Starting phenix.real_space_refine on Tue Nov 18 23:39:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5m3l_3434/11_2025/5m3l_3434.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m3l_3434/11_2025/5m3l_3434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5m3l_3434/11_2025/5m3l_3434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m3l_3434/11_2025/5m3l_3434.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5m3l_3434/11_2025/5m3l_3434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m3l_3434/11_2025/5m3l_3434.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.520 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 69 5.16 5 C 12182 2.51 5 N 3437 2.21 5 O 3307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19007 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1163 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 142} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1095 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 140} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1152 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 143} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1088 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1174 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 142} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "F" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1076 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 140} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "G" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1151 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 143} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "H" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1094 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1168 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 142} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1089 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 139} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "K" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1156 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 143} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "L" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1094 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "M" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "N" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1676 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 215} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 8, 'GLN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "O" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1636 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 205} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASP:plan': 4, 'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.08, per 1000 atoms: 0.27 Number of scatterers: 19007 At special positions: 0 Unit cell: (135.42, 148.74, 134.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 69 16.00 O 3307 8.00 N 3437 7.00 C 12182 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 817.0 milliseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4508 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 7 sheets defined 65.3% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 removed outlier: 3.649A pdb=" N VAL A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 43 removed outlier: 3.511A pdb=" N VAL A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 65 through 82 removed outlier: 4.143A pdb=" N ARG A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 removed outlier: 4.208A pdb=" N SER A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.903A pdb=" N PHE A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.706A pdb=" N HIS A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 142 " --> pdb=" O CYS A 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 20 removed outlier: 3.922A pdb=" N LEU B 10 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 41 removed outlier: 3.922A pdb=" N ILE B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.740A pdb=" N ARG B 45 " --> pdb=" O PRO B 42 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ARG B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS B 52 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 78 removed outlier: 3.662A pdb=" N HIS B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 98 removed outlier: 3.576A pdb=" N LYS B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY B 98 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 121 removed outlier: 3.516A pdb=" N LYS B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 142 removed outlier: 3.510A pdb=" N ALA B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 20 removed outlier: 4.070A pdb=" N HIS C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 14 " --> pdb=" O GLU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 removed outlier: 3.649A pdb=" N ARG C 24 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP C 25 " --> pdb=" O LEU C 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 25' Processing helix chain 'C' and resid 28 through 45 removed outlier: 3.909A pdb=" N LEU C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 40 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 41 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.514A pdb=" N PHE C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG C 56 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 84 removed outlier: 4.154A pdb=" N HIS C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 104 removed outlier: 3.991A pdb=" N LEU C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 93 " --> pdb=" O PRO C 89 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 104 " --> pdb=" O HIS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 128 removed outlier: 4.057A pdb=" N LYS C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Proline residue: C 125 - end of helix removed outlier: 3.707A pdb=" N LEU C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 Processing helix chain 'D' and resid 10 through 26 removed outlier: 4.303A pdb=" N VAL D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 18 " --> pdb=" O SER D 14 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 24 " --> pdb=" O GLN D 20 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 46 removed outlier: 3.785A pdb=" N ASP D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP D 44 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.572A pdb=" N LYS D 50 " --> pdb=" O PRO D 47 " (cutoff:3.500A) Proline residue: D 52 - end of helix removed outlier: 4.134A pdb=" N ARG D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 84 removed outlier: 3.557A pdb=" N LEU D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 103 removed outlier: 3.770A pdb=" N ALA D 91 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D 100 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 127 removed outlier: 4.251A pdb=" N PHE D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP D 112 " --> pdb=" O PRO D 108 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 115 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 121 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP D 124 " --> pdb=" O HIS D 120 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.618A pdb=" N ASP D 140 " --> pdb=" O HIS D 136 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE D 142 " --> pdb=" O CYS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'E' and resid 9 through 24 removed outlier: 3.502A pdb=" N ARG E 13 " --> pdb=" O TYR E 9 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL E 22 " --> pdb=" O ILE E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 43 removed outlier: 3.518A pdb=" N VAL E 35 " --> pdb=" O ARG E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 Processing helix chain 'E' and resid 65 through 82 removed outlier: 4.143A pdb=" N ARG E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 removed outlier: 4.224A pdb=" N SER E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 122 removed outlier: 3.735A pdb=" N ARG E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU E 117 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 120 " --> pdb=" O GLY E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.696A pdb=" N HIS E 140 " --> pdb=" O ASN E 136 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG E 141 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU E 142 " --> pdb=" O CYS E 138 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 20 removed outlier: 3.921A pdb=" N LEU F 10 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS F 13 " --> pdb=" O GLY F 9 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 41 removed outlier: 3.922A pdb=" N ILE F 33 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA F 39 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 52 removed outlier: 3.746A pdb=" N ARG F 45 " --> pdb=" O PRO F 42 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG F 50 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS F 52 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 78 removed outlier: 3.669A pdb=" N HIS F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F 74 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 98 removed outlier: 3.573A pdb=" N LYS F 86 " --> pdb=" O PRO F 82 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN F 93 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN F 95 " --> pdb=" O HIS F 91 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY F 98 " --> pdb=" O VAL F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 121 removed outlier: 3.527A pdb=" N LYS F 110 " --> pdb=" O PHE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 142 removed outlier: 3.508A pdb=" N ALA F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP F 135 " --> pdb=" O ASP F 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 20 removed outlier: 4.073A pdb=" N HIS G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE G 14 " --> pdb=" O GLU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 removed outlier: 3.641A pdb=" N ARG G 24 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP G 25 " --> pdb=" O LEU G 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 21 through 25' Processing helix chain 'G' and resid 28 through 45 removed outlier: 3.909A pdb=" N LEU G 39 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU G 40 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 58 removed outlier: 3.502A pdb=" N PHE G 54 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG G 56 " --> pdb=" O LEU G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 84 removed outlier: 4.142A pdb=" N HIS G 70 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 104 removed outlier: 3.992A pdb=" N LEU G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL G 104 " --> pdb=" O HIS G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 128 removed outlier: 4.063A pdb=" N LYS G 114 " --> pdb=" O LYS G 110 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) Proline residue: G 125 - end of helix removed outlier: 3.717A pdb=" N LEU G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 147 removed outlier: 3.500A pdb=" N LYS G 146 " --> pdb=" O GLY G 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 26 removed outlier: 4.292A pdb=" N VAL H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS H 18 " --> pdb=" O SER H 14 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA H 24 " --> pdb=" O