 0.8812 (mmm-85) REVERT: h 229 ASN cc_start: 0.8758 (t0) cc_final: 0.8367 (t0) REVERT: g 41 ASP cc_start: 0.8791 (p0) cc_final: 0.8531 (p0) REVERT: g 107 ASN cc_start: 0.8901 (t0) cc_final: 0.8624 (t0) REVERT: g 115 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8734 (mm-40) REVERT: g 116 ARG cc_start: 0.8690 (ptm160) cc_final: 0.8161 (ptm160) REVERT: g 120 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8292 (mp0) REVERT: g 123 ASP cc_start: 0.8952 (m-30) cc_final: 0.8603 (m-30) REVERT: g 136 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8609 (mt0) REVERT: g 144 ASP cc_start: 0.7130 (m-30) cc_final: 0.6861 (m-30) REVERT: g 180 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8358 (mm-30) REVERT: g 183 ASP cc_start: 0.9489 (m-30) cc_final: 0.9206 (m-30) REVERT: g 199 GLN cc_start: 0.9215 (mm110) cc_final: 0.8886 (mp10) REVERT: i 14 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8197 (mtm-85) REVERT: i 23 ASN cc_start: 0.9173 (m-40) cc_final: 0.8217 (m-40) REVERT: i 26 GLN cc_start: 0.8411 (pp30) cc_final: 0.8014 (pp30) REVERT: i 151 ASN cc_start: 0.9110 (m-40) cc_final: 0.8829 (m110) REVERT: i 173 ASP cc_start: 0.9113 (p0) cc_final: 0.8754 (p0) REVERT: i 185 MET cc_start: 0.8155 (mmm) cc_final: 0.7946 (mpp) REVERT: i 221 SER cc_start: 0.9643 (t) cc_final: 0.9346 (m) outliers start: 156 outliers final: 66 residues processed: 1276 average time/residue: 1.4722 time to fit residues: 2372.3474 Evaluate side-chains 1187 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1102 time to evaluate : 5.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 181 ASN Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain Q residue 221 ASN Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain U residue 180 GLU Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 91 GLN Chi-restraints excluded: chain V residue 118 SER Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 167 SER Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 91 CYS Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain Y residue 1 THR Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 54 CYS Chi-restraints excluded: chain Z residue 146 GLN Chi-restraints excluded: chain Z residue 166 LEU Chi-restraints excluded: chain a residue 26 MET Chi-restraints excluded: chain a residue 65 GLN Chi-restraints excluded: chain b residue 86 MET Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain c residue 191 GLN Chi-restraints excluded: chain f residue 38 GLN Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 144 GLU Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain g residue 50 ASN Chi-restraints excluded: chain g residue 136 GLN Chi-restraints excluded: chain g residue 162 SER Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 126 GLN Chi-restraints excluded: chain i residue 140 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 246 optimal weight: 9.9990 chunk 660 optimal weight: 0.0030 chunk 145 optimal weight: 10.0000 chunk 430 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 734 optimal weight: 0.9980 chunk 609 optimal weight: 7.9990 chunk 340 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 385 optimal weight: 0.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 16 GLN J 55 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN K 62 GLN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 HIS ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 GLN S 65 HIS S 68 ASN S 121 GLN U 128 ASN V 57 GLN W 80 GLN ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 3 ASN a 47 ASN b 193 GLN ** c 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 136 GLN ** e 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 23 ASN h 38 GLN h 143 GLN h 151 ASN ** h 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 143 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 59176 Z= 0.260 Angle : 0.607 11.564 80293 Z= 0.324 Chirality : 0.043 0.273 9335 Planarity : 0.004 0.079 10242 Dihedral : 4.489 46.916 8442 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.00 % Allowed : 19.00 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: 1.51 (0.09), residues: 7657 helix: 2.28 (0.08), residues: 3441 sheet: 0.20 (0.13), residues: 1467 loop : -0.14 (0.12), residues: 2749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 215 HIS 0.004 0.001 HIS f 192 PHE 0.025 0.001 PHE d 212 TYR 0.031 0.001 TYR G 160 ARG 0.011 0.001 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1342 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1170 time to evaluate : 5.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: A 95 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7730 (tm-30) REVERT: A 106 THR cc_start: 0.9104 (m) cc_final: 0.8791 (m) REVERT: A 120 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8059 (t80) REVERT: A 142 ARG cc_start: 0.8255 (ptm-80) cc_final: 0.8038 (ptm-80) REVERT: A 165 ASN cc_start: 0.8725 (m110) cc_final: 0.8079 (t0) REVERT: A 206 ASN cc_start: 0.8943 (m-40) cc_final: 0.8293 (t160) REVERT: B 26 GLU cc_start: 0.8734 (tp30) cc_final: 0.8045 (tp30) REVERT: B 49 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7878 (ttm110) REVERT: B 50 ARG cc_start: 0.8586 (tpp80) cc_final: 0.7629 (tpp80) REVERT: B 67 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8204 (tttt) REVERT: B 69 ASN cc_start: 0.8600 (t0) cc_final: 0.8241 (t0) REVERT: B 72 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8114 (mtp) REVERT: B 103 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7941 (mt-10) REVERT: B 108 GLU cc_start: 0.8534 (tt0) cc_final: 0.8315 (tt0) REVERT: B 117 ILE cc_start: 0.9313 (mm) cc_final: 0.9096 (mp) REVERT: B 174 MET cc_start: 0.8501 (mtp) cc_final: 0.8184 (ttm) REVERT: B 178 ASP cc_start: 0.9153 (m-30) cc_final: 0.8850 (m-30) REVERT: B 184 MET cc_start: 0.8238 (tpp) cc_final: 0.7925 (mpp) REVERT: C 28 LYS cc_start: 0.9096 (mttm) cc_final: 0.8796 (mttm) REVERT: C 47 LYS cc_start: 0.8315 (mtmm) cc_final: 0.7961 (mtmm) REVERT: C 54 GLN cc_start: 0.8724 (tt0) cc_final: 0.8405 (mm110) REVERT: C 93 SER cc_start: 0.9235 (t) cc_final: 0.8954 (t) REVERT: C 105 GLU cc_start: 0.8634 (tp30) cc_final: 0.8401 (tp30) REVERT: C 137 ASP cc_start: 0.7883 (p0) cc_final: 0.7484 (p0) REVERT: C 146 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: C 206 ILE cc_start: 0.9117 (pt) cc_final: 0.8835 (mp) REVERT: D 5 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7387 (tpt170) REVERT: D 78 MET cc_start: 0.7809 (ppp) cc_final: 0.7597 (ppp) REVERT: D 166 ASP cc_start: 0.8723 (m-30) cc_final: 0.8433 (m-30) REVERT: D 216 GLU cc_start: 0.8247 (tt0) cc_final: 0.8036 (tt0) REVERT: E 60 GLN cc_start: 0.8434 (pt0) cc_final: 0.7588 (pp30) REVERT: E 137 TYR cc_start: 0.9007 (t80) cc_final: 0.8638 (t80) REVERT: E 138 ASP cc_start: 0.7972 (p0) cc_final: 0.7680 (p0) REVERT: E 178 GLU cc_start: 0.8786 (pm20) cc_final: 0.8503 (pm20) REVERT: F 31 GLU cc_start: 0.8292 (mp0) cc_final: 0.8063 (mp0) REVERT: F 70 ASP cc_start: 0.8575 (t0) cc_final: 0.7937 (t0) REVERT: F 93 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7423 (tm-30) REVERT: F 136 MET cc_start: 0.9197 (mtp) cc_final: 0.8887 (mtp) REVERT: F 225 GLU cc_start: 0.8564 (pt0) cc_final: 0.8140 (pp20) REVERT: G 15 ILE cc_start: 0.9523 (pt) cc_final: 0.9291 (pp) REVERT: G 21 ARG cc_start: 0.8529 (mtp180) cc_final: 0.7897 (mtm110) REVERT: G 26 GLU cc_start: 0.8266 (mp0) cc_final: 0.7962 (mp0) REVERT: G 80 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8000 (mmt) REVERT: G 113 MET cc_start: 0.9144 (mmm) cc_final: 0.8889 (mmm) REVERT: G 131 MET cc_start: 0.7712 (ttp) cc_final: 0.7486 (ttp) REVERT: H 139 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: H 143 ARG cc_start: 0.8448 (ptt90) cc_final: 0.8134 (ptt90) REVERT: H 153 ASN cc_start: 0.8875 (m-40) cc_final: 0.8125 (m-40) REVERT: H 157 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8046 (mm-30) REVERT: I 11 MET cc_start: 0.8743 (ttp) cc_final: 0.8513 (tpp) REVERT: I 92 ASN cc_start: 0.8990 (t0) cc_final: 0.8618 (t0) REVERT: I 105 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7995 (mm-30) REVERT: I 123 LEU cc_start: 0.9631 (mp) cc_final: 0.9327 (mt) REVERT: I 190 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7574 (mp0) REVERT: J 8 GLN cc_start: 0.8755 (tt0) cc_final: 0.8301 (tt0) REVERT: J 18 ASP cc_start: 0.8846 (p0) cc_final: 0.8549 (p0) REVERT: J 41 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8836 (mttt) REVERT: J 90 ASP cc_start: 0.8749 (m-30) cc_final: 0.8278 (m-30) REVERT: J 108 ASP cc_start: 0.8360 (t0) cc_final: 0.7897 (t0) REVERT: J 111 GLU cc_start: 0.8395 (mp0) cc_final: 0.8106 (mp0) REVERT: J 161 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7879 (ttp-170) REVERT: J 165 GLU cc_start: 0.8130 (tp30) cc_final: 0.7714 (tp30) REVERT: L 198 VAL cc_start: 0.9621 (OUTLIER) cc_final: 0.9408 (m) REVERT: M 30 TYR cc_start: 0.8546 (t80) cc_final: 0.8280 (t80) REVERT: M 104 ASN cc_start: 0.9026 (t0) cc_final: 0.8452 (t0) REVERT: M 213 HIS cc_start: 0.8828 (m-70) cc_final: 0.8517 (m-70) REVERT: N 61 TYR cc_start: 0.9250 (t80) cc_final: 0.8713 (t80) REVERT: N 165 GLU cc_start: 0.8179 (tp30) cc_final: 0.7885 (tp30) REVERT: O 118 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8748 (tm-30) REVERT: O 224 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: P 22 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: P 26 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8116 (mm-30) REVERT: P 48 GLU cc_start: 0.8354 (tt0) cc_final: 0.8118 (tm-30) REVERT: Q 24 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8050 (tm-30) REVERT: Q 52 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8695 (pttp) REVERT: Q 55 ASP cc_start: 0.7643 (t0) cc_final: 0.7317 (t0) REVERT: Q 90 GLU cc_start: 0.8569 (tp30) cc_final: 0.8166 (tp30) REVERT: Q 99 GLU cc_start: 0.7824 (mp0) cc_final: 0.6999 (mp0) REVERT: Q 116 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8404 (tp40) REVERT: Q 121 SER cc_start: 0.8740 (t) cc_final: 0.8413 (p) REVERT: Q 122 ASN cc_start: 0.8837 (m-40) cc_final: 0.8548 (m-40) REVERT: Q 153 TYR cc_start: 0.9515 (p90) cc_final: 0.9315 (p90) REVERT: R 20 ARG cc_start: 0.8323 (pmm-80) cc_final: 0.7764 (mpp80) REVERT: R 32 LYS cc_start: 0.9134 (mttp) cc_final: 0.8837 (mtmt) REVERT: R 78 MET cc_start: 0.8948 (ptp) cc_final: 0.8420 (ptp) REVERT: R 86 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8518 (mmmm) REVERT: R 166 ASP cc_start: 0.8303 (m-30) cc_final: 0.8051 (m-30) REVERT: S 16 GLN cc_start: 0.8906 (mp-120) cc_final: 0.8419 (mp10) REVERT: S 27 GLU cc_start: 0.8906 (tp30) cc_final: 0.8623 (mm-30) REVERT: S 176 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8060 (tpt) REVERT: S 189 LYS cc_start: 0.9166 (mtmm) cc_final: 0.8818 (mtmp) REVERT: U 88 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8176 (mmm160) REVERT: U 180 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8015 (mm-30) REVERT: U 214 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8345 (tp30) REVERT: V 215 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8852 (ttmm) REVERT: W 105 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: W 150 GLU cc_start: 0.8565 (tp30) cc_final: 0.8117 (tt0) REVERT: W 154 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8316 (pt0) REVERT: W 157 MET cc_start: 0.8981 (mtm) cc_final: 0.8650 (mtp) REVERT: W 164 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8253 (mm-30) REVERT: W 177 ASP cc_start: 0.8648 (t0) cc_final: 0.8155 (t0) REVERT: X 27 GLN cc_start: 0.8553 (pt0) cc_final: 0.7872 (pp30) REVERT: X 35 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7798 (mtt) REVERT: X 37 LYS cc_start: 0.8976 (tttt) cc_final: 0.8761 (tttp) REVERT: X 41 LYS cc_start: 0.9009 (mttp) cc_final: 0.8720 (mttt) REVERT: X 90 ASP cc_start: 0.8703 (m-30) cc_final: 0.8484 (m-30) REVERT: X 108 ASP cc_start: 0.8188 (t0) cc_final: 0.7802 (t0) REVERT: X 144 ASP cc_start: 0.8674 (m-30) cc_final: 0.8369 (m-30) REVERT: X 151 ILE cc_start: 0.9365 (tt) cc_final: 0.8831 (pp) REVERT: X 165 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7945 (mt-10) REVERT: Y 62 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8983 (mm110) REVERT: Y 81 LYS cc_start: 0.9209 (tptm) cc_final: 0.8445 (tptm) REVERT: Z 186 ASP cc_start: 0.8221 (t0) cc_final: 0.7883 (t0) REVERT: a 26 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8287 (mtp) REVERT: a 157 GLN cc_start: 0.8646 (tt0) cc_final: 0.8378 (pt0) REVERT: b 90 TYR cc_start: 0.8840 (m-80) cc_final: 0.8614 (m-80) REVERT: d 36 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9168 (tt) REVERT: d 42 TYR cc_start: 0.8901 (t80) cc_final: 0.8627 (t80) REVERT: d 53 ASN cc_start: 0.9411 (t0) cc_final: 0.9191 (m-40) REVERT: d 56 ASP cc_start: 0.8404 (t70) cc_final: 0.7780 (p0) REVERT: d 173 ASP cc_start: 0.8543 (p0) cc_final: 0.8145 (p0) REVERT: d 185 MET cc_start: 0.8386 (mmp) cc_final: 0.8016 (mmp) REVERT: d 186 ASP cc_start: 0.8687 (p0) cc_final: 0.8282 (p0) REVERT: d 201 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8124 (tp30) REVERT: c 11 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8101 (tp-100) REVERT: c 20 ASP cc_start: 0.9225 (t70) cc_final: 0.8921 (t0) REVERT: c 27 ASN cc_start: 0.9033 (p0) cc_final: 0.8690 (p0) REVERT: c 123 ASP cc_start: 0.8419 (m-30) cc_final: 0.8217 (m-30) REVERT: c 164 HIS cc_start: 0.9096 (t70) cc_final: 0.8856 (t-90) REVERT: c 168 GLU cc_start: 0.8614 (tp30) cc_final: 0.8098 (tp30) REVERT: c 191 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8383 (mm110) REVERT: c 208 GLU cc_start: 0.8915 (tp30) cc_final: 0.8672 (tp30) REVERT: c 228 ASP cc_start: 0.8946 (t70) cc_final: 0.8612 (t70) REVERT: c 229 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8992 (tt) REVERT: c 249 TYR cc_start: 0.8642 (m-80) cc_final: 0.8307 (m-80) REVERT: f 22 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8434 (pp30) REVERT: f 26 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7706 (tp-100) REVERT: f 38 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8675 (mp10) REVERT: f 65 ASP cc_start: 0.8885 (t70) cc_final: 0.8638 (t70) REVERT: f 194 ARG cc_start: 0.8967 (mpt90) cc_final: 0.8756 (mpt-90) REVERT: f 201 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8619 (mm-30) REVERT: f 208 ASP cc_start: 0.8844 (m-30) cc_final: 0.8453 (m-30) REVERT: f 229 ASN cc_start: 0.8831 (t0) cc_final: 0.8586 (t160) REVERT: e 11 GLN cc_start: 0.8913 (tp40) cc_final: 0.8689 (tp40) REVERT: e 115 GLN cc_start: 0.9214 (mm110) cc_final: 0.8980 (tp40) REVERT: e 123 ASP cc_start: 0.8852 (m-30) cc_final: 0.8245 (t0) REVERT: e 147 ASN cc_start: 0.8938 (m-40) cc_final: 0.8721 (m-40) REVERT: e 173 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8727 (tm-30) REVERT: e 191 GLN cc_start: 0.9271 (mp10) cc_final: 0.9027 (mp10) REVERT: h 16 GLN cc_start: 0.8246 (mt0) cc_final: 0.7891 (mt0) REVERT: h 22 GLN cc_start: 0.8848 (mm110) cc_final: 0.8513 (mm110) REVERT: h 61 ARG cc_start: 0.9147 (mtp-110) cc_final: 0.8807 (ttm110) REVERT: h 229 ASN cc_start: 0.8744 (t0) cc_final: 0.8280 (t0) REVERT: g 41 ASP cc_start: 0.8796 (p0) cc_final: 0.8541 (p0) REVERT: g 107 ASN cc_start: 0.8901 (t0) cc_final: 0.8622 (t0) REVERT: g 115 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8733 (mm-40) REVERT: g 116 ARG cc_start: 0.8711 (ptm160) cc_final: 0.8217 (ptm160) REVERT: g 120 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8289 (mp0) REVERT: g 123 ASP cc_start: 0.8956 (m-30) cc_final: 0.8599 (m-30) REVERT: g 128 LEU cc_start: 0.9379 (tp) cc_final: 0.9141 (tt) REVERT: g 144 ASP cc_start: 0.7302 (m-30) cc_final: 0.6977 (m-30) REVERT: g 180 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8354 (mm-30) REVERT: g 183 ASP cc_start: 0.9502 (m-30) cc_final: 0.9226 (m-30) REVERT: g 196 ASP cc_start: 0.8604 (p0) cc_final: 0.8378 (p0) REVERT: g 199 GLN cc_start: 0.9207 (mm110) cc_final: 0.8894 (mp10) REVERT: i 22 GLN cc_start: 0.8308 (pp30) cc_final: 0.7958 (pp30) REVERT: i 23 ASN cc_start: 0.9079 (m-40) cc_final: 0.8828 (m110) REVERT: i 26 GLN cc_start: 0.8426 (pp30) cc_final: 0.8059 (pp30) REVERT: i 33 TYR cc_start: 0.9348 (m-80) cc_final: 0.9076 (m-80) REVERT: i 151 ASN cc_start: 0.9132 (m-40) cc_final: 0.8840 (m110) REVERT: i 173 ASP cc_start: 0.9127 (p0) cc_final: 0.8734 (p0) REVERT: i 208 ASP cc_start: 0.9223 (m-30) cc_final: 0.8956 (m-30) REVERT: i 221 SER cc_start: 0.9645 (t) cc_final: 0.9345 (m) outliers start: 172 outliers final: 79 residues processed: 1264 average time/residue: 1.4492 time to fit residues: 2313.9709 Evaluate side-chains 1200 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1099 time to evaluate : 5.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 181 ASN Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 210 ASP Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain Q residue 221 ASN Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 156 CYS Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 180 GLU Chi-restraints excluded: chain U residue 234 GLU Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 118 SER Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 167 SER Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain X residue 35 MET Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain Y residue 1 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Y residue 138 VAL Chi-restraints excluded: chain Z residue 54 CYS Chi-restraints excluded: chain Z residue 166 LEU Chi-restraints excluded: chain a residue 26 MET Chi-restraints excluded: chain a residue 65 GLN Chi-restraints excluded: chain b residue 7 GLN Chi-restraints excluded: chain b residue 86 MET Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain c residue 191 GLN Chi-restraints excluded: chain c residue 229 ILE Chi-restraints excluded: chain f residue 38 GLN Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 144 GLU Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain h residue 42 TYR Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain g residue 162 SER Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 126 GLN Chi-restraints excluded: chain i residue 127 HIS Chi-restraints excluded: chain i residue 140 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 708 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 418 optimal weight: 3.9990 chunk 536 optimal weight: 4.9990 chunk 415 optimal weight: 9.9990 chunk 618 optimal weight: 10.0000 chunk 410 optimal weight: 7.9990 chunk 731 optimal weight: 0.8980 chunk 457 optimal weight: 7.9990 chunk 446 optimal weight: 5.9990 chunk 337 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN E 16 GLN H 57 GLN H 172 ASN J 55 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 HIS ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 GLN S 65 HIS S 68 ASN S 121 GLN V 57 GLN W 80 GLN W 156 ASN ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 189 HIS ** Z 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 ASN a 108 ASN b 193 GLN c 129 ASN ** c 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 23 ASN h 38 GLN h 143 GLN ** g 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 127 HIS i 143 GLN ** i 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 59176 Z= 0.361 Angle : 0.645 10.583 80293 Z= 0.345 Chirality : 0.044 0.270 9335 Planarity : 0.004 0.064 10242 Dihedral : 4.552 47.124 8442 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.09 % Allowed : 19.74 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.09), residues: 7657 helix: 2.22 (0.08), residues: 3440 sheet: 0.16 (0.13), residues: 1465 loop : -0.17 (0.12), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 215 HIS 0.005 0.001 HIS S 175 PHE 0.034 0.002 PHE F 135 TYR 0.033 0.002 TYR G 160 ARG 0.015 0.001 ARG h 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1300 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1123 time to evaluate : 5.