GLN H 20 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY H 26 " --> pdb=" O ALA H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 46 removed outlier: 3.791A pdb=" N ASP H 41 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE H 42 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 56 removed outlier: 3.575A pdb=" N LYS H 50 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Proline residue: H 52 - end of helix removed outlier: 4.130A pdb=" N ARG H 55 " --> pdb=" O PRO H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 84 removed outlier: 3.560A pdb=" N LEU H 77 " --> pdb=" O VAL H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 103 removed outlier: 3.776A pdb=" N ALA H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN H 93 " --> pdb=" O MET H 89 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN H 100 " --> pdb=" O HIS H 96 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU H 103 " --> pdb=" O VAL H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 127 removed outlier: 4.267A pdb=" N PHE H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 115 " --> pdb=" O PHE H 111 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS H 116 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY H 123 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP H 124 " --> pdb=" O HIS H 120 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG H 125 " --> pdb=" O VAL H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.614A pdb=" N ASP H 140 " --> pdb=" O HIS H 136 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE H 142 " --> pdb=" O CYS H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'I' and resid 9 through 24 removed outlier: 3.500A pdb=" N ARG I 13 " --> pdb=" O TYR I 9 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL I 22 " --> pdb=" O ILE I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 43 removed outlier: 3.522A pdb=" N VAL I 35 " --> pdb=" O ARG I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 52 Processing helix chain 'I' and resid 65 through 82 removed outlier: 4.144A pdb=" N ARG I 72 " --> pdb=" O SER I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 103 removed outlier: 4.215A pdb=" N SER I 92 " --> pdb=" O LEU I 88 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS I 101 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 122 removed outlier: 3.905A pdb=" N PHE I 112 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG I 113 " --> pdb=" O LYS I 109 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU I 117 " --> pdb=" O ARG I 113 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA I 120 " --> pdb=" O GLY I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 127 removed outlier: 3.539A pdb=" N VAL I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.701A pdb=" N HIS I 140 " --> pdb=" O ASN I 136 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG I 141 " --> pdb=" O ARG I 137 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU I 142 " --> pdb=" O CYS I 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 20 removed outlier: 3.917A pdb=" N LEU J 10 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL J 12 " --> pdb=" O GLU J 8 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS J 13 " --> pdb=" O GLY J 9 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY J 17 " --> pdb=" O LYS J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 41 removed outlier: 3.925A pdb=" N ILE J 33 " --> pdb=" O PHE J 29 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA J 39 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.740A pdb=" N ARG J 45 " --> pdb=" O PRO J 42 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ARG J 50 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS J 52 " --> pdb=" O LYS J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 78 removed outlier: 3.671A pdb=" N HIS J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 98 removed outlier: 3.573A pdb=" N LYS J 86 " --> pdb=" O PRO J 82 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN J 93 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN J 95 " --> pdb=" O HIS J 91 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY J 98 " --> pdb=" O VAL J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 121 removed outlier: 3.518A pdb=" N LYS J 110 " --> pdb=" O PHE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 142 removed outlier: 3.500A pdb=" N ALA J 132 " --> pdb=" O GLU J 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS J 133 " --> pdb=" O ALA J 129 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP J 135 " --> pdb=" O ASP J 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 20 removed outlier: 4.066A pdb=" N HIS K 12 " --> pdb=" O SER K 8 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG K 13 " --> pdb=" O GLU K 9 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE K 14 " --> pdb=" O GLU K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 25 removed outlier: 3.640A pdb=" N ARG K 24 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP K 25 " --> pdb=" O LEU K 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 21 through 25' Processing helix chain 'K' and resid 28 through 45 removed outlier: 3.914A pdb=" N LEU K 39 " --> pdb=" O PHE K 35 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU K 40 " --> pdb=" O GLY K 36 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR K 41 " --> pdb=" O ARG K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 58 removed outlier: 3.501A pdb=" N PHE K 54 " --> pdb=" O ASN K 51 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG K 56 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 84 removed outlier: 4.150A pdb=" N HIS K 70 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA K 81 " --> pdb=" O GLY K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 104 removed outlier: 3.980A pdb=" N LEU K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA K 93 " --> pdb=" O PRO K 89 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU K 98 " --> pdb=" O ALA K 94 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL K 104 " --> pdb=" O HIS K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 128 removed outlier: 4.062A pdb=" N LYS K 114 " --> pdb=" O LYS K 110 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS K 115 " --> pdb=" O ALA K 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Proline residue: K 125 - end of helix removed outlier: 3.713A pdb=" N LEU K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 147 removed outlier: 3.501A pdb=" N LYS K 146 " --> pdb=" O GLY K 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 26 removed outlier: 4.321A pdb=" N VAL L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS L 18 " --> pdb=" O SER L 14 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA L 24 " --> pdb=" O GLN L 20 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 46 removed outlier: 3.795A pdb=" N ASP L 41 " --> pdb=" O GLU L 37 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE L 42 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP L 44 " --> pdb=" O ARG L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 56 removed outlier: 3.581A pdb=" N LYS L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Proline residue: L 52 - end of helix removed outlier: 4.139A pdb=" N ARG L 55 " --> pdb=" O PRO L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 84 removed outlier: 3.561A pdb=" N LEU L 77 " --> pdb=" O VAL L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 103 removed outlier: 3.774A pdb=" N ALA L 91 " --> pdb=" O PRO L 87 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA L 92 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN L 93 " --> pdb=" O MET L 89 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL L 99 " --> pdb=" O ALA L 95 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN L 100 " --> pdb=" O HIS L 96 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS L 101 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU L 103 " --> pdb=" O VAL L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 127 removed outlier: 4.259A pdb=" N PHE L 111 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP L 112 " --> pdb=" O PRO L 108 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU L 115 " --> pdb=" O PHE L 111 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS L 116 " --> pdb=" O ASP L 112 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL L 121 " --> pdb=" O HIS L 117 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU L 122 " --> pdb=" O LEU L 118 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP L 124 " --> pdb=" O HIS L 120 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG L 125 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 144 removed outlier: 3.616A pdb=" N ASP L 140 " --> pdb=" O HIS L 136 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN L 141 " --> pdb=" O ASP L 137 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE L 142 " --> pdb=" O CYS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 147 No H-bonds generated for 'chain 'L' and resid 145 through 147' Processing helix chain 'M' and resid 10 through 37 removed outlier: 3.856A pdb=" N LEU M 24 " --> pdb=" O HIS M 20 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS M 29 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU M 33 " --> pdb=" O HIS M 29 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU M 34 " --> pdb=" O ASP M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 56 removed outlier: 4.193A pdb=" N ILE M 47 " --> pdb=" O ASP M 43 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA M 52 " --> pdb=" O ARG M 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG M 53 " --> pdb=" O GLN M 49 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE M 54 " --> pdb=" O LEU M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 82 No H-bonds generated for 'chain 'M' and resid 80 through 82' Processing helix chain 'M' and resid 92 through 95 removed outlier: 3.718A pdb=" N GLU M 95 " --> pdb=" O GLY M 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 92 through 95' Processing helix chain 'M' and resid 96 through 101 Processing helix chain 'M' and resid 102 through 106 removed outlier: 3.970A pdb=" N HIS M 106 " --> pdb=" O ASN M 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 34 removed outlier: 4.052A pdb=" N PHE N 19 " --> pdb=" O GLY N 15 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU N 31 " --> pdb=" O ILE N 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG N 32 " --> pdb=" O ILE N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 58 removed outlier: 4.019A pdb=" N SER N 48 " --> pdb=" O GLU N 44 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS N 56 " --> pdb=" O ALA N 52 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE N 57 " --> pdb=" O ARG N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 92 through 95 Processing helix chain 'N' and resid 96 through 101 Processing helix chain 'O' and resid 9 through 13 Processing helix chain 'O' and resid 14 through 40 removed outlier: 3.528A pdb=" N ILE O 18 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG O 20 " --> pdb=" O LYS O 16 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER O 27 " --> pdb=" O LYS O 23 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL O 31 " --> pdb=" O SER O 27 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER O 33 " --> pdb=" O SER O 29 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG O 38 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU O 39 " --> pdb=" O LEU O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 58 removed outlier: 4.074A pdb=" N ILE O 44 " --> pdb=" O ASP O 40 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU O 50 " --> pdb=" O LYS O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 82 No H-bonds generated for 'chain 'O' and resid 80 through 82' Processing sheet with id=AA1, first strand: chain 'M' and resid 66 through 68 removed outlier: 3.670A pdb=" N ILE M 77 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 116 through 117 removed outlier: 3.602A pdb=" N THR M 116 " --> pdb=" O HIS M 219 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU M 177 " --> pdb=" O ASN M 172 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN M 172 " --> pdb=" O GLU M 177 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA M 134 " --> pdb=" O ARG M 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 removed outlier: 3.602A pdb=" N THR M 116 " --> pdb=" O HIS M 219 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU M 177 " --> pdb=" O ASN M 172 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN M 172 " --> pdb=" O GLU M 177 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA M 134 " --> pdb=" O ARG M 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'N' and resid 111 through 115 removed outlier: 3.783A pdb=" N HIS N 126 " --> pdb=" O SER N 115 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE N 222 " --> pdb=" O THR N 114 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR N 114 " --> pdb=" O PHE N 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 66 through 68 Processing sheet with id=AA7, first strand: chain 'O' and resid 107 through 114 removed outlier: 6.774A pdb=" N HIS O 145 " --> pdb=" O GLU O 130 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER O 132 " --> pdb=" O ASP O 143 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP O 143 " --> pdb=" O SER O 132 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU O 168 " --> pdb=" O THR O 177 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG O 175 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA O 214 " --> pdb=" O ILE O 204 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N HIS O 206 " --> pdb=" O VAL O 212 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL O 212 " --> pdb=" O HIS O 206 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU O 215 " --> pdb=" O CYS O 113 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2703 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: 3.03 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 6782 1.37 - 1.56: 12587 1.56 - 1.76: 29 1.76 - 1.95: 88 1.95 - 2.14: 36 Bond restraints: 19522 Sorted by residual: bond pdb=" N PRO E 151 " pdb=" CD PRO E 151 " ideal model delta sigma weight residual 1.473 1.581 -0.108 1.40e-02 5.10e+03 5.98e+01 bond pdb=" CA GLU O 160 " pdb=" C GLU O 160 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.25e-02 6.40e+03 2.67e+01 bond pdb=" C ARG N 137 " pdb=" O ARG N 137 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.22e-02 6.72e+03 2.09e+01 bond pdb=" CA ILE M 129 " pdb=" CB ILE M 129 " ideal model delta sigma weight residual 1.545 1.480 0.065 1.51e-02 4.39e+03 1.84e+01 bond pdb=" CA VAL M 107 " pdb=" C VAL M 107 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.14e-02 7.69e+03 1.83e+01 ... (remaining 19517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.21: 26622 10.21 - 20.41: 9 20.41 - 30.62: 0 30.62 - 40.82: 0 40.82 - 51.03: 1 Bond angle restraints: 26632 Sorted by residual: angle pdb=" C LEU E 150 " pdb=" N PRO E 151 " pdb=" CD PRO E 151 " ideal model delta sigma weight residual 125.00 73.97 51.03 4.10e+00 5.95e-02 1.55e+02 angle pdb=" N LYS E 109 " pdb=" CA LYS E 109 " pdb=" C LYS E 109 " ideal model delta sigma weight residual 111.28 97.98 13.30 1.09e+00 8.42e-01 1.49e+02 angle pdb=" N LEU M 123 " pdb=" CA LEU M 123 " pdb=" C LEU M 123 " ideal model delta sigma weight residual 113.01 122.30 -9.29 1.20e+00 6.94e-01 5.99e+01 angle pdb=" N GLU E 110 " pdb=" CA GLU E 110 " pdb=" C GLU E 110 " ideal model delta sigma weight residual 111.75 121.64 -9.89 1.28e+00 6.10e-01 5.97e+01 angle pdb=" C GLU O 160 " pdb=" N VAL O 161 " pdb=" CA VAL O 161 " ideal model delta sigma weight residual 121.96 111.64 10.32 1.34e+00 5.57e-01 5.93e+01 ... (remaining 26627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10612 18.00 - 35.99: 509 35.99 - 53.99: 106 53.99 - 71.99: 15 71.99 - 89.98: 27 Dihedral angle restraints: 11269 sinusoidal: 4347 harmonic: 6922 Sorted by residual: dihedral pdb=" N LEU H 10 " pdb=" C LEU H 10 " pdb=" CA LEU H 10 " pdb=" CB LEU H 10 " ideal model delta harmonic sigma weight residual 122.80 138.38 -15.58 0 2.50e+00 1.60e-01 3.88e+01 dihedral pdb=" CA THR O 139 " pdb=" C THR O 139 " pdb=" N PRO O 140 " pdb=" CA PRO O 140 " ideal model delta harmonic sigma weight residual 180.00 149.74 30.26 0 5.00e+00 4.00e-02 3.66e+01 dihedral pdb=" CA SER N 103 " pdb=" C SER N 103 " pdb=" N VAL N 104 " pdb=" CA VAL N 104 " ideal model delta harmonic sigma weight residual 180.00 151.97 28.03 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 11266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2459 0.110 - 0.220: 377 0.220 - 0.329: 31 0.329 - 0.439: 7 0.439 - 0.549: 2 Chirality restraints: 2876 Sorted by residual: chirality pdb=" CA LEU H 10 " pdb=" N LEU H 10 " pdb=" C LEU H 10 " pdb=" CB LEU H 10 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" CA ASP O 157 " pdb=" N ASP O 157 " pdb=" C ASP O 157 " pdb=" CB ASP O 157 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA ARG C 73 " pdb=" N ARG C 73 " pdb=" C ARG C 73 " pdb=" CB ARG C 73 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 ... (remaining 2873 not shown) Planarity restraints: 3376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 150 " 0.195 5.00e-02 4.00e+02 2.54e-01 1.04e+02 pdb=" N PRO E 151 " -0.428 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.188 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 120 " 0.027 2.00e-02 2.50e+03 5.49e-02 3.01e+01 pdb=" C ALA E 120 " -0.095 2.00e-02 2.50e+03 pdb=" O ALA E 120 " 0.036 2.00e-02 2.50e+03 pdb=" N ARG E 121 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM C 201 " 0.036 2.00e-02 2.50e+03 3.29e-02 2.43e+01 pdb=" C2A HEM C 201 " 0.031 2.00e-02 2.50e+03 pdb=" C3A HEM C 201 " 0.023 2.00e-02 2.50e+03 pdb=" C4A HEM C 201 " 0.046 2.00e-02 2.50e+03 pdb=" CAA HEM C 201 " -0.040 2.00e-02 2.50e+03 pdb=" CHA HEM C 201 " -0.023 2.00e-02 2.50e+03 pdb=" CHB HEM C 201 " -0.048 2.00e-02 2.50e+03 pdb=" CMA HEM C 201 " -0.005 2.00e-02 2.50e+03 pdb=" NA HEM C 201 " -0.020 2.00e-02 2.50e+03 ... (remaining 3373 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 11 2.13 - 2.83: 4822 2.83 - 3.52: 26615 3.52 - 4.21: 38813 4.21 - 4.90: 67944 Nonbonded interactions: 138205 Sorted by model distance: nonbonded pdb=" OG1 THR E 108 " pdb=" CD2 TYR E 111 " model vdw 1.442 3.340 nonbonded pdb=" OD2 ASP E 41 " pdb=" NH2 ARG E 121 " model vdw 1.682 3.120 nonbonded pdb=" O PRO I 124 " pdb=" N VAL I 126 " model vdw 1.784 3.120 nonbonded pdb=" OG1 THR E 108 " pdb=" CG TYR E 111 " model vdw 1.820 3.260 nonbonded pdb=" CE2 PHE E 112 " pdb=" CD1 ILE E 146 " model vdw 1.903 3.760 ... (remaining 138200 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 5 or (resid 6 through 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 13 or (resid 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (name \ N or name CA or name C or name O or name CB )) or resid 55 through 69 or (resid \ 70 and (name N or name CA or name C or name O or name CB )) or resid 71 through \ 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) or r \ esid 106 through 109 or (resid 110 and (name N or name CA or name C or name O or \ name CB )) or resid 111 through 116 or (resid 117 through 118 and (name N or na \ me CA or name C or name O or name CB )) or resid 119 through 142 or (resid 143 t \ hrough 145 and (name N or name CA or name C or name O or name CB )) or resid 146 \ through 150 or (resid 151 and (name N or name CA or name C or name O or name CB \ or name CG or name CD )) or resid 201)) selection = (chain 'E' and (resid 5 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 23 or (resid 24 through 25 a \ nd (name N or name CA or name C or name O or name CB )) or resid 26 through 28 o \ r (resid 29 and (name N or name CA or name C or name O or name CB )) or resid 30 \ through 39 or (resid 40 through 41 and (name N or name CA or name C or name O o \ r name CB )) or resid 42 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 77 or (resid 78 and (name N or nam \ e CA or name C or name O or name CB )) or resid 79 through 99 or (resid 100 and \ (name N or name CA or name C or name O or name CB )) or resid 101 through 102 or \ (resid 103 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 4 or (resid 105 and (name N or name CA or name C or name O or name CB )) or resi \ d 106 through 127 or (resid 128 and (name N or name CA or name C or name O or na \ me CB )) or resid 129 through 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 or (resid 143 through 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 150 or (resid 151 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) o \ r resid 201)) selection = (chain 'I' and (resid 5 or (resid 6 through 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 24 or (resid 25 and (name \ N or name CA or name C or name O or name CB )) or resid 26 through 48 or (resid \ 49 and (name N or name CA or name C or name O or name CB )) or resid 50 through \ 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or res \ id 55 through 69 or (resid 70 and (name N or name CA or name C or name O or name \ CB )) or resid 71 through 99 or (resid 100 and (name N or name CA or name C or \ name O or name CB )) or resid 101 through 102 or (resid 103 and (name N or name \ CA or name C or name O or name CB )) or resid 104 through 116 or (resid 117 thro \ ugh 118 and (name N or name CA or name C or name O or name CB )) or resid 119 th \ rough 132 or (resid 133 through 134 and (name N or name CA or name C or name O o \ r name CB )) or resid 135 through 140 or (resid 141 and (name N or name CA or na \ me C or name O or name CB )) or resid 142 through 201)) } ncs_group { reference = (chain 'B' and ((resid 2 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 7 or (resid 8 and (name N or name CA or name C or \ name O or name CB )) or resid 9 through 14 or (resid 15 and (name N or name CA \ or name C or name O or name CB )) or resid 16 through 26 or (resid 27 through 28 \ and (name N or name CA or name C or name O or name CB )) or resid 29 through 42 \ or (resid 43 through 44 and (name N or name CA or name C or name O or name CB ) \ ) or resid 45 through 48 or (resid 49 and (name N or name CA or name C or name O \ or name CB )) or resid 50 through 125 or (resid 126 and (name N or name CA or n \ ame C or name O or name CB )) or resid 127 through 130 or (resid 131 through 132 \ and (name N or name CA or name C or name O or name CB )) or resid 133 through 1 \ 34 or (resid 135 through 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 or (resid 138 and (name N or name CA or name C or name O or n \ ame CB )) or resid 139 through 144 or (resid 145 and (name N or name CA or name \ C or name O or name CB )) or resid 201)) selection = (chain 'F' and ((resid 2 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 7 or (resid 8 and (name N or name CA or name C or \ name O or name