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: A 95 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7819 (tm-30) REVERT: A 142 ARG cc_start: 0.8254 (ptm-80) cc_final: 0.7996 (ptm-80) REVERT: A 165 ASN cc_start: 0.8759 (m110) cc_final: 0.8265 (t0) REVERT: B 26 GLU cc_start: 0.8723 (tp30) cc_final: 0.8159 (OUTLIER) REVERT: B 49 ARG cc_start: 0.8315 (mtp-110) cc_final: 0.7873 (ttm110) REVERT: B 50 ARG cc_start: 0.8595 (tpp80) cc_final: 0.7631 (tpp80) REVERT: B 67 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8207 (tttt) REVERT: B 69 ASN cc_start: 0.8821 (t0) cc_final: 0.8441 (t0) REVERT: B 72 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8273 (mtp) REVERT: B 103 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 108 GLU cc_start: 0.8583 (tt0) cc_final: 0.8283 (tt0) REVERT: B 117 ILE cc_start: 0.9328 (mm) cc_final: 0.9108 (mp) REVERT: B 174 MET cc_start: 0.8514 (mtp) cc_final: 0.8132 (ttm) REVERT: B 178 ASP cc_start: 0.9164 (m-30) cc_final: 0.8837 (m-30) REVERT: C 28 LYS cc_start: 0.9094 (mttm) cc_final: 0.8822 (mttm) REVERT: C 54 GLN cc_start: 0.8734 (tt0) cc_final: 0.8430 (mm110) REVERT: C 55 ASP cc_start: 0.8579 (t0) cc_final: 0.8364 (t0) REVERT: C 93 SER cc_start: 0.9221 (t) cc_final: 0.8940 (t) REVERT: C 105 GLU cc_start: 0.8668 (tp30) cc_final: 0.8410 (tp30) REVERT: C 137 ASP cc_start: 0.7942 (p0) cc_final: 0.7652 (p0) REVERT: D 5 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7413 (tpt170) REVERT: D 166 ASP cc_start: 0.8736 (m-30) cc_final: 0.8431 (m-30) REVERT: E 60 GLN cc_start: 0.8479 (pt0) cc_final: 0.7592 (pp30) REVERT: E 137 TYR cc_start: 0.9037 (t80) cc_final: 0.8667 (t80) REVERT: E 138 ASP cc_start: 0.7977 (p0) cc_final: 0.7698 (p0) REVERT: E 178 GLU cc_start: 0.8797 (pm20) cc_final: 0.8501 (pm20) REVERT: F 70 ASP cc_start: 0.8634 (t0) cc_final: 0.8010 (t0) REVERT: F 93 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7464 (tm-30) REVERT: F 181 MET cc_start: 0.9596 (pmm) cc_final: 0.9280 (pmm) REVERT: G 15 ILE cc_start: 0.9542 (pt) cc_final: 0.9300 (pp) REVERT: G 21 ARG cc_start: 0.8526 (mtp180) cc_final: 0.7987 (mtm110) REVERT: G 26 GLU cc_start: 0.8314 (mp0) cc_final: 0.7930 (mp0) REVERT: G 80 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8049 (mmt) REVERT: G 83 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8121 (mtm) REVERT: G 113 MET cc_start: 0.9160 (mmm) cc_final: 0.8875 (mmm) REVERT: G 131 MET cc_start: 0.7746 (ttp) cc_final: 0.7540 (ttp) REVERT: H 139 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: H 143 ARG cc_start: 0.8474 (ptt90) cc_final: 0.8046 (ptt90) REVERT: H 153 ASN cc_start: 0.8888 (m-40) cc_final: 0.8007 (m-40) REVERT: H 157 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8040 (mm-30) REVERT: I 92 ASN cc_start: 0.9005 (t0) cc_final: 0.8634 (t0) REVERT: I 105 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7985 (mm-30) REVERT: I 190 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7642 (mp0) REVERT: J 8 GLN cc_start: 0.8805 (tt0) cc_final: 0.8421 (tt0) REVERT: J 18 ASP cc_start: 0.8872 (p0) cc_final: 0.8597 (p0) REVERT: J 41 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8877 (mttt) REVERT: J 90 ASP cc_start: 0.8756 (m-30) cc_final: 0.8294 (m-30) REVERT: J 108 ASP cc_start: 0.8453 (t0) cc_final: 0.8031 (t0) REVERT: J 111 GLU cc_start: 0.8509 (mp0) cc_final: 0.8274 (mp0) REVERT: J 161 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7895 (ttp-170) REVERT: J 165 GLU cc_start: 0.8172 (tp30) cc_final: 0.7747 (tp30) REVERT: K 125 THR cc_start: 0.8993 (m) cc_final: 0.8771 (m) REVERT: L 198 VAL cc_start: 0.9632 (OUTLIER) cc_final: 0.9402 (m) REVERT: M 30 TYR cc_start: 0.8650 (t80) cc_final: 0.8346 (t80) REVERT: M 104 ASN cc_start: 0.9037 (t0) cc_final: 0.8487 (t0) REVERT: M 210 ASP cc_start: 0.8464 (p0) cc_final: 0.8258 (p0) REVERT: N 61 TYR cc_start: 0.9298 (t80) cc_final: 0.8786 (t80) REVERT: N 71 ASN cc_start: 0.8798 (t0) cc_final: 0.8577 (t0) REVERT: N 165 GLU cc_start: 0.8233 (tp30) cc_final: 0.7936 (tp30) REVERT: N 167 ASP cc_start: 0.8615 (t0) cc_final: 0.8330 (t0) REVERT: O 118 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8839 (tm-30) REVERT: O 224 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: P 22 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7853 (mp0) REVERT: P 26 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8171 (mm-30) REVERT: P 48 GLU cc_start: 0.8390 (tt0) cc_final: 0.8092 (tm-30) REVERT: P 108 GLU cc_start: 0.8436 (tp30) cc_final: 0.8235 (tp30) REVERT: Q 24 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7997 (tm-30) REVERT: Q 52 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8691 (pttp) REVERT: Q 55 ASP cc_start: 0.7618 (t0) cc_final: 0.7293 (t0) REVERT: Q 90 GLU cc_start: 0.8590 (tp30) cc_final: 0.8170 (tp30) REVERT: Q 99 GLU cc_start: 0.7825 (mp0) cc_final: 0.7122 (mp0) REVERT: Q 121 SER cc_start: 0.8791 (t) cc_final: 0.8467 (p) REVERT: Q 122 ASN cc_start: 0.8844 (m-40) cc_final: 0.8516 (m-40) REVERT: Q 153 TYR cc_start: 0.9520 (p90) cc_final: 0.9295 (p90) REVERT: R 20 ARG cc_start: 0.8336 (pmm-80) cc_final: 0.7720 (mpp80) REVERT: R 32 LYS cc_start: 0.9134 (mttp) cc_final: 0.8746 (mtmt) REVERT: R 86 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8542 (mmmm) REVERT: R 166 ASP cc_start: 0.8299 (m-30) cc_final: 0.8068 (m-30) REVERT: S 16 GLN cc_start: 0.8920 (mp-120) cc_final: 0.8410 (mp10) REVERT: S 176 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8198 (tpt) REVERT: S 189 LYS cc_start: 0.9196 (mtmm) cc_final: 0.8919 (mtmm) REVERT: U 88 ARG cc_start: 0.8503 (mmm160) cc_final: 0.8199 (mmm160) REVERT: U 180 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8131 (mm-30) REVERT: U 214 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8298 (tp30) REVERT: W 105 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: W 150 GLU cc_start: 0.8588 (tp30) cc_final: 0.8160 (tt0) REVERT: W 154 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8418 (mt-10) REVERT: W 157 MET cc_start: 0.8972 (mtm) cc_final: 0.8558 (mtp) REVERT: W 164 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8255 (mm-30) REVERT: W 177 ASP cc_start: 0.8690 (t0) cc_final: 0.8230 (t0) REVERT: X 27 GLN cc_start: 0.8532 (pt0) cc_final: 0.7890 (pp30) REVERT: X 35 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7880 (mtt) REVERT: X 37 LYS cc_start: 0.9007 (tttt) cc_final: 0.8756 (tttp) REVERT: X 41 LYS cc_start: 0.9074 (mttp) cc_final: 0.8787 (mttt) REVERT: X 90 ASP cc_start: 0.8689 (m-30) cc_final: 0.8417 (m-30) REVERT: X 108 ASP cc_start: 0.8193 (t0) cc_final: 0.7850 (t0) REVERT: X 151 ILE cc_start: 0.9381 (tt) cc_final: 0.8853 (pp) REVERT: X 165 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7992 (mt-10) REVERT: Y 62 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8993 (mm110) REVERT: Y 81 LYS cc_start: 0.9237 (tptm) cc_final: 0.8485 (tptm) REVERT: Z 186 ASP cc_start: 0.8300 (t0) cc_final: 0.7894 (t0) REVERT: a 26 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8322 (mtp) REVERT: a 59 ASP cc_start: 0.8833 (m-30) cc_final: 0.8572 (m-30) REVERT: a 157 GLN cc_start: 0.8667 (tt0) cc_final: 0.8404 (pt0) REVERT: a 215 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7676 (pp) REVERT: b 90 TYR cc_start: 0.8884 (m-80) cc_final: 0.8634 (m-80) REVERT: d 36 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9235 (tt) REVERT: d 53 ASN cc_start: 0.9410 (t0) cc_final: 0.9185 (m-40) REVERT: d 56 ASP cc_start: 0.8357 (t70) cc_final: 0.7750 (p0) REVERT: d 173 ASP cc_start: 0.8558 (p0) cc_final: 0.8151 (p0) REVERT: d 185 MET cc_start: 0.8435 (mmp) cc_final: 0.7790 (mmp) REVERT: d 186 ASP cc_start: 0.8688 (p0) cc_final: 0.8298 (p0) REVERT: d 201 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8138 (tp30) REVERT: c 11 GLN cc_start: 0.8653 (tp-100) cc_final: 0.8067 (tp-100) REVERT: c 15 ASP cc_start: 0.8797 (m-30) cc_final: 0.8137 (m-30) REVERT: c 18 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8967 (ttp-110) REVERT: c 20 ASP cc_start: 0.9248 (t70) cc_final: 0.8947 (t0) REVERT: c 26 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7988 (pp20) REVERT: c 27 ASN cc_start: 0.9054 (p0) cc_final: 0.8666 (p0) REVERT: c 123 ASP cc_start: 0.8416 (m-30) cc_final: 0.7796 (m-30) REVERT: c 127 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8369 (mp10) REVERT: c 146 ASN cc_start: 0.9389 (t0) cc_final: 0.9026 (t160) REVERT: c 164 HIS cc_start: 0.9134 (t70) cc_final: 0.8886 (t-90) REVERT: c 168 GLU cc_start: 0.8630 (tp30) cc_final: 0.8096 (tp30) REVERT: c 171 HIS cc_start: 0.9266 (OUTLIER) cc_final: 0.8878 (t-90) REVERT: c 191 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8466 (mm110) REVERT: c 208 GLU cc_start: 0.8926 (tp30) cc_final: 0.8721 (tp30) REVERT: c 228 ASP cc_start: 0.8851 (t70) cc_final: 0.8596 (t70) REVERT: c 229 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8996 (tt) REVERT: c 249 TYR cc_start: 0.8652 (m-80) cc_final: 0.8332 (m-80) REVERT: f 26 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7759 (tp-100) REVERT: f 38 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8681 (mp10) REVERT: f 65 ASP cc_start: 0.8914 (t70) cc_final: 0.8682 (t70) REVERT: f 194 ARG cc_start: 0.8967 (mpt90) cc_final: 0.8640 (mpt-90) REVERT: f 201 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8625 (mm-30) REVERT: f 208 ASP cc_start: 0.8836 (m-30) cc_final: 0.8428 (m-30) REVERT: f 229 ASN cc_start: 0.8831 (t0) cc_final: 0.8568 (t160) REVERT: e 11 GLN cc_start: 0.9004 (tp40) cc_final: 0.8618 (tp40) REVERT: e 115 GLN cc_start: 0.9235 (mm110) cc_final: 0.9007 (tp40) REVERT: e 123 ASP cc_start: 0.8838 (m-30) cc_final: 0.8302 (t0) REVERT: e 147 ASN cc_start: 0.8993 (m-40) cc_final: 0.8774 (m-40) REVERT: e 173 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8751 (tm-30) REVERT: h 22 GLN cc_start: 0.8885 (mm110) cc_final: 0.8535 (mm-40) REVERT: h 205 MET cc_start: 0.9022 (mmm) cc_final: 0.8802 (mmt) REVERT: h 229 ASN cc_start: 0.8712 (t0) cc_final: 0.8223 (t0) REVERT: g 41 ASP cc_start: 0.8809 (p0) cc_final: 0.8527 (p0) REVERT: g 107 ASN cc_start: 0.8928 (t0) cc_final: 0.8652 (t0) REVERT: g 115 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8720 (mm-40) REVERT: g 116 ARG cc_start: 0.8715 (ptm160) cc_final: 0.8216 (ptm160) REVERT: g 120 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8272 (mp0) REVERT: g 123 ASP cc_start: 0.8964 (m-30) cc_final: 0.8614 (m-30) REVERT: g 180 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8389 (mm-30) REVERT: g 183 ASP cc_start: 0.9491 (m-30) cc_final: 0.9218 (m-30) REVERT: g 196 ASP cc_start: 0.8664 (p0) cc_final: 0.8420 (p0) REVERT: g 199 GLN cc_start: 0.9214 (mm110) cc_final: 0.8876 (mp10) REVERT: i 14 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8164 (mtm-85) REVERT: i 22 GLN cc_start: 0.8348 (pp30) cc_final: 0.8142 (pp30) REVERT: i 23 ASN cc_start: 0.9071 (m-40) cc_final: 0.8691 (m-40) REVERT: i 26 GLN cc_start: 0.8497 (pp30) cc_final: 0.8112 (pp30) REVERT: i 33 TYR cc_start: 0.9355 (m-80) cc_final: 0.9094 (m-80) REVERT: i 151 ASN cc_start: 0.9142 (m-40) cc_final: 0.8861 (m110) REVERT: i 173 ASP cc_start: 0.9140 (p0) cc_final: 0.8725 (p0) REVERT: i 208 ASP cc_start: 0.9216 (m-30) cc_final: 0.8950 (m-30) REVERT: i 221 SER cc_start: 0.9653 (t) cc_final: 0.9346 (m) outliers start: 177 outliers final: 81 residues processed: 1220 average time/residue: 1.4454 time to fit residues: 2224.0943 Evaluate side-chains 1188 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1085 time to evaluate : 5.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 181 ASN Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 173 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 107 CYS Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain Q residue 221 ASN Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain S residue 156 CYS Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 180 GLU Chi-restraints excluded: chain U residue 234 GLU Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 118 SER Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 167 SER Chi-restraints excluded: chain W residue 186 VAL Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain X residue 35 MET Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain Y residue 1 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 54 CYS Chi-restraints excluded: chain Z residue 166 LEU Chi-restraints excluded: chain a residue 26 MET Chi-restraints excluded: chain a residue 65 GLN Chi-restraints excluded: chain a residue 215 ILE Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 171 HIS Chi-restraints excluded: chain c residue 191 GLN Chi-restraints excluded: chain c residue 229 ILE Chi-restraints excluded: chain f residue 38 GLN Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 144 GLU Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain g residue 50 ASN Chi-restraints excluded: chain g residue 162 SER Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 126 GLN Chi-restraints excluded: chain i residue 140 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 452 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 436 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 465 optimal weight: 9.9990 chunk 498 optimal weight: 0.9990 chunk 361 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 575 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN J 55 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 HIS ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 GLN S 65 HIS S 68 ASN S 121 GLN V 57 GLN W 80 GLN ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 3 ASN a 47 ASN b 193 GLN c 129 ASN ** c 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 16 GLN ** h 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 GLN h 143 GLN h 151 ASN g 199 GLN i 143 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 59176 Z= 0.209 Angle : 0.625 11.455 80293 Z= 0.333 Chirality : 0.043 0.275 9335 Planarity : 0.004 0.063 10242 Dihedral : 4.462 45.762 8442 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.20 % Allowed : 21.26 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: 1.48 (0.10), residues: 7657 helix: 2.28 (0.08), residues: 3441 sheet: 0.16 (0.13), residues: 1466 loop : -0.18 (0.12), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 215 HIS 0.003 0.001 HIS D 73 PHE 0.030 0.001 PHE Q 171 TYR 0.032 0.001 TYR G 160 ARG 0.014 0.001 ARG h 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1183 time to evaluate : 5.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: A 95 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 106 THR cc_start: 0.9073 (m) cc_final: 0.8748 (m) REVERT: A 120 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8007 (t80) REVERT: A 142 ARG cc_start: 0.8263 (ptm-80) cc_final: 0.8042 (ptm-80) REVERT: A 165 ASN cc_start: 0.8719 (m110) cc_final: 0.8348 (t0) REVERT: B 26 GLU cc_start: 0.8716 (tp30) cc_final: 0.8038 (OUTLIER) REVERT: B 49 ARG cc_start: 0.8320 (mtp-110) cc_final: 0.7878 (ttm110) REVERT: B 50 ARG cc_start: 0.8608 (tpp80) cc_final: 0.7632 (tpp80) REVERT: B 69 ASN cc_start: 0.8641 (t0) cc_final: 0.8363 (t0) REVERT: B 72 MET cc_start: 0.8447 (ptm) cc_final: 0.8122 (mtp) REVERT: B 103 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 108 GLU cc_start: 0.8464 (tt0) cc_final: 0.8227 (tt0) REVERT: B 174 MET cc_start: 0.8504 (mtp) cc_final: 0.8144 (ttm) REVERT: B 178 ASP cc_start: 0.9144 (m-30) cc_final: 0.8841 (m-30) REVERT: B 184 MET cc_start: 0.8310 (tpp) cc_final: 0.7929 (mpt) REVERT: C 28 LYS cc_start: 0.9092 (mttm) cc_final: 0.8752 (mttm) REVERT: C 54 GLN cc_start: 0.8726 (tt0) cc_final: 0.8493 (mm110) REVERT: C 93 SER cc_start: 0.9222 (t) cc_final: 0.8936 (t) REVERT: C 105 GLU cc_start: 0.8666 (tp30) cc_final: 0.8414 (tp30) REVERT: C 137 ASP cc_start: 0.7853 (p0) cc_final: 0.7435 (p0) REVERT: C 206 ILE cc_start: 0.9120 (pt) cc_final: 0.8897 (mp) REVERT: D 5 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7447 (tpt170) REVERT: D 52 LYS cc_start: 0.9065 (mmtp) cc_final: 0.8846 (mmtm) REVERT: D 78 MET cc_start: 0.7873 (ppp) cc_final: 0.7629 (ppp) REVERT: D 166 ASP cc_start: 0.8706 (m-30) cc_final: 0.8406 (m-30) REVERT: D 216 GLU cc_start: 0.8327 (tt0) cc_final: 0.7619 (mt-10) REVERT: E 60 GLN cc_start: 0.8501 (pt0) cc_final: 0.7606 (pp30) REVERT: E 137 TYR cc_start: 0.8999 (t80) cc_final: 0.8604 (t80) REVERT: E 138 ASP cc_start: 0.8010 (p0) cc_final: 0.7743 (p0) REVERT: E 178 GLU cc_start: 0.8766 (pm20) cc_final: 0.8466 (pm20) REVERT: F 70 ASP cc_start: 0.8531 (t0) cc_final: 0.7883 (t0) REVERT: F 93 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7325 (tm-30) REVERT: F 181 MET cc_start: 0.9590 (pmm) cc_final: 0.9294 (pmm) REVERT: G 15 ILE cc_start: 0.9517 (pt) cc_final: 0.9286 (pp) REVERT: G 21 ARG cc_start: 0.8508 (mtp180) cc_final: 0.7898 (mtm110) REVERT: G 26 GLU cc_start: 0.8250 (mp0) cc_final: 0.7982 (mp0) REVERT: G 80 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8278 (mmt) REVERT: G 113 MET cc_start: 0.9083 (mmm) cc_final: 0.8799 (mmm) REVERT: G 131 MET cc_start: 0.7709 (ttp) cc_final: 0.7500 (ttp) REVERT: H 139 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: H 143 ARG cc_start: 0.8435 (ptt90) cc_final: 0.8183 (ptt90) REVERT: H 153 ASN cc_start: 0.8860 (m-40) cc_final: 0.8008 (m-40) REVERT: I 11 MET cc_start: 0.8765 (ttp) cc_final: 0.8540 (tpp) REVERT: I 92 ASN cc_start: 0.8945 (t0) cc_final: 0.8583 (t0) REVERT: I 105 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7978 (mm-30) REVERT: I 190 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7540 (mp0) REVERT: J 8 GLN cc_start: 0.8763 (tt0) cc_final: 0.8282 (tt0) REVERT: J 18 ASP cc_start: 0.8864 (p0) cc_final: 0.8612 (p0) REVERT: J 90 ASP cc_start: 0.8732 (m-30) cc_final: 0.8289 (m-30) REVERT: J 108 ASP cc_start: 0.8484 (t0) cc_final: 0.7946 (t0) REVERT: J 111 GLU cc_start: 0.8518 (mp0) cc_final: 0.8227 (mp0) REVERT: J 161 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7842 (ttp-170) REVERT: J 165 GLU cc_start: 0.8178 (tp30) cc_final: 0.7665 (tp30) REVERT: L 198 VAL cc_start: 0.9618 (OUTLIER) cc_final: 0.9403 (m) REVERT: M 30 TYR cc_start: 0.8554 (t80) cc_final: 0.8310 (t80) REVERT: M 104 ASN cc_start: 0.9036 (t0) cc_final: 0.8490 (t0) REVERT: N 61 TYR cc_start: 0.9242 (t80) cc_final: 0.8631 (t80) REVERT: N 167 ASP cc_start: 0.8609 (t0) cc_final: 0.8288 (t0) REVERT: O 22 GLU cc_start: 0.8408 (tt0) cc_final: 0.8050 (tm-30) REVERT: O 118 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8788 (tm-30) REVERT: O 224 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8361 (mp0) REVERT: P 22 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7821 (mp0) REVERT: P 26 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8099 (mm-30) REVERT: P 48 GLU cc_start: 0.8363 (tt0) cc_final: 0.8100 (tm-30) REVERT: P 108 GLU cc_start: 0.8455 (tp30) cc_final: 0.8035 (tp30) REVERT: Q 23 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8840 (mm110) REVERT: Q 24 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8021 (tm-30) REVERT: Q 52 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8707 (pttp) REVERT: Q 55 ASP cc_start: 0.7554 (t0) cc_final: 0.7243 (t0) REVERT: Q 90 GLU cc_start: 0.8513 (tp30) cc_final: 0.8161 (tp30) REVERT: Q 99 GLU cc_start: 0.7822 (mp0) cc_final: 0.7011 (mp0) REVERT: Q 116 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8479 (tp40) REVERT: Q 121 SER cc_start: 0.8749 (t) cc_final: 0.8425 (p) REVERT: Q 122 ASN cc_start: 0.8768 (m-40) cc_final: 0.8394 (m-40) REVERT: Q 153 TYR cc_start: 0.9516 (p90) cc_final: 0.9295 (p90) REVERT: R 20 ARG cc_start: 0.8346 (pmm-80) cc_final: 0.7742 (mpp80) REVERT: R 32 LYS cc_start: 0.9145 (mttp) cc_final: 0.8830 (mtmt) REVERT: R 86 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8523 (mmmm) REVERT: S 16 GLN cc_start: 0.8888 (mp-120) cc_final: 0.8384 (mp10) REVERT: S 39 LYS cc_start: 0.9204 (pttp) cc_final: 0.8945 (pttp) REVERT: S 189 LYS cc_start: 0.9170 (mtmm) cc_final: 0.8955 (mtmm) REVERT: T 184 MET cc_start: 0.8293 (ptp) cc_final: 0.7843 (ptp) REVERT: T 225 GLU cc_start: 0.7880 (pp20) cc_final: 0.7455 (pp20) REVERT: U 88 ARG cc_start: 0.8524 (mmm160) cc_final: 0.8217 (mmm160) REVERT: U 159 TYR cc_start: 0.7974 (t80) cc_final: 0.7739 (t80) REVERT: U 180 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: U 214 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8303 (tp30) REVERT: V 51 ASP cc_start: 0.8813 (m-30) cc_final: 0.8463 (m-30) REVERT: W 105 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: W 154 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8406 (mt-10) REVERT: W 157 MET cc_start: 0.8976 (mtm) cc_final: 0.8587 (mtp) REVERT: W 164 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8280 (mm-30) REVERT: W 177 ASP cc_start: 0.8641 (t0) cc_final: 0.8163 (t0) REVERT: X 27 GLN cc_start: 0.8606 (pt0) cc_final: 0.7912 (pp30) REVERT: X 35 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7751 (mtt) REVERT: X 37 LYS cc_start: 0.9046 (tttt) cc_final: 0.8805 (tttp) REVERT: X 41 LYS cc_start: 0.9023 (mttp) cc_final: 0.8777 (mttt) REVERT: X 90 ASP cc_start: 0.8701 (m-30) cc_final: 0.8472 (m-30) REVERT: X 108 ASP cc_start: 0.8144 (t0) cc_final: 0.7779 (t0) REVERT: X 144 ASP cc_start: 0.8597 (m-30) cc_final: 0.8384 (m-30) REVERT: X 151 ILE cc_start: 0.9377 (tt) cc_final: 0.8849 (pp) REVERT: X 165 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7936 (mt-10) REVERT: X 166 GLU cc_start: 0.8599 (tp30) cc_final: 0.8313 (tp30) REVERT: Y 62 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8996 (mm110) REVERT: Y 81 LYS cc_start: 0.9188 (tptm) cc_final: 0.8397 (tptm) REVERT: Z 91 MET cc_start: 0.8770 (tmm) cc_final: 0.8560 (ttm) REVERT: Z 146 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8531 (tm-30) REVERT: Z 186 ASP cc_start: 0.8139 (t0) cc_final: 0.7840 (t0) REVERT: a 157 GLN cc_start: 0.8681 (tt0) cc_final: 0.8439 (pt0) REVERT: b 90 TYR cc_start: 0.8771 (m-80) cc_final: 0.8544 (m-80) REVERT: d 38 GLN cc_start: 0.9315 (mm110) cc_final: 0.9114 (mm-40) REVERT: d 53 ASN cc_start: 0.9381 (t0) cc_final: 0.9159 (m-40) REVERT: d 56 ASP cc_start: 0.8362 (t70) cc_final: 0.7842 (p0) REVERT: d 185 MET cc_start: 0.8404 (mmp) cc_final: 0.7773 (mmp) REVERT: d 186 ASP cc_start: 0.8688 (p0) cc_final: 0.8292 (p0) REVERT: d 201 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8142 (tp30) REVERT: c 11 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8103 (tp-100) REVERT: c 18 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8942 (ttp-110) REVERT: c 20 ASP cc_start: 0.9185 (t70) cc_final: 0.8869 (t0) REVERT: c 27 ASN cc_start: 0.9021 (p0) cc_final: 0.8690 (p0) REVERT: c 123 ASP cc_start: 0.8377 (m-30) cc_final: 0.8051 (m-30) REVERT: c 127 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8618 (mp10) REVERT: c 146 ASN cc_start: 0.9383 (t0) cc_final: 0.9017 (t160) REVERT: c 164 HIS cc_start: 0.9100 (t70) cc_final: 0.8872 (t-90) REVERT: c 168 GLU cc_start: 0.8619 (tp30) cc_final: 0.8061 (tp30) REVERT: c 191 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8408 (mm110) REVERT: c 228 ASP cc_start: 0.8965 (t70) cc_final: 0.8599 (t70) REVERT: f 23 ASN cc_start: 0.8919 (m110) cc_final: 0.8499 (m-40) REVERT: f 26 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7729 (tp-100) REVERT: f 38 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8828 (mp10) REVERT: f 65 ASP cc_start: 0.8900 (t70) cc_final: 0.8662 (t70) REVERT: f 194 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8682 (mpt-90) REVERT: f 201 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8599 (mm-30) REVERT: f 208 ASP cc_start: 0.8791 (m-30) cc_final: 0.8356 (m-30) REVERT: f 229 ASN cc_start: 0.8831 (t0) cc_final: 0.8566 (t160) REVERT: e 11 GLN cc_start: 0.9056 (tp40) cc_final: 0.8761 (tp40) REVERT: e 115 GLN cc_start: 0.9183 (mm110) cc_final: 0.8970 (tp40) REVERT: e 123 ASP cc_start: 0.8812 (m-30) cc_final: 0.8257 (t0) REVERT: e 136 GLN cc_start: 0.9289 (mm110) cc_final: 0.9000 (mm-40) REVERT: e 173 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8725 (tm-30) REVERT: e 191 GLN cc_start: 0.9349 (mp10) cc_final: 0.9104 (mm110) REVERT: h 22 GLN cc_start: 0.8888 (mm110) cc_final: 0.8492 (mm-40) REVERT: h 182 THR cc_start: 0.9067 (p) cc_final: 0.8838 (p) REVERT: h 185 MET cc_start: 0.8547 (mmm) cc_final: 0.7568 (mmm) REVERT: h 205 MET cc_start: 0.8981 (mmm) cc_final: 0.8669 (mmt) REVERT: h 229 ASN cc_start: 0.8641 (t0) cc_final: 0.8162 (t0) REVERT: g 11 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8463 (tp40) REVERT: g 15 ASP cc_start: 0.9043 (t0) cc_final: 0.8814 (m-30) REVERT: g 41 ASP cc_start: 0.8799 (p0) cc_final: 0.8529 (p0) REVERT: g 107 ASN cc_start: 0.8865 (t0) cc_final: 0.8613 (t0) REVERT: g 115 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8703 (mm-40) REVERT: g 116 ARG cc_start: 0.8679 (ptm160) cc_final: 0.8149 (ptm160) REVERT: g 120 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8375 (mp0) REVERT: g 123 ASP cc_start: 0.8951 (m-30) cc_final: 0.8587 (m-30) REVERT: g 180 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8371 (mm-30) REVERT: g 183 ASP cc_start: 0.9499 (m-30) cc_final: 0.9225 (m-30) REVERT: g 196 ASP cc_start: 0.8795 (p0) cc_final: 0.8578 (p0) REVERT: g 199 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8869 (mp10) REVERT: i 14 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8142 (mtm-85) REVERT: i 22 GLN cc_start: 0.8479 (pp30) cc_final: 0.8260 (pp30) REVERT: i 23 ASN cc_start: 0.9022 (m-40) cc_final: 0.8524 (m-40) REVERT: i 26 GLN cc_start: 0.8472 (pp30) cc_final: 0.8087 (pp30) REVERT: i 33 TYR cc_start: 0.9346 (m-80) cc_final: 0.9079 (m-80) REVERT: i 151 ASN cc_start: 0.9155 (m-40) cc_final: 0.8877 (m110) REVERT: i 161 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8724 (mm-40) REVERT: i 173 ASP cc_start: 0.9118 (p0) cc_final: 0.8696 (p0) REVERT: i 185 MET cc_start: 0.8256 (mmm) cc_final: 0.7812 (mpp) REVERT: i 221 SER cc_start: 0.9675 (t) cc_final: 0.9380 (m) outliers start: 126 outliers final: 71 residues processed: 1249 average time/residue: 1.4341 time to fit residues: 2262.0286 Evaluate side-chains 1195 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1110 time to evaluate : 5.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 173 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain P residue 107 CYS Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain Q residue 221 ASN Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 144 ASP Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 180 GLU Chi-restraints excluded: chain U residue 234 GLU Chi-restraints excluded: chain V residue 118 SER Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 167 SER Chi-restraints excluded: chain W residue 186 VAL Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain X residue 35 MET Chi-restraints excluded: chain X residue 91 CYS Chi-restraints excluded: chain Y residue 1 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 54 CYS Chi-restraints excluded: chain Z residue 166 LEU Chi-restraints excluded: chain a residue 65 GLN Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 191 GLN Chi-restraints excluded: chain f residue 38 GLN Chi-restraints excluded: chain f residue 144 GLU Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain f residue 194 ARG Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain g residue 162 SER Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 140 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 665 optimal weight: 10.0000 chunk 700 optimal weight: 6.9990 chunk 639 optimal weight: 0.9990 chunk 681 optimal weight: 2.9990 chunk 410 optimal weight: 4.9990 chunk 296 optimal weight: 0.9990 chunk 535 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 616 optimal weight: 10.0000 chunk 644 optimal weight: 0.7980 chunk 679 optimal weight: 0.4980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN I 39 GLN J 55 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 GLN S 65 HIS S 68 ASN S 121 GLN V 57 GLN W 80 GLN ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 ASN a 108 ASN b 193 GLN c 105 ASN c 129 ASN c 221 ASN f 16 GLN e 136 GLN ** e 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 23 ASN ** h 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 GLN h 143 GLN i 143 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 59176 Z= 0.212 Angle : 0.638 12.252 80293 Z= 0.341 Chirality : 0.043 0.279 9335 Planarity : 0.004 0.063 10242 Dihedral : 4.434 45.137 8442 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.97 % Allowed : 22.01 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: 1.48 (0.10), residues: 7657 helix: 2.29 (0.09), residues: 3437 sheet: 0.15 (0.13), residues: 1482 loop : -0.17 (0.12), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP h 112 HIS 0.009 0.001 HIS f 192 PHE 0.034 0.001 PHE F 135 TYR 0.032 0.001 TYR G 160 ARG 0.013 0.001 ARG h 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1161 time to evaluate : 5.