CB )) or resid 9 through 29 or (resid 30 and (name N or name CA \ or name C or name O or name CB )) or resid 31 through 53 or (resid 54 through 55 \ and (name N or name CA or name C or name O or name CB )) or resid 56 through 76 \ or (resid 77 and (name N or name CA or name C or name O or name CB )) or resid \ 78 through 92 or (resid 93 and (name N or name CA or name C or name O or name CB \ )) or resid 94 through 122 or (resid 123 and (name N or name CA or name C or na \ me O or name CB )) or resid 124 through 127 or (resid 128 through 129 and (name \ N or name CA or name C or name O or name CB )) or resid 130 through 201)) selection = (chain 'J' and ((resid 2 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 or (resid 30 and (name N or name \ CA or name C or name O or name CB )) or resid 31 through 42 or (resid 43 through \ 44 and (name N or name CA or name C or name O or name CB )) or resid 45 through \ 48 or (resid 49 and (name N or name CA or name C or name O or name CB )) or res \ id 50 through 54 or (resid 55 and (name N or name CA or name C or name O or name \ CB )) or resid 56 through 72 or (resid 73 and (name N or name CA or name C or n \ ame O or name CB )) or resid 74 through 76 or (resid 77 and (name N or name CA o \ r name C or name O or name CB )) or resid 78 through 79 or (resid 80 and (name N \ or name CA or name C or name O or name CB )) or resid 81 through 122 or (resid \ 123 and (name N or name CA or name C or name O or name CB )) or resid 124 throug \ h 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) or \ resid 127 or (resid 128 through 129 and (name N or name CA or name C or name O o \ r name CB )) or resid 130 or (resid 131 through 132 and (name N or name CA or na \ me C or name O or name CB )) or resid 133 through 134 or (resid 135 through 136 \ and (name N or name CA or name C or name O or name CB )) or resid 137 through 14 \ 4 or (resid 145 and (name N or name CA or name C or name O or name CB )) or resi \ d 201)) } ncs_group { reference = (chain 'C' and (resid 3 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 26 or (resid 27 through 28 and (nam \ e N or name CA or name C or name O or name CB )) or resid 29 through 51 or (resi \ d 52 through 53 and (name N or name CA or name C or name O or name CB )) or resi \ d 54 or (resid 55 through 56 and (name N or name CA or name C or name O or name \ CB )) or resid 57 through 59 or (resid 60 and (name N or name CA or name C or na \ me O or name CB )) or resid 61 through 128 or (resid 129 through 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 or (resid 132 through \ 133 and (name N or name CA or name C or name O or name CB )) or resid 134 throu \ gh 201)) selection = (chain 'G' and (resid 3 through 7 or (resid 8 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 27 or (resid 28 and (name \ N or name CA or name C or name O or name CB )) or resid 29 through 51 or (resid \ 52 through 53 and (name N or name CA or name C or name O or name CB )) or resid \ 54 through 86 or (resid 87 and (name N or name CA or name C or name O or name CB \ )) or resid 88 through 91 or (resid 92 through 94 and (name N or name CA or nam \ e C or name O or name CB )) or resid 95 or (resid 96 and (name N or name CA or n \ ame C or name O or name CB )) or resid 97 through 117 or (resid 118 and (name N \ or name CA or name C or name O or name CB )) or resid 119 through 121 or (resid \ 122 and (name N or name CA or name C or name O or name CB )) or resid 123 throug \ h 129 or (resid 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 or (resid 132 through 133 and (name N or name CA or name C or name O o \ r name CB )) or resid 134 through 147 or (resid 148 and (name N or name CA or na \ me C or name O or name CB )) or resid 149 through 201)) selection = (chain 'K' and (resid 3 through 7 or (resid 8 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 17 or (resid 18 and (name \ N or name CA or name C or name O or name CB )) or resid 19 through 27 or (resid \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 54 or (resid 55 through 56 and (name N or name CA or name C or name O or name CB \ )) or resid 57 through 86 or (resid 87 and (name N or name CA or name C or name \ O or name CB )) or resid 88 through 91 or (resid 92 through 94 and (name N or n \ ame CA or name C or name O or name CB )) or resid 95 or (resid 96 and (name N or \ name CA or name C or name O or name CB )) or resid 97 through 117 or (resid 118 \ and (name N or name CA or name C or name O or name CB )) or resid 119 through 1 \ 21 or (resid 122 and (name N or name CA or name C or name O or name CB )) or res \ id 123 through 201)) } ncs_group { reference = (chain 'D' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 or (resid 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 through 12 or (resid 13 and (name N or name CA or name C or name \ O or name CB )) or resid 14 through 43 or (resid 44 through 45 and (name N or na \ me CA or name C or name O or name CB )) or resid 46 through 64 or (resid 65 and \ (name N or name CA or name C or name O or name CB )) or resid 66 through 77 or ( \ resid 78 and (name N or name CA or name C or name O or name CB )) or resid 79 th \ rough 84 or (resid 85 through 86 and (name N or name CA or name C or name O or n \ ame CB )) or resid 87 through 96 or (resid 97 through 98 and (name N or name CA \ or name C or name O or name CB )) or resid 99 through 102 or (resid 103 and (nam \ e N or name CA or name C or name O or name CB )) or resid 104 through 115 or (re \ sid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 th \ rough 119 or (resid 120 and (name N or name CA or name C or name O or name CB )) \ or resid 121 through 136 or (resid 137 and (name N or name CA or name C or name \ O or name CB )) or resid 138 through 146 or (resid 147 and (name N or name CA o \ r name C or name O or name CB )) or resid 201)) selection = (chain 'H' and ((resid 8 and (name N or name CA or name C or 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 through 44 or (resid 45 and (name N or name CA or name \ C or name O or name CB )) or resid 46 through 64 or (resid 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 79 or (resid 80 and \ (name N or name CA or name C or name O or name CB )) or resid 81 or (resid 82 an \ d (name N or name CA or name C or name O or name CB )) or resid 83 through 84 or \ (resid 85 through 86 and (name N or name CA or name C or name O or name CB )) o \ r resid 87 through 97 or (resid 98 and (name N or name CA or name C or name O or \ name CB )) or resid 99 or (resid 100 and (name N or name CA or name C or name O \ or name CB )) or resid 101 through 108 or (resid 109 and (name N or name CA or \ name C or name O or name CB )) or resid 110 through 111 or (resid 112 and (name \ N or name CA or name C or name O or name CB )) or resid 113 through 118 or (resi \ d 119 through 120 and (name N or name CA or name C or name O or name CB )) or re \ sid 121 through 124 or (resid 125 and (name N or name CA or name C or name O or \ name CB )) or resid 126 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 201)) selection = (chain 'L' and (resid 8 through 43 or (resid 44 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 through 81 or (resid 82 and (nam \ e N or name CA or name C or name O or name CB )) or resid 83 through 96 or (resi \ d 97 through 98 and (name N or name CA or name C or name O or name CB )) or resi \ d 99 or (resid 100 and (name N or name CA or name C or name O or name CB )) or r \ esid 101 through 102 or (resid 103 and (name N or name CA or name C or name O or \ name CB )) or resid 104 through 108 or (resid 109 and (name N or name CA or nam \ e C or name O or name CB )) or resid 110 through 111 or (resid 112 and (name N o \ r name CA or name C or name O or name CB )) or resid 113 through 115 or (resid 1 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 117 through \ 118 or (resid 119 through 120 and (name N or name CA or name C or name O or nam \ e CB )) or resid 121 through 124 or (resid 125 and (name N or name CA or name C \ or name O or name CB )) or resid 126 through 130 or (resid 131 and (name N or na \ me CA or name C or name O or name CB )) or resid 132 through 136 or (resid 137 a \ nd (name N or name CA or name C or name O or name CB )) or resid 138 through 139 \ or (resid 140 and (name N or name CA or name C or name O or name CB )) or resid \ 141 through 146 or (resid 147 and (name N or name CA or name C or name O or nam \ e CB )) or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.500 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.015 0.536 19534 Z= 0.735 Angle : 1.532 51.025 26632 Z= 0.927 Chirality : 0.080 0.549 2876 Planarity : 0.008 0.254 3376 Dihedral : 12.484 89.983 6761 Min Nonbonded Distance : 1.442 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.40 % Favored : 91.46 % Rotamer: Outliers : 0.59 % Allowed : 4.42 % Favored : 94.99 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.14), residues: 2364 helix: -3.88 (0.08), residues: 1228 sheet: -2.99 (0.29), residues: 205 loop : -1.98 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG I 137 TYR 0.041 0.005 TYR M 153 PHE 0.032 0.004 PHE M 215 TRP 0.031 0.005 TRP F 34 HIS 0.016 0.003 HIS C 3 Details of bonding type rmsd covalent geometry : bond 0.01257 (19522) covalent geometry : angle 1.53210 (26632) hydrogen bonds : bond 0.32284 ( 945) hydrogen bonds : angle 10.84933 ( 2703) Misc. bond : bond 0.36407 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 804 time to evaluate : 0.772 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: A 31 ARG cc_start: 0.7685 (ptp-170) cc_final: 0.7480 (ptp-170) REVERT: A 62 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7554 (pm20) REVERT: A 79 LEU cc_start: 0.8636 (tp) cc_final: 0.8082 (tp) REVERT: A 125 GLN cc_start: 0.8179 (mt0) cc_final: 0.7623 (mm110) REVERT: B 18 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8287 (ttm110) REVERT: B 50 ARG cc_start: 0.8673 (tpt170) cc_final: 0.8311 (mtt-85) REVERT: C 17 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8254 (ttpt) REVERT: C 103 GLU cc_start: 0.7656 (tp30) cc_final: 0.7347 (tp30) REVERT: D 57 ARG cc_start: 0.7394 (mtp-110) cc_final: 0.6601 (tpt-90) REVERT: D 65 GLU cc_start: 0.7820 (tt0) cc_final: 0.7212 (tp30) REVERT: D 72 ARG cc_start: 0.7716 (mtm180) cc_final: 0.7332 (mtm-85) REVERT: D 126 LEU cc_start: 0.7915 (mp) cc_final: 0.7683 (mp) REVERT: D 138 CYS cc_start: 0.8908 (t) cc_final: 0.8468 (m) REVERT: E 12 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7806 (mtm-85) REVERT: E 62 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6597 (pm20) REVERT: E 79 LEU cc_start: 0.7895 (tp) cc_final: 0.7571 (tp) REVERT: E 100 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7824 (tp40) REVERT: E 131 ASN cc_start: 0.7179 (t0) cc_final: 0.6746 (t0) REVERT: E 148 LYS cc_start: 0.7115 (tptp) cc_final: 0.6702 (tttt) REVERT: F 41 VAL cc_start: 0.8687 (t) cc_final: 0.8360 (m) REVERT: F 95 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7637 (mm-40) REVERT: F 120 GLN cc_start: 0.8983 (tp40) cc_final: 0.8681 (tp-100) REVERT: G 17 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8203 (tttt) REVERT: G 66 LYS cc_start: 0.8070 (tptt) cc_final: 0.7588 (tptm) REVERT: G 112 HIS cc_start: 0.7595 (m170) cc_final: 0.6716 (m-70) REVERT: G 115 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7680 (mmtp) REVERT: G 130 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.6053 (m-30) REVERT: G 146 