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: A 95 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 106 THR cc_start: 0.9155 (m) cc_final: 0.8810 (m) REVERT: A 120 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.7933 (t80) REVERT: A 142 ARG cc_start: 0.8204 (ptm-80) cc_final: 0.7991 (ptm-80) REVERT: A 165 ASN cc_start: 0.8709 (m110) cc_final: 0.8339 (t0) REVERT: B 15 GLU cc_start: 0.8494 (mp0) cc_final: 0.8225 (pm20) REVERT: B 26 GLU cc_start: 0.8709 (tp30) cc_final: 0.7999 (OUTLIER) REVERT: B 49 ARG cc_start: 0.8317 (mtp-110) cc_final: 0.7875 (ttm110) REVERT: B 50 ARG cc_start: 0.8612 (tpp80) cc_final: 0.7676 (tpp80) REVERT: B 69 ASN cc_start: 0.8607 (t0) cc_final: 0.8339 (t0) REVERT: B 72 MET cc_start: 0.8409 (ptm) cc_final: 0.8107 (mtp) REVERT: B 103 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7942 (mt-10) REVERT: B 108 GLU cc_start: 0.8437 (tt0) cc_final: 0.8234 (tt0) REVERT: B 174 MET cc_start: 0.8503 (mtp) cc_final: 0.8154 (ttm) REVERT: B 178 ASP cc_start: 0.9144 (m-30) cc_final: 0.8845 (m-30) REVERT: B 184 MET cc_start: 0.8253 (tpp) cc_final: 0.7997 (mpt) REVERT: C 28 LYS cc_start: 0.9089 (mttm) cc_final: 0.8793 (mttm) REVERT: C 54 GLN cc_start: 0.8790 (tt0) cc_final: 0.8320 (mm110) REVERT: C 66 ASP cc_start: 0.8133 (m-30) cc_final: 0.7847 (m-30) REVERT: C 93 SER cc_start: 0.9216 (t) cc_final: 0.8941 (t) REVERT: C 105 GLU cc_start: 0.8669 (tp30) cc_final: 0.8430 (tp30) REVERT: C 137 ASP cc_start: 0.7842 (p0) cc_final: 0.7424 (p0) REVERT: D 5 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7531 (tpt170) REVERT: D 78 MET cc_start: 0.7876 (ppp) cc_final: 0.7628 (ppp) REVERT: D 166 ASP cc_start: 0.8700 (m-30) cc_final: 0.8399 (m-30) REVERT: D 193 GLU cc_start: 0.8457 (mp0) cc_final: 0.8213 (pm20) REVERT: E 47 VAL cc_start: 0.9537 (OUTLIER) cc_final: 0.9327 (p) REVERT: E 60 GLN cc_start: 0.8499 (pt0) cc_final: 0.7605 (pp30) REVERT: E 137 TYR cc_start: 0.8986 (t80) cc_final: 0.8604 (t80) REVERT: E 138 ASP cc_start: 0.8021 (p0) cc_final: 0.7719 (p0) REVERT: E 178 GLU cc_start: 0.8761 (pm20) cc_final: 0.8460 (pm20) REVERT: F 70 ASP cc_start: 0.8522 (t0) cc_final: 0.7872 (t0) REVERT: F 93 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7346 (tm-30) REVERT: G 15 ILE cc_start: 0.9508 (pt) cc_final: 0.9287 (pp) REVERT: G 21 ARG cc_start: 0.8484 (mtp180) cc_final: 0.7841 (mtm110) REVERT: G 26 GLU cc_start: 0.8240 (mp0) cc_final: 0.7967 (mp0) REVERT: G 80 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8276 (mmt) REVERT: G 113 MET cc_start: 0.9063 (mmm) cc_final: 0.8767 (mmm) REVERT: H 139 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: H 153 ASN cc_start: 0.8664 (m-40) cc_final: 0.8006 (m-40) REVERT: I 92 ASN cc_start: 0.8933 (t0) cc_final: 0.8538 (t0) REVERT: I 105 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7982 (mm-30) REVERT: I 190 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7528 (mp0) REVERT: J 8 GLN cc_start: 0.8746 (tt0) cc_final: 0.8297 (tt0) REVERT: J 18 ASP cc_start: 0.8875 (p0) cc_final: 0.8620 (p0) REVERT: J 90 ASP cc_start: 0.8737 (m-30) cc_final: 0.8293 (m-30) REVERT: J 108 ASP cc_start: 0.8471 (t0) cc_final: 0.7914 (t0) REVERT: J 111 GLU cc_start: 0.8577 (mp0) cc_final: 0.8282 (mp0) REVERT: J 161 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7890 (ttp-170) REVERT: J 165 GLU cc_start: 0.8167 (tp30) cc_final: 0.7697 (tp30) REVERT: L 184 GLU cc_start: 0.8258 (tp30) cc_final: 0.8042 (tp30) REVERT: L 198 VAL cc_start: 0.9618 (OUTLIER) cc_final: 0.9400 (m) REVERT: M 104 ASN cc_start: 0.9033 (t0) cc_final: 0.8509 (t0) REVERT: N 61 TYR cc_start: 0.9273 (t80) cc_final: 0.8646 (t80) REVERT: N 167 ASP cc_start: 0.8611 (t0) cc_final: 0.8305 (t0) REVERT: O 108 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8972 (mm110) REVERT: O 118 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8755 (tm-30) REVERT: O 224 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8335 (mp0) REVERT: P 22 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7821 (mp0) REVERT: P 26 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8096 (mm-30) REVERT: P 48 GLU cc_start: 0.8378 (tt0) cc_final: 0.8061 (tm-30) REVERT: P 108 GLU cc_start: 0.8503 (tp30) cc_final: 0.8096 (tp30) REVERT: P 184 MET cc_start: 0.8483 (mmm) cc_final: 0.7965 (mpt) REVERT: Q 24 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7938 (tm-30) REVERT: Q 52 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8702 (pttp) REVERT: Q 55 ASP cc_start: 0.7535 (t0) cc_final: 0.7221 (t0) REVERT: Q 90 GLU cc_start: 0.8504 (tp30) cc_final: 0.8119 (tp30) REVERT: Q 99 GLU cc_start: 0.7785 (mp0) cc_final: 0.6976 (mp0) REVERT: Q 116 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8467 (tp40) REVERT: Q 121 SER cc_start: 0.8748 (t) cc_final: 0.8431 (p) REVERT: Q 122 ASN cc_start: 0.8762 (m-40) cc_final: 0.8397 (m-40) REVERT: Q 153 TYR cc_start: 0.9508 (p90) cc_final: 0.9302 (p90) REVERT: Q 215 GLN cc_start: 0.8932 (mt0) cc_final: 0.8446 (mp10) REVERT: R 20 ARG cc_start: 0.8329 (pmm-80) cc_final: 0.7717 (mpp80) REVERT: R 32 LYS cc_start: 0.9161 (mttp) cc_final: 0.8854 (mtmt) REVERT: R 86 LYS cc_start: 0.8935 (mmmt) cc_final: 0.8577 (mmmm) REVERT: R 231 LYS cc_start: 0.9172 (ttpp) cc_final: 0.8893 (tmmt) REVERT: S 16 GLN cc_start: 0.8896 (mp-120) cc_final: 0.8405 (mp10) REVERT: S 39 LYS cc_start: 0.9209 (pttp) cc_final: 0.8962 (pttp) REVERT: S 189 LYS cc_start: 0.9173 (mtmm) cc_final: 0.8956 (mtmm) REVERT: T 184 MET cc_start: 0.8343 (ptp) cc_final: 0.7975 (ptp) REVERT: T 225 GLU cc_start: 0.7958 (pp20) cc_final: 0.7570 (pp20) REVERT: U 88 ARG cc_start: 0.8537 (mmm160) cc_final: 0.8220 (mmm160) REVERT: U 180 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8045 (mm-30) REVERT: U 214 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8354 (tp30) REVERT: W 105 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: W 150 GLU cc_start: 0.8528 (tp30) cc_final: 0.8026 (tt0) REVERT: W 154 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8406 (mt-10) REVERT: W 157 MET cc_start: 0.8990 (mtm) cc_final: 0.8628 (mtp) REVERT: W 164 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8309 (mm-30) REVERT: W 177 ASP cc_start: 0.8655 (t0) cc_final: 0.8146 (t0) REVERT: X 27 GLN cc_start: 0.8596 (pt0) cc_final: 0.7930 (pp30) REVERT: X 35 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7765 (mtt) REVERT: X 37 LYS cc_start: 0.9071 (tttt) cc_final: 0.8830 (tttp) REVERT: X 41 LYS cc_start: 0.9027 (mttp) cc_final: 0.8810 (mttt) REVERT: X 90 ASP cc_start: 0.8704 (m-30) cc_final: 0.8464 (m-30) REVERT: X 108 ASP cc_start: 0.8131 (t0) cc_final: 0.7781 (t0) REVERT: X 151 ILE cc_start: 0.9357 (tt) cc_final: 0.8785 (pp) REVERT: X 165 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7947 (mt-10) REVERT: X 166 GLU cc_start: 0.8586 (tp30) cc_final: 0.8287 (tp30) REVERT: Y 62 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8942 (mm110) REVERT: Y 81 LYS cc_start: 0.9195 (tptm) cc_final: 0.8382 (tptm) REVERT: Z 146 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8497 (tm-30) REVERT: Z 186 ASP cc_start: 0.8104 (t0) cc_final: 0.7801 (t0) REVERT: a 157 GLN cc_start: 0.8671 (tt0) cc_final: 0.8436 (pt0) REVERT: a 215 ILE cc_start: 0.7840 (pp) cc_final: 0.7541 (pt) REVERT: b 90 TYR cc_start: 0.8757 (m-80) cc_final: 0.8544 (m-80) REVERT: b 107 GLU cc_start: 0.6413 (tm-30) cc_final: 0.5813 (tm-30) REVERT: d 38 GLN cc_start: 0.9311 (mm110) cc_final: 0.9105 (mm-40) REVERT: d 53 ASN cc_start: 0.9366 (t0) cc_final: 0.9154 (m-40) REVERT: d 56 ASP cc_start: 0.8379 (t70) cc_final: 0.7848 (p0) REVERT: d 185 MET cc_start: 0.8361 (mmp) cc_final: 0.7737 (mmp) REVERT: d 186 ASP cc_start: 0.8690 (p0) cc_final: 0.8302 (p0) REVERT: d 201 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8176 (tp30) REVERT: c 11 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8100 (tp-100) REVERT: c 20 ASP cc_start: 0.9186 (t70) cc_final: 0.8866 (t0) REVERT: c 26 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8142 (pp20) REVERT: c 27 ASN cc_start: 0.9037 (p0) cc_final: 0.8603 (p0) REVERT: c 123 ASP cc_start: 0.8373 (m-30) cc_final: 0.8048 (m-30) REVERT: c 127 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8724 (mp10) REVERT: c 146 ASN cc_start: 0.9388 (t0) cc_final: 0.9013 (t160) REVERT: c 164 HIS cc_start: 0.9102 (t70) cc_final: 0.8882 (t-90) REVERT: c 168 GLU cc_start: 0.8599 (tp30) cc_final: 0.8028 (tp30) REVERT: c 191 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8464 (mm110) REVERT: c 228 ASP cc_start: 0.8961 (t70) cc_final: 0.8604 (t70) REVERT: f 23 ASN cc_start: 0.8868 (m110) cc_final: 0.8557 (m-40) REVERT: f 26 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7701 (tp-100) REVERT: f 38 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8837 (mp10) REVERT: f 65 ASP cc_start: 0.8889 (t70) cc_final: 0.8650 (t70) REVERT: f 113 THR cc_start: 0.9611 (m) cc_final: 0.9403 (p) REVERT: f 194 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8694 (mpt-90) REVERT: f 201 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8603 (mm-30) REVERT: f 208 ASP