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7742 (tptp) REVERT: H 31 ARG cc_start: 0.6852 (ttm170) cc_final: 0.6573 (ttm170) REVERT: H 129 HIS cc_start: 0.8228 (m90) cc_final: 0.7551 (m170) REVERT: I 17 HIS cc_start: 0.8048 (m90) cc_final: 0.7688 (m-70) REVERT: I 46 TYR cc_start: 0.7497 (m-80) cc_final: 0.7179 (m-10) REVERT: I 119 PHE cc_start: 0.8435 (m-80) cc_final: 0.8085 (m-10) REVERT: J 26 ARG cc_start: 0.7812 (ttm170) cc_final: 0.7270 (ttm170) REVERT: J 45 ARG cc_start: 0.6945 (mtt180) cc_final: 0.6542 (ttm110) REVERT: K 4 GLU cc_start: 0.5070 (tt0) cc_final: 0.3772 (mm-30) REVERT: K 12 HIS cc_start: 0.8132 (p-80) cc_final: 0.7135 (p-80) REVERT: K 70 HIS cc_start: 0.7688 (t70) cc_final: 0.7426 (t-90) REVERT: K 92 ASP cc_start: 0.7845 (t70) cc_final: 0.7601 (t0) REVERT: K 110 LYS cc_start: 0.6704 (tttt) cc_final: 0.5803 (mptt) REVERT: K 141 LYS cc_start: 0.6841 (mttt) cc_final: 0.6619 (mmmt) REVERT: K 146 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7480 (mptt) REVERT: L 138 CYS cc_start: 0.7866 (t) cc_final: 0.7665 (m) REVERT: M 15 LYS cc_start: 0.7964 (tptt) cc_final: 0.7499 (tmmt) REVERT: M 68 GLU cc_start: 0.8892 (pm20) cc_final: 0.8621 (pm20) REVERT: M 69 CYS cc_start: 0.8836 (m) cc_final: 0.8416 (m) REVERT: M 77 ILE cc_start: 0.8756 (mp) cc_final: 0.8532 (mp) REVERT: M 86 GLU cc_start: 0.7621 (mp0) cc_final: 0.7216 (mp0) REVERT: M 89 CYS cc_start: 0.7920 (m) cc_final: 0.7633 (m) REVERT: M 138 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8310 (mmmt) REVERT: M 146 TRP cc_start: 0.8850 (m100) cc_final: 0.8421 (m100) REVERT: M 215 PHE cc_start: 0.7689 (t80) cc_final: 0.7407 (t80) REVERT: N 42 ASP cc_start: 0.8207 (p0) cc_final: 0.7908 (p0) REVERT: N 49 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8258 (tm-30) REVERT: N 69 CYS cc_start: 0.8142 (m) cc_final: 0.7410 (m) REVERT: N 73 GLU cc_start: 0.8454 (pm20) cc_final: 0.8106 (pm20) REVERT: N 75 GLU cc_start: 0.8854 (pm20) cc_final: 0.8635 (pm20) REVERT: N 77 ILE cc_start: 0.8773 (mt) cc_final: 0.8551 (mm) REVERT: N 86 HIS cc_start: 0.7495 (m-70) cc_final: 0.7171 (m90) REVERT: N 106 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8410 (ttmt) REVERT: N 131 THR cc_start: 0.8625 (t) cc_final: 0.8303 (p) REVERT: N 139 LYS cc_start: 0.8003 (pttm) cc_final: 0.7423 (ttmt) REVERT: N 153 SER cc_start: 0.8810 (m) cc_final: 0.8586 (m) REVERT: N 169 LYS cc_start: 0.8437 (mttt) cc_final: 0.8066 (mtpt) REVERT: N 177 ARG cc_start: 0.8602 (mtp85) cc_final: 0.8341 (ttm110) REVERT: N 206 GLU cc_start: 0.8224 (mp0) cc_final: 0.7969 (mp0) REVERT: N 207 CYS cc_start: 0.8305 (m) cc_final: 0.8050 (m) REVERT: N 210 VAL cc_start: 0.8956 (m) cc_final: 0.8674 (p) REVERT: N 226 GLU cc_start: 0.8277 (tp30) cc_final: 0.7941 (tp30) REVERT: N 228 HIS cc_start: 0.5657 (m170) cc_final: 0.5372 (m170) REVERT: O 30 HIS cc_start: 0.8081 (t70) cc_final: 0.7793 (t70) REVERT: O 56 GLU cc_start: 0.7849 (tt0) cc_final: 0.7599 (tt0) REVERT: O 58 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7822 (tp30) REVERT: O 81 PHE cc_start: 0.8579 (m-10) cc_final: 0.8279 (m-10) REVERT: O 83 CYS cc_start: 0.8532 (m) cc_final: 0.8039 (t) REVERT: O 119 LYS cc_start: 0.5512 (pttm) cc_final: 0.4520 (pttm) REVERT: O 133 SER cc_start: 0.8193 (m) cc_final: 0.7823 (t) REVERT: O 144 LEU cc_start: 0.8719 (mt) cc_final: 0.8502 (mp) REVERT: O 191 GLU cc_start: 0.8321 (tt0) cc_final: 0.7966 (tt0) REVERT: O 210 GLU cc_start: 0.8241 (tp30) cc_final: 0.7737 (tt0) REVERT: O 215 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7919 (mm-30) outliers start: 11 outliers final: 2 residues processed: 810 average time/residue: 0.1725 time to fit residues: 201.6844 Evaluate side-chains 639 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 636 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 PRO Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain O residue 173 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 69 HIS A 75 ASN A 82 ASN ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS B 64 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS E 75 ASN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS F 93 GLN G 16 GLN G 70 HIS G 76 ASN G 100 HIS ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 HIS H 117 HIS H 129 HIS ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 ASN I 96 HIS J 40 GLN J 145 HIS K 76 ASN K 83 ASN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 HIS ** M 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS M 127 HIS N 17 ASN N 86 HIS ** O 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 206 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.144497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.115678 restraints weight = 29532.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.119171 restraints weight = 18685.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.119834 restraints weight = 13772.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.120307 restraints weight = 10605.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.121033 restraints weight = 9768.522| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 19534 Z= 0.192 Angle : 0.815 11.576 26632 Z= 0.407 Chirality : 0.045 0.221 2876 Planarity : 0.006 0.156 3376 Dihedral : 8.929 86.569 2663 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.78 % Favored : 94.97 % Rotamer: Outliers : 4.10 % Allowed : 13.53 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.16), residues: 2364 helix: -1.22 (0.12), residues: 1338 sheet: -2.15 (0.32), residues: 200 loop : -1.51 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 121 TYR 0.017 0.002 TYR E 111 PHE 0.021 0.002 PHE L 132 TRP 0.019 0.002 TRP B 34 HIS 0.012 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00414 (19522) covalent geometry : angle 0.81475 (26632) hydrogen bonds : bond 0.07316 ( 945) hydrogen bonds : angle 6.09320 ( 2703) Misc. bond : bond 0.13553 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 673 time to evaluate : 1.132 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: A 79 LEU cc_start: 0.8468 (tp) cc_final: 0.7903 (tp) REVERT: A 96 HIS cc_start: 0.7693 (t-90) cc_final: 0.7385 (t-170) REVERT: A 97 LEU cc_start: 0.8220 (tt) cc_final: 0.7853 (mp) REVERT: A 137 ARG cc_start: 0.7400 (mmt-90) cc_final: 0.7146 (mtt90) REVERT: B 31 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8164 (mt0) REVERT: C 17 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8356 (ttpp) REVERT: C 103 GLU cc_start: 0.7640 (tp30) cc_final: 0.7263 (tp30) REVERT: D 31 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7815 (ttm170) REVERT: D 65 GLU cc_start: 0.7596 (tt0) cc_final: 0.6999 (tp30) REVERT: D 72 ARG cc_start: 0.7733 (mtm180) cc_final: 0.7331 (mtm-85) REVERT: D 126 LEU cc_start: 0.8333 (mp) cc_final: 0.8002 (mp) REVERT: D 137 ASP cc_start: 0.7128 (p0) cc_final: 0.6903 (p0) REVERT: D 141 GLN cc_start: 0.7967 (tt0) cc_final: 0.7465 (tm-30) REVERT: E 79 LEU cc_start: 0.8059 (tp) cc_final: 0.7825 (tp) REVERT: E 131 ASN cc_start: 0.7286 (t0) cc_final: 0.6488 (t0) REVERT: E 137 ARG cc_start: 0.7024 (ttp-110) cc_final: 0.6803 (ttm110) REVERT: E 148 LYS cc_start: 0.6511 (tptp) cc_final: 0.6214 (tttt) REVERT: F 67 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7409 (mtm-85) REVERT: G 23 TRP cc_start: 0.7423 (m-90) cc_final: 0.7019 (m-90) REVERT: G 76 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7458 (t0) REVERT: G 114 LYS cc_start: 0.7378 (tptm) cc_final: 0.6671 (mtpp) REVERT: H 93 GLN cc_start: 0.6854 (mm-40) cc_final: 0.6504 (mm110) REVERT: J 20 TYR cc_start: 0.7895 (t80) cc_final: 0.7606 (t80) REVERT: J 26 ARG cc_start: 0.7734 (ttm170) cc_final: 0.6945 (ttm170) REVERT: J 34 TRP cc_start: 0.8307 (m100) cc_final: 0.7773 (m100) REVERT: K 4 GLU cc_start: 0.4366 (tt0) cc_final: 0.3651 (mm-30) REVERT: K 12 HIS cc_start: 0.7652 (p-80) cc_final: 0.6390 (p-80) REVERT: K 23 TRP cc_start: 0.7464 (m-90) cc_final: 0.7175 (m100) REVERT: K 30 LYS cc_start: 0.7151 (ttmt) cc_final: 0.6479 (tppt) REVERT: K 92 ASP cc_start: 0.7899 (t70) cc_final: 0.7485 (t0) REVERT: K 110 LYS cc_start: 0.6996 (tttt) cc_final: 0.6210 (mptt) REVERT: K 116 PHE cc_start: 0.6613 (t80) cc_final: 0.6084 (t80) REVERT: K 146 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7380 (mptt) REVERT: L 16 LYS cc_start: 0.8312 (ttpt) cc_final: 0.8054 (ttpt) REVERT: L 49 ILE cc_start: 0.7782 (mm) cc_final: 0.7424 (mt) REVERT: L 138 CYS cc_start: 0.7981 (t) cc_final: 0.7668 (m) REVERT: M 68 GLU cc_start: 0.8087 (pm20) cc_final: 0.7825 (pm20) REVERT: M 69 CYS cc_start: 0.8218 (m) cc_final: 0.7154 (m) REVERT: M 89 CYS cc_start: 0.6607 (m) cc_final: 0.6249 (m) REVERT: N 32 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7527 (mtt-85) REVERT: N 46 PHE cc_start: 0.7567 (t80) cc_final: 0.7357 (t80) REVERT: N 49 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7854 (tm-30) REVERT: N 94 ASP cc_start: 0.8780 (p0) cc_final: 0.8485 (p0) REVERT: N 129 ARG cc_start: 0.6998 (ptt180) cc_final: 0.6505 (ptm160) REVERT: N 131 THR cc_start: 0.8674 (t) cc_final: 0.8307 (p) REVERT: N 139 LYS cc_start: 0.7542 (pttm) cc_final: 0.7151 (ttmt) REVERT: N 153 SER cc_start: 0.8329 (m) cc_final: 0.7734 (p) REVERT: N 169 LYS cc_start: 0.8432 (mttt) cc_final: 0.7849 (mtpt) REVERT: N 226 GLU cc_start: 0.8108 (tp30) cc_final: 0.7372 (mm-30) REVERT: O 30 HIS cc_start: 0.7772 (t70) cc_final: 0.7254 (t70) REVERT: O 56 GLU cc_start: 0.7413 (tt0) cc_final: 0.7026 (tt0) REVERT: O 83 CYS cc_start: 0.7977 (m) cc_final: 0.7587 (t) REVERT: O 133 SER cc_start: 0.7980 (m) cc_final: 0.7765 (t) REVERT: O 191 GLU cc_start: 0.7290 (tt0) cc_final: 0.6958 (tt0) REVERT: O 215 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7678 (mm-30) outliers start: 76 outliers final: 39 residues processed: 699 average time/residue: 0.1719 time to fit residues: 173.6456 Evaluate side-chains 638 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 598 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 CYS Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 216 HIS Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 203 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 203 optimal weight: 0.0670 chunk 78 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 214 optimal weight: 0.1980 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 93 HIS ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS D 46 HIS D 96 HIS E 69 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN G 16 GLN ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 HIS J 64 HIS ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS ** M 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS N 202 ASN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 145 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.148244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.119775 restraints weight = 29663.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.123671 restraints weight = 19465.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.124147 restraints weight = 14017.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.124601 restraints weight = 10731.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.125045 restraints weight = 10017.276| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 19534 Z= 0.157 Angle : 0.722 9.632 26632 Z= 0.351 Chirality : 0.042 0.204 2876 Planarity : 0.005 0.117 3376 Dihedral : 8.549 86.764 2656 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 4.53 % Allowed : 17.52 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2364 helix: 0.09 (0.14), residues: 1351 sheet: -1.43 (0.34), residues: 197 loop : -1.23 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 12 TYR 0.016 0.002 TYR F 20 PHE 0.019 0.002 PHE B 29 TRP 0.016 0.002 TRP B 34 HIS 0.012 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00395 (19522) covalent geometry : angle 0.72219 (26632) hydrogen bonds : bond 0.05136 ( 945) hydrogen bonds : angle 5.19766 ( 2703) Misc. bond : bond 0.08830 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 655 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8277 (m) cc_final: 0.7532 (p) REVERT: A 79 LEU cc_start: 0.8534 (tp) cc_final: 0.8008 (tp) REVERT: A 96 HIS cc_start: 0.7764 (t-90) cc_final: 0.7443 (t-170) REVERT: A 97 LEU cc_start: 0.8236 (tt) cc_final: 0.7831 (mt) REVERT: A 113 ARG cc_start: 0.6981 (ttp80) cc_final: 0.6645 (ttt-90) REVERT: A 137 ARG cc_start: 0.7543 (mmt-90) cc_final: 0.7167 (mtt90) REVERT: B 31 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8176 (mt0) REVERT: B 89 LEU cc_start: 0.8419 (tt) cc_final: 0.7955 (mt) REVERT: B 107 ASP cc_start: 0.8078 (t70) cc_final: 0.7764 (t70) REVERT: C 17 LYS cc_start: 0.8978 (ttmm) cc_final: 0.8672 (ttpp) REVERT: C 57 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8106 (t) REVERT: C 73 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7617 (ttm170) REVERT: C 103 GLU cc_start: 0.7584 (tp30) cc_final: 0.7054 (tp30) REVERT: D 57 ARG cc_start: 0.7740 (mtp-110) cc_final: 0.7453 (mmm-85) REVERT: D 65 GLU cc_start: 0.7596 (tt0) cc_final: 0.7241 (tp30) REVERT: D 72 ARG cc_start: 0.7606 (mtm180) cc_final: 0.7072 (mtm-85) REVERT: D 85 ASP cc_start: 0.7221 (p0) cc_final: 0.6919 (p0) REVERT: D 126 LEU cc_start: 0.8377 (mp) cc_final: 0.8096 (mp) REVERT: E 79 LEU cc_start: 0.8162 (tp) cc_final: 0.7950 (tp) REVERT: E 113 ARG cc_start: 0.6939 (mmm-85) cc_final: 0.6629 (mmm-85) REVERT: E 131 ASN cc_start: 0.7504 (t0) cc_final: 0.6676 (t0) REVERT: E 137 ARG cc_start: 0.7165 (ttp-110) cc_final: 0.6862 (ttm110) REVERT: E 148 LYS cc_start: 0.6617 (tptp) cc_final: 0.6285 (tttt) REVERT: F 11 LYS cc_start: 0.7889 (tptm) cc_final: 0.7631 (tptm) REVERT: F 72 LEU cc_start: 0.8965 (tt) cc_final: 0.8711 (tt) REVERT: F 120 GLN cc_start: 0.8422 (tp40) cc_final: 0.8219 (tp-100) REVERT: F 134 ILE cc_start: 0.8199 (pp) cc_final: 0.7849 (mt) REVERT: G 23 TRP cc_start: 0.7470 (m-90) cc_final: 0.7115 (m-90) REVERT: G 114 LYS cc_start: 0.7474 (tptm) cc_final: 0.6728 (mtpp) REVERT: G 124 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8682 (mm) REVERT: G 136 TRP cc_start: 0.7809 (m100) cc_final: 0.7575 (m100) REVERT: G 140 LEU cc_start: 0.6700 (mm) cc_final: 0.6494 (mm) REVERT: H 129 HIS cc_start: 0.7010 (m-70) cc_final: 0.6441 (m-70) REVERT: I 20 ASP cc_start: 0.7197 (t0) cc_final: 0.6762 (m-30) REVERT: I 137 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7619 (ttm-80) REVERT: J 131 ASP cc_start: 0.8164 (t0) cc_final: 0.7770 (t0) REVERT: K 12 HIS cc_start: 0.7587 (p-80) cc_final: 0.6351 (p-80) REVERT: K 30 LYS cc_start: 0.7232 (ttmt) cc_final: 0.6600 (tppt) REVERT: K 42 LYS cc_start: 0.7057 (mtpp) cc_final: 0.6829 (mtpp) REVERT: K 73 ARG cc_start: 0.7679 (ttm170) cc_final: 0.7291 (ttm170) REVERT: K 110 LYS cc_start: 0.6969 (tttt) cc_final: 0.6231 (mptt) REVERT: K 146 LYS cc_start: 0.7638 (ttmm) cc_final: 0.7133 (mptt) REVERT: L 16 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7923 (ttpt) REVERT: L 94 LEU cc_start: 0.8127 (mm) cc_final: 0.7840 (mm) REVERT: M 22 ASP cc_start: 0.7346 (t70) cc_final: 0.7122 (t0) REVERT: M 70 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7694 (mtm-85) REVERT: M 106 HIS cc_start: 0.7811 (t-90) cc_final: 0.7480 (t-170) REVERT: N 32 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7413 (mtt-85) REVERT: N 49 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7827 (tm-30) REVERT: N 84 ASP cc_start: 0.6700 (p0) cc_final: 0.6389 (p0) REVERT: N 131 THR cc_start: 0.8915 (t) cc_final: 0.8665 (p) REVERT: N 139 LYS cc_start: 0.7530 (pttm) cc_final: 0.7135 (ttmt) REVERT: N 169 LYS cc_start: 0.8646 (mttt) cc_final: 0.8077 (mtpt) REVERT: N 206 GLU cc_start: 0.7171 (mp0) cc_final: 0.6586 (mp0) REVERT: N 226 GLU cc_start: 0.8070 (tp30) cc_final: 0.7298 (mm-30) REVERT: O 30 HIS cc_start: 0.7572 (t70) cc_final: 0.7115 (t-90) REVERT: O 36 ASP cc_start: 0.7103 (t70) cc_final: 0.6702 (t0) REVERT: O 56 GLU cc_start: 0.7487 (tt0) cc_final: 0.7084 (tt0) REVERT: O 133 SER cc_start: 0.8108 (m) cc_final: 0.7840 (t) REVERT: O 191 GLU cc_start: 0.7290 (tt0) cc_final: 0.7009 (tt0) REVERT: O 215 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7769 (mm-30) outliers start: 84 outliers final: 53 residues processed: 675 average time/residue: 0.1617 time to fit residues: 160.1539 Evaluate side-chains 668 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 613 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 CYS Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 216 HIS Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 38 optimal weight: 50.0000 chunk 79 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 198 optimal weight: 0.0070 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 209 optimal weight: 0.0030 chunk 230 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 overall best weight: 1.8014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS C 76 ASN D 27 HIS D 69 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 GLN M 29 HIS M 60 HIS ** M 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 ASN ** O 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 145 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.146348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.116426 restraints weight = 29245.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.120685 restraints weight = 17758.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.122956 restraints weight = 10130.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.123533 restraints weight = 7931.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.123925 restraints weight = 7487.961| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 19534 Z= 0.141 Angle : 0.690 10.532 26632 Z= 0.332 Chirality : 0.040 0.166 2876 Planarity : 0.004 0.098 3376 Dihedral : 8.450 86.627 2656 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.18 % Rotamer: Outliers : 5.39 % Allowed : 19.08 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.18), residues: 2364 helix: 0.57 (0.14), residues: 1332 sheet: -1.10 (0.35), residues: 196 loop : -0.96 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 121 TYR 0.014 0.001 TYR F 20 PHE 0.021 0.002 PHE J 29 TRP 0.015 0.001 TRP G 19 HIS 0.020 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00361 (19522) covalent geometry : angle 0.68954 (26632) hydrogen bonds : bond 0.04624 ( 945) hydrogen bonds : angle 4.80581 ( 2703) Misc. bond : bond 0.07067 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 647 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8358 (m) cc_final: 0.7617 (p) REVERT: A 62 GLU cc_start: 0.7093 (pm20) cc_final: 0.6478 (pm20) REVERT: A 79 LEU cc_start: 0.8560 (tp) cc_final: 0.8070 (tp) REVERT: A 96 HIS cc_start: 0.7833 (t-90) cc_final: 0.7586 (t-170) REVERT: A 97 LEU cc_start: 0.8275 (tt) cc_final: 0.7947 (mt) REVERT: A 137 ARG cc_start: 0.7490 (mmt-90) cc_final: 0.7203 (mtt90) REVERT: B 31 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8058 (mt0) REVERT: B 89 LEU cc_start: 0.8506 (tt) cc_final: 0.8043 (mt) REVERT: B 107 ASP cc_start: 0.8066 (t70) cc_final: 0.7791 (t70) REVERT: C 17 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8682 (ttpp) REVERT: C 57 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8146 (t) REVERT: C 103 GLU cc_start: 0.7632 (tp30) cc_final: 0.7030 (tp30) REVERT: C 105 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7964 (mmt90) REVERT: C 151 LEU cc_start: 0.7615 (mt) cc_final: 0.7319 (mt) REVERT: D 57 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7479 (mmm-85) REVERT: D 72 ARG cc_start: 0.7613 (mtm180) cc_final: 0.7122 (mtm-85) REVERT: D 85 ASP cc_start: 0.7215 (p0) cc_final: 0.6874 (p0) REVERT: D 126 LEU cc_start: 0.8445 (mp) cc_final: 0.8143 (mp) REVERT: E 67 LYS cc_start: 0.6497 (mtpt) cc_final: 0.5639 (mttt) REVERT: E 79 LEU cc_start: 0.8162 (tp) cc_final: 0.7856 (tp) REVERT: E 90 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7440 (tt) REVERT: E 94 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7714 (mp) REVERT: E 113 ARG cc_start: 0.6969 (mmm-85) cc_final: 0.6700 (mmm-85) REVERT: E 121 ARG cc_start: 0.7183 (ttp-110) cc_final: 0.6698 (ttp-110) REVERT: E 131 ASN cc_start: 0.7492 (t0) cc_final: 0.6654 (t0) REVERT: E 137 ARG cc_start: 0.7258 (ttp-110) cc_final: 0.6980 (ttm110) REVERT: F 11 LYS cc_start: 0.7984 (tptm) cc_final: 0.7738 (tttt) REVERT: F 120 GLN cc_start: 0.8458 (tp40) cc_final: 0.8147 (tp-100) REVERT: F 123 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5915 (ptp-170) REVERT: F 134 ILE cc_start: 0.8395 (pp) cc_final: 0.8043 (mt) REVERT: G 23 TRP cc_start: 0.7583 (m-90) cc_final: 0.7283 (m-90) REVERT: G 114 LYS cc_start: 0.7517 (tptm) cc_final: 0.6800 (mtpp) REVERT: G 124 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8631 (mm) REVERT: H 93 GLN cc_start: 0.6897 (mm110) cc_final: 0.6679 (mm-40) REVERT: H 98 LYS cc_start: 0.7296 (tmtt) cc_final: 0.6283 (ttmm) REVERT: I 85 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.5842 (t70) REVERT: I 137 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7680 (ttp-110) REVERT: J 26 ARG cc_start: 0.7679 (ttm170) cc_final: 0.6956 (ttt180) REVERT: J 131 ASP cc_start: 0.8190 (t0) cc_final: 0.7904 (t0) REVERT: K 6 CYS cc_start: 0.7002 (m) cc_final: 0.6752 (p) REVERT: K 12 HIS cc_start: 0.7547 (p-80) cc_final: 0.6391 (p-80) REVERT: K 30 LYS cc_start: 0.7134 (ttmt) cc_final: 0.6539 (tppt) REVERT: K 42 LYS cc_start: 0.7123 (mtpp) cc_final: 0.6795 (mtpp) REVERT: K 73 ARG cc_start: 0.7720 (ttm170) cc_final: 0.7332 (ttm170) REVERT: K 110 LYS cc_start: 0.6943 (tttt) cc_final: 0.6204 (mptt) REVERT: K 146 LYS cc_start: 0.7684 (ttmm) cc_final: 0.7142 (mptt) REVERT: L 94 LEU cc_start: 0.8250 (mm) cc_final: 0.7937 (mt) REVERT: L 132 PHE cc_start: 0.7079 (t80) cc_final: 0.6468 (t80) REVERT: M 22 ASP cc_start: 0.7406 (t70) cc_final: 0.7182 (t0) REVERT: M 70 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7627 (mtm-85) REVERT: M 200 ASP cc_start: 0.7563 (t0) cc_final: 0.7189 (t70) REVERT: N 65 ARG cc_start: 0.7382 (tmm-80) cc_final: 0.6882 (ttp-170) REVERT: N 84 ASP cc_start: 0.6549 (p0) cc_final: 0.6210 (p0) REVERT: N 139 LYS cc_start: 0.7449 (pttm) cc_final: 0.7119 (ttmt) REVERT: N 169 LYS cc_start: 0.8587 (mttt) cc_final: 0.8034 (mtpt) REVERT: N 226 GLU cc_start: 0.8093 (tp30) cc_final: 0.7488 (mm-30) REVERT: O 30 HIS cc_start: 0.7565 (t70) cc_final: 0.7223 (t-90) REVERT: O 36 ASP cc_start: 0.7120 (t70) cc_final: 0.6696 (t0) REVERT: O 50 LEU cc_start: 0.8747 (tt) cc_final: 0.8527 (tt) REVERT: O 56 GLU cc_start: 0.7438 (tt0) cc_final: 0.7063 (tt0) REVERT: O 77 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8187 (pt) REVERT: O 103 LYS cc_start: 0.7818 (tppp) cc_final: 0.7222 (ptpp) REVERT: O 191 GLU cc_start: 0.7268 (tt0) cc_final: 0.7001 (tt0) outliers start: 100 outliers final: 68 residues processed: 687 average time/residue: 0.1627 time to fit residues: 163.6867 Evaluate side-chains 695 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 620 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 123 ARG Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 70 HIS Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 CYS Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 208 HIS Chi-restraints excluded: chain N residue 216 HIS Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 145 HIS Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 177 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 121 optimal weight: 40.0000 chunk 144 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS B 120 GLN C 76 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN G 16 GLN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS M 56 ASN M 65 HIS M 78 HIS M 106 HIS N 126 HIS N 202 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.141979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.113495 restraints weight = 29465.