cc_start: 0.8802 (m-30) cc_final: 0.8449 (m-30) REVERT: f 229 ASN cc_start: 0.8838 (t0) cc_final: 0.8582 (t160) REVERT: e 115 GLN cc_start: 0.9160 (mm110) cc_final: 0.8916 (tp40) REVERT: e 136 GLN cc_start: 0.9290 (mm-40) cc_final: 0.9038 (mm-40) REVERT: e 173 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8786 (tm-30) REVERT: e 191 GLN cc_start: 0.9370 (mp10) cc_final: 0.9164 (mm110) REVERT: h 22 GLN cc_start: 0.8899 (mm110) cc_final: 0.8540 (mm-40) REVERT: h 26 GLN cc_start: 0.8276 (pp30) cc_final: 0.8075 (pp30) REVERT: h 182 THR cc_start: 0.9058 (p) cc_final: 0.8822 (p) REVERT: h 185 MET cc_start: 0.8527 (mmm) cc_final: 0.7547 (mmm) REVERT: h 229 ASN cc_start: 0.8623 (t0) cc_final: 0.8150 (t0) REVERT: g 11 GLN cc_start: 0.8986 (tp-100) cc_final: 0.8504 (tp40) REVERT: g 15 ASP cc_start: 0.9046 (t0) cc_final: 0.8823 (m-30) REVERT: g 41 ASP cc_start: 0.8764 (p0) cc_final: 0.8500 (p0) REVERT: g 107 ASN cc_start: 0.8852 (t0) cc_final: 0.8603 (t0) REVERT: g 115 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8700 (mm-40) REVERT: g 116 ARG cc_start: 0.8675 (ptm160) cc_final: 0.8191 (ptm160) REVERT: g 120 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8254 (mp0) REVERT: g 123 ASP cc_start: 0.8954 (m-30) cc_final: 0.8590 (m-30) REVERT: g 180 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8419 (mm-30) REVERT: g 183 ASP cc_start: 0.9501 (m-30) cc_final: 0.9226 (m-30) REVERT: g 196 ASP cc_start: 0.8802 (p0) cc_final: 0.8580 (p0) REVERT: g 199 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8849 (mp10) REVERT: g 215 MET cc_start: 0.8719 (ttm) cc_final: 0.8333 (mtt) REVERT: i 14 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.8208 (mtm-85) REVERT: i 23 ASN cc_start: 0.9024 (m-40) cc_final: 0.8747 (m110) REVERT: i 26 GLN cc_start: 0.8464 (pp30) cc_final: 0.8044 (pp30) REVERT: i 33 TYR cc_start: 0.9344 (m-80) cc_final: 0.9084 (m-80) REVERT: i 58 THR cc_start: 0.9378 (p) cc_final: 0.9088 (t) REVERT: i 151 ASN cc_start: 0.9154 (m-40) cc_final: 0.8871 (m110) REVERT: i 161 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8526 (mm-40) REVERT: i 173 ASP cc_start: 0.9091 (p0) cc_final: 0.8759 (p0) REVERT: i 221 SER cc_start: 0.9673 (t) cc_final: 0.9379 (m) outliers start: 113 outliers final: 74 residues processed: 1222 average time/residue: 1.4501 time to fit residues: 2243.6066 Evaluate side-chains 1196 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1108 time to evaluate : 5.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 181 ASN Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain M residue 173 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain M residue 210 ASP Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain P residue 72 MET Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 CYS Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain Q residue 221 ASN Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain T residue 31 GLU Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 180 GLU Chi-restraints excluded: chain U residue 234 GLU Chi-restraints excluded: chain V residue 118 SER Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 167 SER Chi-restraints excluded: chain W residue 186 VAL Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain X residue 35 MET Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain Y residue 1 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 54 CYS Chi-restraints excluded: chain Z residue 166 LEU Chi-restraints excluded: chain a residue 65 GLN Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain c residue 191 GLN Chi-restraints excluded: chain f residue 38 GLN Chi-restraints excluded: chain f residue 144 GLU Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain f residue 194 ARG Chi-restraints excluded: chain h residue 163 THR Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain g residue 162 SER Chi-restraints excluded: chain i residue 140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 447 optimal weight: 2.9990 chunk 720 optimal weight: 2.9990 chunk 439 optimal weight: 0.0980 chunk 341 optimal weight: 0.9990 chunk 501 optimal weight: 0.3980 chunk 756 optimal weight: 0.9990 chunk 695 optimal weight: 1.9990 chunk 602 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 465 optimal weight: 10.0000 chunk 369 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 182 GLN E 16 GLN I 30 GLN I 39 GLN J 27 GLN J 55 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 198 ASN Q 23 GLN S 60 GLN S 65 HIS S 68 ASN S 121 GLN W 80 GLN ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 3 ASN a 47 ASN a 108 ASN b 193 GLN ** d 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 16 GLN ** e 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 GLN h 143 GLN h 151 ASN i 143 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 59176 Z= 0.197 Angle : 0.646 12.882 80293 Z= 0.345 Chirality : 0.043 0.283 9335 Planarity : 0.004 0.063 10242 Dihedral : 4.404 44.447 8442 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.76 % Allowed : 22.71 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: 1.47 (0.10), residues: 7657 helix: 2.29 (0.09), residues: 3437 sheet: 0.16 (0.13), residues: 1479 loop : -0.19 (0.12), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP h 112 HIS 0.013 0.001 HIS N 38 PHE 0.032 0.001 PHE d 212 TYR 0.031 0.001 TYR G 160 ARG 0.012 0.001 ARG h 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1168 time to evaluate : 5.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8252 (pm20) REVERT: A 95 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7697 (tm-30) REVERT: A 106 THR cc_start: 0.9094 (m) cc_final: 0.8742 (m) REVERT: A 120 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.7901 (t80) REVERT: A 165 ASN cc_start: 0.8694 (m110) cc_final: 0.8335 (t0) REVERT: B 15 GLU cc_start: 0.8643 (mp0) cc_final: 0.8413 (pm20) REVERT: B 26 GLU cc_start: 0.8680 (tp30) cc_final: 0.7903 (OUTLIER) REVERT: B 49 ARG cc_start: 0.8309 (mtp-110) cc_final: 0.7870 (ttm110) REVERT: B 50 ARG cc_start: 0.8505 (tpp80) cc_final: 0.7584 (tpp80) REVERT: B 67 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8274 (tttt) REVERT: B 69 ASN cc_start: 0.8559 (t0) cc_final: 0.8292 (t0) REVERT: B 72 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7999 (mtp) REVERT: B 174 MET cc_start: 0.8479 (mtp) cc_final: 0.8160 (ttm) REVERT: B 178 ASP cc_start: 0.9136 (m-30) cc_final: 0.8834 (m-30) REVERT: B 180 LYS cc_start: 0.9211 (mtmm) cc_final: 0.8969 (ptpp) REVERT: B 184 MET cc_start: 0.8185 (tpp) cc_final: 0.7805 (mpt) REVERT: C 28 LYS cc_start: 0.9091 (mttm) cc_final: 0.8838 (mttm) REVERT: C 54 GLN cc_start: 0.8755 (tt0) cc_final: 0.8309 (mm110) REVERT: C 93 SER cc_start: 0.9219 (t) cc_final: 0.8946 (t) REVERT: C 105 GLU cc_start: 0.8676 (tp30) cc_final: 0.8448 (tp30) REVERT: C 137 ASP cc_start: 0.7788 (p0) cc_final: 0.7342 (p0) REVERT: D 78 MET cc_start: 0.7856 (ppp) cc_final: 0.7610 (ppp) REVERT: D 166 ASP cc_start: 0.8692 (m-30) cc_final: 0.8389 (m-30) REVERT: D 193 GLU cc_start: 0.8452 (mp0) cc_final: 0.8214 (pm20) REVERT: E 47 VAL cc_start: 0.9525 (OUTLIER) cc_final: 0.9324 (p) REVERT: E 60 GLN cc_start: 0.8498 (pt0) cc_final: 0.7642 (pp30) REVERT: E 116 THR cc_start: 0.9393 (m) cc_final: 0.9121 (p) REVERT: E 137 TYR cc_start: 0.8967 (t80) cc_final: 0.8592 (t80) REVERT: E 138 ASP cc_start: 0.8030 (p0) cc_final: 0.7736 (p0) REVERT: E 178 GLU cc_start: 0.8754 (pm20) cc_final: 0.8455 (pm20) REVERT: F 70 ASP cc_start: 0.8492 (t0) cc_final: 0.7840 (t0) REVERT: F 93 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7382 (tm-30) REVERT: G 15 ILE cc_start: 0.9491 (pt) cc_final: 0.9274 (pp) REVERT: G 21 ARG cc_start: 0.8453 (mtp180) cc_final: 0.7817 (mtm110) REVERT: G 26 GLU cc_start: 0.8228 (mp0) cc_final: 0.7952 (mp0) REVERT: G 80 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8271 (mmt) REVERT: G 113 MET cc_start: 0.9107 (mmm) cc_final: 0.8853 (mmm) REVERT: H 139 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: H 153 ASN cc_start: 0.8546 (m-40) cc_final: 0.8188 (m110) REVERT: I 92 ASN cc_start: 0.8937 (t0) cc_final: 0.8552 (t0) REVERT: I 105 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7954 (mm-30) REVERT: J 8 GLN cc_start: 0.8738 (tt0) cc_final: 0.8304 (tt0) REVERT: J 11 ASP cc_start: 0.9001 (p0) cc_final: 0.8754 (p0) REVERT: J 18 ASP cc_start: 0.8862 (p0) cc_final: 0.8628 (p0) REVERT: J 61 GLN cc_start: 0.9496 (tt0) cc_final: 0.9175 (tt0) REVERT: J 90 ASP cc_start: 0.8693 (m-30) cc_final: 0.8269 (m-30) REVERT: J 108 ASP cc_start: 0.8456 (t0) cc_final: 0.8137 (t70) REVERT: J 161 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7949 (ttp-170) REVERT: J 165 GLU cc_start: 0.8120 (tp30) cc_final: 0.7655 (tp30) REVERT: K 56 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8780 (mm-30) REVERT: L 184 GLU cc_start: 0.8223 (tp30) cc_final: 0.8008 (tp30) REVERT: L 198 VAL cc_start: 0.9613 (OUTLIER) cc_final: 0.9397 (m) REVERT: M 104 ASN cc_start: 0.9021 (t0) cc_final: 0.8507 (t0) REVERT: M 127 MET cc_start: 0.8992 (ttm) cc_final: 0.8759 (ttm) REVERT: N 61 TYR cc_start: 0.9265 (t80) cc_final: 0.8639 (t80) REVERT: N 119 MET cc_start: 0.8317 (ppp) cc_final: 0.8078 (ttt) REVERT: O 108 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8949 (mm110) REVERT: O 118 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8693 (tm-30) REVERT: O 211 ILE cc_start: 0.9547 (pt) cc_final: 0.9326 (pp) REVERT: O 224 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8323 (mp0) REVERT: P 22 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8084 (mp0) REVERT: P 26 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8082 (mm-30) REVERT: P 48 GLU cc_start: 0.8369 (tt0) cc_final: 0.8070 (tm-30) REVERT: P 108 GLU cc_start: 0.8441 (tp30) cc_final: 0.8061 (tp30) REVERT: P 184 MET cc_start: 0.8506 (mmm) cc_final: 0.8020 (mpt) REVERT: Q 24 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7897 (tm-30) REVERT: Q 55 ASP cc_start: 0.7610 (t0) cc_final: 0.7234 (t0) REVERT: Q 90 GLU cc_start: 0.8483 (tp30) cc_final: 0.8114 (tp30) REVERT: Q 99 GLU cc_start: 0.7696 (mp0) cc_final: 0.7039 (mp0) REVERT: Q 116 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8535 (tp40) REVERT: Q 121 SER cc_start: 0.8722 (t) cc_final: 0.8406 (p) REVERT: Q 122 ASN cc_start: 0.8764 (m-40) cc_final: 0.8421 (m-40) REVERT: Q 215 GLN cc_start: 0.8875 (mt0) cc_final: 0.8450 (mp10) REVERT: R 20 ARG cc_start: 0.8320 (pmm-80) cc_final: 0.7707 (mpp80) REVERT: R 32 LYS cc_start: 0.9143 (mttp) cc_final: 0.8938 (mtmt) REVERT: R 86 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8596 (mmmm) REVERT: R 231 LYS cc_start: 0.9169 (ttpp) cc_final: 0.8956 (tmmt) REVERT: S 16 GLN cc_start: 0.8888 (mp-120) cc_final: 0.8400 (mp10) REVERT: S 39 LYS cc_start: 0.9186 (pttp) cc_final: 0.8946 (pttp) REVERT: S 189 LYS cc_start: 0.9163 (mtmm) cc_final: 0.8924 (mtmm) REVERT: T 184 MET cc_start: 0.8324 (ptp) cc_final: 0.7959 (ptp) REVERT: T 225 GLU cc_start: 0.7983 (pp20) cc_final: 0.7568 (pp20) REVERT: U 88 ARG cc_start: 0.8544 (mmm160) cc_final: 0.8212 (mmm160) REVERT: U 174 GLU cc_start: 0.9002 (mp0) cc_final: 0.8733 (mp0) REVERT: U 180 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: W 79 ARG cc_start: 0.9080 (ppt-90) cc_final: 0.8860 (ppt-90) REVERT: W 105 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: W 150 GLU cc_start: 0.8490 (tp30) cc_final: 0.7959 (tt0) REVERT: W 154 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8394 (mt-10) REVERT: W 157 MET cc_start: 0.8980 (mtm) cc_final: 0.8605 (mtp) REVERT: W 164 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8299 (mm-30) REVERT: W 177 ASP cc_start: 0.8670 (t0) cc_final: 0.8137 (t0) REVERT: X 27 GLN cc_start: 0.8585 (pt0) cc_final: 0.7973 (pp30) REVERT: X 37 LYS cc_start: 0.9033 (tttt) cc_final: 0.8796 (tttp) REVERT: X 90 ASP cc_start: 0.8732 (m-30) cc_final: 0.8499 (m-30) REVERT: X 108 ASP cc_start: 0.8117 (t0) cc_final: 0.7800 (t0) REVERT: X 151 ILE cc_start: 0.9356 (tt) cc_final: 0.8784 (pp) REVERT: X 165 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7947 (mt-10) REVERT: X 166 GLU cc_start: 0.8585 (tp30) cc_final: 0.8281 (tp30) REVERT: Y 81 LYS cc_start: 0.9151 (tptm) cc_final: 0.8334 (tptm) REVERT: Z 146 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8437 (tm-30) REVERT: Z 186 ASP cc_start: 0.8050 (t0) cc_final: 0.7710 (t0) REVERT: a 157 GLN cc_start: 0.8718 (tt0) cc_final: 0.8490 (pt0) REVERT: a 215 ILE cc_start: 0.7681 (pp) cc_final: 0.7397 (pt) REVERT: b 90 TYR cc_start: 0.8717 (m-80) cc_final: 0.8512 (m-80) REVERT: d 34 ARG cc_start: 0.9000 (mpp80) cc_final: 0.8761 (mtt-85) REVERT: d 38 GLN cc_start: 0.9326 (mm110) cc_final: 0.9123 (mm-40) REVERT: d 53 ASN cc_start: 0.9377 (t0) cc_final: 0.9163 (m-40) REVERT: d 56 ASP cc_start: 0.8359 (t70) cc_final: 0.7818 (p0) REVERT: d 185 MET cc_start: 0.8324 (mmp) cc_final: 0.7713 (mmp) REVERT: d 186 ASP cc_start: 0.8671 (p0) cc_final: 0.8280 (p0) REVERT: d 201 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8162 (tp30) REVERT: c 11 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8150 (tp-100) REVERT: c 20 ASP cc_start: 0.9154 (t70) cc_final: 0.8826 (t0) REVERT: c 26 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8144 (pp20) REVERT: c 115 GLN cc_start: 0.8524 (pp30) cc_final: 0.8242 (pp30) REVERT: c 123 ASP cc_start: 0.8346 (m-30) cc_final: 0.8019 (m-30) REVERT: c 146 ASN cc_start: 0.9380 (t0) cc_final: 0.9009 (t160) REVERT: c 164 HIS cc_start: 0.9088 (t70) cc_final: 0.8875 (t-90) REVERT: c 168 GLU cc_start: 0.8602 (tp30) cc_final: 0.7986 (tp30) REVERT: c 191 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8458 (mm110) REVERT: c 228 ASP cc_start: 0.8978 (t70) cc_final: 0.8626 (t70) REVERT: f 22 GLN cc_start: 0.8554 (pp30) cc_final: 0.8265 (pp30) REVERT: f 23 ASN cc_start: 0.8887 (m110) cc_final: 0.8492 (m-40) REVERT: f 26 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7675 (tp-100) REVERT: f 38 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8854 (mp10) REVERT: f 65 ASP cc_start: 0.8878 (t70) cc_final: 0.8635 (t70) REVERT: f 113 THR cc_start: 0.9601 (m) cc_final: 0.9397 (p) REVERT: f 194 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8697 (mpt-90) REVERT: f 201 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8604 (mm-30) REVERT: f 208 ASP cc_start: 0.8801 (m-30) cc_final: 0.8454 (m-30) REVERT: f 229 ASN cc_start: 0.8845 (t0) cc_final: 0.8589 (t160) REVERT: e 115 GLN cc_start: 0.9099 (mm110) cc_final: 0.8869 (tp40) REVERT: e 173 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8697 (tm-30) REVERT: e 191 GLN cc_start: 0.9340 (mp10) cc_final: 0.9128 (mm110) REVERT: e 199 GLN cc_start: 0.9312 (tp40) cc_final: 0.9038 (tp40) REVERT: h 22 GLN cc_start: 0.8874 (mm110) cc_final: 0.8519 (mm-40) REVERT: h 182 THR cc_start: 0.9011 (p) cc_final: 0.8765 (p) REVERT: h 185 MET cc_start: 0.8480 (mmm) cc_final: 0.7552 (mmm) REVERT: h 229 ASN cc_start: 0.8620 (t0) cc_final: 0.8178 (t0) REVERT: g 107 ASN cc_start: 0.8834 (t0) cc_final: 0.8591 (t0) REVERT: g 115 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8658 (mm-40) REVERT: g 116 ARG cc_start: 0.8670 (ptm160) cc_final: 0.8229 (ptm160) REVERT: g 120 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8233 (mp0) REVERT: g 123 ASP cc_start: 0.8971 (m-30) cc_final: 0.8625 (m-30) REVERT: g 180 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8409 (mm-30) REVERT: g 183 ASP cc_start: 0.9493 (m-30) cc_final: 0.9218 (m-30) REVERT: g 196 ASP cc_start: 0.8846 (p0) cc_final: 0.8623 (p0) REVERT: g 199 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8850 (mp10) REVERT: g 215 MET cc_start: 0.8738 (ttm) cc_final: 0.8372 (mtt) REVERT: i 14 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8213 (mtm-85) REVERT: i 23 ASN cc_start: 0.9086 (m-40) cc_final: 0.8781 (m110) REVERT: i 26 GLN cc_start: 0.8430 (pp30) cc_final: 0.8046 (pp30) REVERT: i 58 THR cc_start: 0.9345 (p) cc_final: 0.9060 (t) REVERT: i 151 ASN cc_start: 0.9150 (m-40) cc_final: 0.8869 (m110) REVERT: i 161 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8544 (mm-40) REVERT: i 173 ASP cc_start: 0.9077 (p0) cc_final: 0.8748 (p0) REVERT: i 221 SER cc_start: 0.9664 (t) cc_final: 0.9377 (m) outliers start: 101 outliers final: 65 residues processed: 1225 average time/residue: 1.4310 time to fit residues: 2220.2436 Evaluate side-chains 1198 residues out of total 6522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1121 time to evaluate : 5.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 181 ASN Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain M residue 173 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain P residue 72 MET Chi-restraints excluded: chain P residue 107 CYS Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain Q residue 221 ASN Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain T residue 31 GLU Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain U residue 180 GLU Chi-restraints excluded: chain U residue 234 GLU Chi-restraints excluded: chain V residue 118 SER Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 167 SER Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain Y residue 1 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 54 CYS Chi-restraints excluded: chain Z residue 166 LEU Chi-restraints excluded: chain a residue 65 GLN Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain c residue 191 GLN Chi-restraints excluded: chain f residue 38 GLN Chi-restraints excluded: chain f residue 144 GLU Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain f residue 194 ARG Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain g residue 162 SER Chi-restraints excluded: chain i residue 140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 478 optimal weight: 1.9990 chunk 641 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 chunk 555 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 603 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 619 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN E 16 GLN I 30 GLN J 27 GLN J 55 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN L 157 ASN O 95 GLN ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 GLN S 65 HIS S 68 ASN S 121 GLN V 57 GLN W 80 GLN W 172 ASN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 ASN a 108 ASN b 193 GLN c 105 ASN e 129 ASN ** e 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.072054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.058257 restraints weight = 153117.357| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.94 r_work: 0.2737 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 59176 Z= 0.212 Angle : 0.655 12.932 80293 Z= 0.350 Chirality : 0.043 0.294 9335 Planarity : 0.005 0.118 10242 Dihedral : 4.394 43.968 8442 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.69 % Allowed : 23.67 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: 1.47 (0.10), residues: 7657 helix: 2.27 (0.09), residues: 3423 sheet: 0.17 (0.13), residues: 1487 loop : -0.17 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP h 112 HIS 0.010 0.001 HIS f 192 PHE 0.034 0.001 PHE d 212 TYR 0.030 0.001 TYR G 160 ARG 0.012 0.001 ARG O 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29471.63 seconds wall clock time: 501 minutes 13.78 seconds (30073.78 seconds total)