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.116089 restraints weight = 17233.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.117302 restraints weight = 12295.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.117793 restraints weight = 9925.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.118059 restraints weight = 9574.663| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 19534 Z= 0.210 Angle : 0.765 11.458 26632 Z= 0.371 Chirality : 0.043 0.191 2876 Planarity : 0.005 0.084 3376 Dihedral : 8.584 88.036 2656 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.29 % Favored : 94.59 % Rotamer: Outliers : 6.15 % Allowed : 20.65 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2364 helix: 0.29 (0.14), residues: 1364 sheet: -1.13 (0.35), residues: 205 loop : -0.90 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 18 TYR 0.019 0.002 TYR F 20 PHE 0.038 0.002 PHE F 106 TRP 0.017 0.002 TRP G 136 HIS 0.045 0.002 HIS O 145 Details of bonding type rmsd covalent geometry : bond 0.00532 (19522) covalent geometry : angle 0.76545 (26632) hydrogen bonds : bond 0.05250 ( 945) hydrogen bonds : angle 5.01170 ( 2703) Misc. bond : bond 0.07853 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 652 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7175 (tpp80) REVERT: A 79 LEU cc_start: 0.8339 (tp) cc_final: 0.7818 (tp) REVERT: A 97 LEU cc_start: 0.8495 (tt) cc_final: 0.7998 (mt) REVERT: A 137 ARG cc_start: 0.7567 (mmt-90) cc_final: 0.7367 (mtm-85) REVERT: B 89 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8010 (mt) REVERT: B 107 ASP cc_start: 0.8047 (t70) cc_final: 0.7759 (t70) REVERT: C 17 LYS cc_start: 0.9001 (ttmm) cc_final: 0.8334 (tttm) REVERT: C 57 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8225 (t) REVERT: C 76 ASN cc_start: 0.8573 (t0) cc_final: 0.8236 (t0) REVERT: C 86 ASP cc_start: 0.6395 (OUTLIER) cc_final: 0.5588 (t0) REVERT: C 103 GLU cc_start: 0.7565 (tp30) cc_final: 0.7251 (tp30) REVERT: D 50 LYS cc_start: 0.6333 (OUTLIER) cc_final: 0.6094 (ptmt) REVERT: D 57 ARG cc_start: 0.7952 (mtp-110) cc_final: 0.7650 (mmm-85) REVERT: D 72 ARG cc_start: 0.7731 (mtm180) cc_final: 0.7261 (mtm-85) REVERT: D 85 ASP cc_start: 0.7578 (p0) cc_final: 0.7349 (p0) REVERT: D 126 LEU cc_start: 0.8460 (mp) cc_final: 0.8255 (mp) REVERT: E 67 LYS cc_start: 0.6522 (mtpt) cc_final: 0.5730 (mttt) REVERT: E 79 LEU cc_start: 0.8311 (tp) cc_final: 0.8034 (tp) REVERT: E 94 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7963 (mp) REVERT: E 113 ARG cc_start: 0.7085 (mmm-85) cc_final: 0.6749 (mmm-85) REVERT: E 131 ASN cc_start: 0.7491 (t0) cc_final: 0.6692 (t0) REVERT: F 11 LYS cc_start: 0.8138 (tptm) cc_final: 0.7926 (tttt) REVERT: F 120 GLN cc_start: 0.8604 (tp40) cc_final: 0.8262 (tp-100) REVERT: F 123 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.6079 (ptp-170) REVERT: G 38 LEU cc_start: 0.6871 (tt) cc_final: 0.6513 (mp) REVERT: G 83 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.7864 (m-40) REVERT: G 103 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7111 (tm-30) REVERT: G 124 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8738 (tp) REVERT: H 31 ARG cc_start: 0.6678 (ttm170) cc_final: 0.6288 (ttm170) REVERT: H 88 ASP cc_start: 0.7790 (p0) cc_final: 0.7450 (p0) REVERT: H 93 GLN cc_start: 0.7029 (mm110) cc_final: 0.6797 (mm-40) REVERT: H 129 HIS cc_start: 0.7135 (m-70) cc_final: 0.6225 (m-70) REVERT: I 20 ASP cc_start: 0.7550 (t0) cc_final: 0.6906 (m-30) REVERT: I 36 ARG cc_start: 0.7959 (ttp80) cc_final: 0.6724 (ttm170) REVERT: I 94 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7982 (tp) REVERT: I 131 ASN cc_start: 0.8019 (t0) cc_final: 0.7657 (t0) REVERT: I 137 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7850 (ttm-80) REVERT: J 114 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8178 (tp) REVERT: J 131 ASP cc_start: 0.8185 (t0) cc_final: 0.7927 (t0) REVERT: K 6 CYS cc_start: 0.7137 (m) cc_final: 0.6800 (p) REVERT: K 10 GLU cc_start: 0.7405 (tp30) cc_final: 0.6841 (tp30) REVERT: K 12 HIS cc_start: 0.7628 (p-80) cc_final: 0.6466 (p-80) REVERT: K 30 LYS cc_start: 0.7163 (ttmt) cc_final: 0.6576 (tppt) REVERT: K 110 LYS cc_start: 0.6910 (tttt) cc_final: 0.6220 (mptt) REVERT: K 146 LYS cc_start: 0.7924 (ttmm) cc_final: 0.7387 (mptt) REVERT: L 36 LEU cc_start: 0.8099 (tt) cc_final: 0.7821 (tp) REVERT: L 94 LEU cc_start: 0.8386 (mm) cc_final: 0.8051 (mt) REVERT: L 138 CYS cc_start: 0.7525 (m) cc_final: 0.7049 (m) REVERT: M 17 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8138 (mm-40) REVERT: M 69 CYS cc_start: 0.8246 (m) cc_final: 0.7931 (t) REVERT: M 88 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: M 200 ASP cc_start: 0.7760 (t0) cc_final: 0.7295 (t70) REVERT: N 65 ARG cc_start: 0.7448 (tmm-80) cc_final: 0.6940 (ttp-170) REVERT: N 83 CYS cc_start: 0.8610 (t) cc_final: 0.8353 (t) REVERT: N 139 LYS cc_start: 0.7602 (pttm) cc_final: 0.7381 (ttmt) REVERT: N 169 LYS cc_start: 0.8580 (mttt) cc_final: 0.7974 (ptmt) REVERT: N 216 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7851 (p-80) REVERT: N 226 GLU cc_start: 0.8197 (tp30) cc_final: 0.7720 (mm-30) REVERT: O 30 HIS cc_start: 0.7668 (t70) cc_final: 0.7180 (t-90) REVERT: O 36 ASP cc_start: 0.7318 (t70) cc_final: 0.6930 (t0) REVERT: O 56 GLU cc_start: 0.7302 (tt0) cc_final: 0.7101 (tt0) REVERT: O 75 GLN cc_start: 0.8106 (tp40) cc_final: 0.7886 (tp-100) REVERT: O 77 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8144 (pt) REVERT: O 139 THR cc_start: 0.8501 (t) cc_final: 0.8192 (p) REVERT: O 191 GLU cc_start: 0.7205 (tt0) cc_final: 0.6979 (tt0) REVERT: O 203 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.6698 (p-80) REVERT: O 210 GLU cc_start: 0.7299 (tp30) cc_final: 0.7060 (tp30) outliers start: 114 outliers final: 74 residues processed: 699 average time/residue: 0.1671 time to fit residues: 170.0196 Evaluate side-chains 712 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 624 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 123 ARG Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 70 HIS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 CYS Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 208 HIS Chi-restraints excluded: chain N residue 216 HIS Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 203 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 217 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS D 27 HIS ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 HIS K 100 HIS L 96 HIS M 29 HIS M 60 HIS N 126 HIS N 202 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.145345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.117169 restraints weight = 28927.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.119913 restraints weight = 17550.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.121169 restraints weight = 12316.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.121741 restraints weight = 9888.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.123017 restraints weight = 9570.103| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 19534 Z= 0.135 Angle : 0.686 11.543 26632 Z= 0.327 Chirality : 0.041 0.260 2876 Planarity : 0.004 0.063 3376 Dihedral : 8.423 88.739 2656 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 5.23 % Allowed : 23.40 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.18), residues: 2364 helix: 0.69 (0.14), residues: 1333 sheet: -1.01 (0.36), residues: 204 loop : -0.78 (0.24), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 121 TYR 0.016 0.002 TYR J 20 PHE 0.026 0.002 PHE J 29 TRP 0.015 0.001 TRP G 19 HIS 0.009 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00342 (19522) covalent geometry : angle 0.68559 (26632) hydrogen bonds : bond 0.04258 ( 945) hydrogen bonds : angle 4.59317 ( 2703) Misc. bond : bond 0.05854 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 637 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7653 (tpp80) cc_final: 0.7323 (tpp80) REVERT: A 97 LEU cc_start: 0.8303 (tt) cc_final: 0.7883 (mt) REVERT: A 137 ARG cc_start: 0.7470 (mmt-90) cc_final: 0.7026 (mtt90) REVERT: B 10 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7766 (pp) REVERT: B 31 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7986 (mt0) REVERT: B 107 ASP cc_start: 0.8073 (t70) cc_final: 0.7796 (t70) REVERT: C 17 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8463 (tttm) REVERT: C 86 ASP cc_start: 0.6105 (OUTLIER) cc_final: 0.5364 (t0) REVERT: D 36 LEU cc_start: 0.8335 (tt) cc_final: 0.7989 (tp) REVERT: D 57 ARG cc_start: 0.7873 (mtp-110) cc_final: 0.7618 (mmm-85) REVERT: D 72 ARG cc_start: 0.7638 (mtm180) cc_final: 0.6909 (mtm-85) REVERT: D 116 LYS cc_start: 0.8107 (tppt) cc_final: 0.7899 (tptt) REVERT: D 126 LEU cc_start: 0.8320 (mp) cc_final: 0.8087 (mp) REVERT: E 67 LYS cc_start: 0.6406 (mtpt) cc_final: 0.5607 (mttt) REVERT: E 79 LEU cc_start: 0.8255 (tp) cc_final: 0.8003 (tp) REVERT: E 113 ARG cc_start: 0.7045 (mmm-85) cc_final: 0.6721 (mmm-85) REVERT: E 131 ASN cc_start: 0.7497 (t0) cc_final: 0.6669 (t0) REVERT: F 120 GLN cc_start: 0.8561 (tp40) cc_final: 0.8218 (tp-100) REVERT: F 123 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.6014 (ptp-170) REVERT: G 38 LEU cc_start: 0.6865 (tt) cc_final: 0.6477 (mp) REVERT: G 103 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7360 (tm-30) REVERT: G 124 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8693 (tp) REVERT: H 69 HIS cc_start: 0.7805 (t-90) cc_final: 0.7209 (t-90) REVERT: H 88 ASP cc_start: 0.7838 (p0) cc_final: 0.7418 (p0) REVERT: I 20 ASP cc_start: 0.7663 (t0) cc_final: 0.7164 (m-30) REVERT: I 36 ARG cc_start: 0.7975 (ttp80) cc_final: 0.6690 (ttm170) REVERT: I 44 LYS cc_start: 0.7285 (tttm) cc_final: 0.7046 (tttm) REVERT: I 86 ASP cc_start: 0.8803 (t0) cc_final: 0.8587 (t0) REVERT: I 94 LEU cc_start: 0.8181 (tp) cc_final: 0.7919 (tp) REVERT: I 131 ASN cc_start: 0.7856 (t0) cc_final: 0.7626 (t0) REVERT: I 137 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7647 (ttm-80) REVERT: J 33 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8395 (mp) REVERT: J 34 TRP cc_start: 0.8042 (m100) cc_final: 0.7545 (m100) REVERT: J 114 LEU cc_start: 0.8424 (mp) cc_final: 0.8174 (tp) REVERT: J 131 ASP cc_start: 0.8072 (t0) cc_final: 0.7854 (t0) REVERT: K 6 CYS cc_start: 0.6896 (m) cc_final: 0.6594 (p) REVERT: K 12 HIS cc_start: 0.7546 (p-80) cc_final: 0.6355 (p-80) REVERT: K 30 LYS cc_start: 0.7106 (ttmt) cc_final: 0.6521 (tppt) REVERT: K 110 LYS cc_start: 0.6917 (tttt) cc_final: 0.6210 (mptt) REVERT: K 146 LYS cc_start: 0.7674 (ttmm) cc_final: 0.7178 (mptt) REVERT: L 36 LEU cc_start: 0.7886 (tt) cc_final: 0.7652 (tp) REVERT: L 94 LEU cc_start: 0.8309 (mm) cc_final: 0.8030 (mt) REVERT: L 129 HIS cc_start: 0.6138 (m-70) cc_final: 0.5737 (m90) REVERT: L 138 CYS cc_start: 0.7434 (m) cc_final: 0.6982 (m) REVERT: M 17 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8111 (mm-40) REVERT: M 68 GLU cc_start: 0.8237 (pm20) cc_final: 0.7954 (pm20) REVERT: M 88 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: M 200 ASP cc_start: 0.7799 (t0) cc_final: 0.7436 (t70) REVERT: M 207 LYS cc_start: 0.8352 (ptpt) cc_final: 0.8081 (ptpp) REVERT: M 208 ILE cc_start: 0.8752 (mm) cc_final: 0.8462 (mm) REVERT: N 49 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7796 (tm-30) REVERT: N 65 ARG cc_start: 0.7356 (tmm-80) cc_final: 0.6788 (ttp-170) REVERT: N 74 GLN cc_start: 0.8320 (pt0) cc_final: 0.7926 (pt0) REVERT: N 139 LYS cc_start: 0.7428 (pttm) cc_final: 0.7224 (ttmt) REVERT: N 169 LYS cc_start: 0.8517 (mttt) cc_final: 0.7922 (ptmt) REVERT: N 216 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7744 (p-80) REVERT: O 30 HIS cc_start: 0.7651 (t70) cc_final: 0.7155 (t-90) REVERT: O 36 ASP cc_start: 0.7325 (t70) cc_final: 0.6807 (t0) REVERT: O 75 GLN cc_start: 0.7956 (tp40) cc_final: 0.7679 (tp-100) REVERT: O 139 THR cc_start: 0.8357 (t) cc_final: 0.8092 (p) REVERT: O 153 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6551 (tm-30) REVERT: O 191 GLU cc_start: 0.7143 (tt0) cc_final: 0.6910 (tt0) REVERT: O 203 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.6597 (p-80) REVERT: O 210 GLU cc_start: 0.7378 (tp30) cc_final: 0.7123 (tp30) outliers start: 97 outliers final: 65 residues processed: 679 average time/residue: 0.1692 time to fit residues: 167.7611 Evaluate side-chains 680 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 607 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 123 ARG Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain K residue 70 HIS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 CYS Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain N residue 208 HIS Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 216 HIS Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 203 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 187 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 121 optimal weight: 50.0000 chunk 77 optimal weight: 0.5980 chunk 164 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 chunk 220 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN D 117 HIS ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN G 97 HIS ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN L 141 GLN M 40 HIS M 60 HIS N 202 ASN O 145 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.142425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.113964 restraints weight = 29312.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.116679 restraints weight = 17409.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.117971 restraints weight = 12278.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.118568 restraints weight = 9926.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.119712 restraints weight = 9589.793| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.166 19534 Z= 0.187 Angle : 0.743 11.132 26632 Z= 0.357 Chirality : 0.043 0.188 2876 Planarity : 0.005 0.052 3376 Dihedral : 8.466 89.532 2656 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.20 % Favored : 94.67 % Rotamer: Outliers : 5.61 % Allowed : 24.74 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.18), residues: 2364 helix: 0.39 (0.14), residues: 1377 sheet: -0.98 (0.36), residues: 204 loop : -0.84 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 121 TYR 0.019 0.002 TYR B 20 PHE 0.025 0.002 PHE J 29 TRP 0.012 0.002 TRP F 34 HIS 0.015 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00481 (19522) covalent geometry : angle 0.74272 (26632) hydrogen bonds : bond 0.04838 ( 945) hydrogen bonds : angle 4.77333 ( 2703) Misc. bond : bond 0.08167 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 632 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7594 (tpp80) cc_final: 0.7109 (tpp80) REVERT: A 60 GLU cc_start: 0.6782 (tp30) cc_final: 0.6540 (tp30) REVERT: A 62 GLU cc_start: 0.6954 (pm20) cc_final: 0.6317 (pm20) REVERT: A 82 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7802 (t0) REVERT: A 97 LEU cc_start: 0.8412 (tt) cc_final: 0.7938 (mt) REVERT: A 137 ARG cc_start: 0.7567 (mmt-90) cc_final: 0.7061 (ttm110) REVERT: A 148 LYS cc_start: 0.7522 (pttp) cc_final: 0.6694 (ptmt) REVERT: B 89 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8005 (mt) REVERT: B 107 ASP cc_start: 0.8097 (t70) cc_final: 0.7885 (t70) REVERT: C 17 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8360 (tttm) REVERT: C 56 ARG cc_start: 0.7322 (tmm-80) cc_final: 0.7045 (tmm-80) REVERT: C 86 ASP cc_start: 0.6317 (OUTLIER) cc_final: 0.5413 (t0) REVERT: D 31 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7846 (ttm170) REVERT: D 57 ARG cc_start: 0.7830 (mtp-110) cc_final: 0.7623 (mmm-85) REVERT: D 62 TYR cc_start: 0.7986 (m-80) cc_final: 0.7527 (m-80) REVERT: D 72 ARG cc_start: 0.7686 (mtm180) cc_final: 0.7005 (mtm-85) REVERT: D 116 LYS cc_start: 0.8010 (tppt) cc_final: 0.7794 (tptt) REVERT: D 126 LEU cc_start: 0.8397 (mp) cc_final: 0.8168 (mp) REVERT: D 141 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7758 (tm-30) REVERT: E 45 HIS cc_start: 0.7389 (m90) cc_final: 0.6919 (m90) REVERT: E 67 LYS cc_start: 0.6335 (mtpt) cc_final: 0.5524 (mttt) REVERT: E 79 LEU cc_start: 0.8389 (tp) cc_final: 0.8180 (tp) REVERT: E 97 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8038 (tt) REVERT: E 113 ARG cc_start: 0.7142 (mmm-85) cc_final: 0.6767 (mmm-85) REVERT: E 121 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.6896 (ttp-110) REVERT: F 120 GLN cc_start: 0.8633 (tp40) cc_final: 0.8252 (tp-100) REVERT: F 123 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6075 (ptp-170) REVERT: G 38 LEU cc_start: 0.7171 (tt) cc_final: 0.6785 (mp) REVERT: G 103 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7550 (tm-30) REVERT: G 114 LYS cc_start: 0.7919 (tptm) cc_final: 0.7209 (mtpp) REVERT: G 124 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8670 (tp) REVERT: H 69 HIS cc_start: 0.7886 (t-90) cc_final: 0.7300 (t-90) REVERT: H 88 ASP cc_start: 0.7906 (p0) cc_final: 0.7456 (p0) REVERT: H 98 LYS cc_start: 0.7261 (tmtt) cc_final: 0.6173 (ttmm) REVERT: I 20 ASP cc_start: 0.7776 (t0) cc_final: 0.7117 (m-30) REVERT: I 36 ARG cc_start: 0.8075 (ttp80) cc_final: 0.6907 (ttm170) REVERT: I 44 LYS cc_start: 0.7303 (tttm) cc_final: 0.7066 (tttm) REVERT: I 94 LEU cc_start: 0.8403 (tp) cc_final: 0.8110 (tp) REVERT: I 131 ASN cc_start: 0.8100 (t0) cc_final: 0.7791 (t0) REVERT: I 137 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7657 (ttm-80) REVERT: J 33 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8445 (mp) REVERT: J 114 LEU cc_start: 0.8507 (mp) cc_final: 0.8234 (tp) REVERT: J 131 ASP cc_start: 0.7955 (t0) cc_final: 0.7624 (t0) REVERT: K 6 CYS cc_start: 0.6912 (m) cc_final: 0.6666 (p) REVERT: K 10 GLU cc_start: 0.7268 (tp30) cc_final: 0.6914 (tp30) REVERT: K 30 LYS cc_start: 0.7023 (ttmt) cc_final: 0.6437 (tppt) REVERT: K 110 LYS cc_start: 0.6919 (tttt) cc_final: 0.6234 (mptt) REVERT: K 146 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7322 (mptt) REVERT: L 36 LEU cc_start: 0.8057 (tt) cc_final: 0.7844 (tp) REVERT: L 94 LEU cc_start: 0.8359 (mm) cc_final: 0.8026 (mt) REVERT: L 138 CYS cc_start: 0.7452 (m) cc_final: 0.6997 (m) REVERT: M 17 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8117 (mm-40) REVERT: M 88 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: M 200 ASP cc_start: 0.7649 (t0) cc_final: 0.7270 (t70) REVERT: M 206 CYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8180 (m) REVERT: M 207 LYS cc_start: 0.8388 (ptpt) cc_final: 0.8185 (ptpp) REVERT: M 208 ILE cc_start: 0.8843 (mm) cc_final: 0.8580 (mm) REVERT: N 65 ARG cc_start: 0.7361 (tmm-80) cc_final: 0.6730 (ttp-170) REVERT: N 74 GLN cc_start: 0.8318 (pt0) cc_final: 0.7935 (pt0) REVERT: N 139 LYS cc_start: 0.7570 (pttm) cc_final: 0.7362 (ttmt) REVERT: N 169 LYS cc_start: 0.8567 (mttt) cc_final: 0.8052 (ptmt) REVERT: N 216 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7668 (p-80) REVERT: N 226 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8329 (mm-30) REVERT: O 30 HIS cc_start: 0.7733 (t70) cc_final: 0.7207 (t-90) REVERT: O 36 ASP cc_start: 0.7146 (t70) cc_final: 0.6572 (t0) REVERT: O 139 THR cc_start: 0.8318 (t) cc_final: 0.8081 (p) REVERT: O 203 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.6646 (p-80) REVERT: O 210 GLU cc_start: 0.7299 (tp30) cc_final: 0.7004 (tp30) outliers start: 104 outliers final: 80 residues processed: 677 average time/residue: 0.1684 time to fit residues: 166.1910 Evaluate side-chains 713 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 622 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 123 ARG Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain K residue 70 HIS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 CYS Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 206 CYS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain N residue 208 HIS Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 216 HIS Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 203 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 133 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 173 optimal weight: 0.2980 chunk 196 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 94 optimal weight: 50.0000 chunk 48 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 100 optimal weight: 0.0980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 93 GLN ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS M 60 HIS O 145 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.146045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.116572 restraints weight = 28920.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.121050 restraints weight = 16652.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.123101 restraints weight = 9597.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.123043 restraints weight = 7860.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.123408 restraints weight = 7651.269| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 19534 Z= 0.129 Angle : 0.680 11.725 26632 Z= 0.325 Chirality : 0.040 0.176 2876 Planarity : 0.004 0.045 3376 Dihedral : 8.284 89.440 2656 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 4.69 % Allowed : 26.36 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2364 helix: 0.70 (0.14), residues: 1350 sheet: -0.99 (0.36), residues: 204 loop : -0.80 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 144 TYR 0.015 0.001 TYR F 20 PHE 0.026 0.001 PHE J 29 TRP 0.016 0.001 TRP G 19 HIS 0.010 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00322 (19522) covalent geometry : angle 0.67994 (26632) hydrogen bonds : bond 0.04004 ( 945) hydrogen bonds : angle 4.46570 ( 2703) Misc. bond : bond 0.06332 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 625 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7362 (tpp80) REVERT: A 62 GLU cc_start: 0.6979 (pm20) cc_final: 0.6520 (pm20) REVERT: A 82 ASN cc_start: 0.8447 (m-40) cc_final: 0.7904 (t0) REVERT: A 97 LEU cc_start: 0.8235 (tt) cc_final: 0.7795 (mt) REVERT: A 113 ARG cc_start: 0.6490 (ttp80) cc_final: 0.6182 (mmm-85) REVERT: A 137 ARG cc_start: 0.7553 (mmt-90) cc_final: 0.7051 (ttm110) REVERT: B 31 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8145 (mm-40) REVERT: B 89 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7919 (mt) REVERT: C 17 LYS cc_start: 0.8986 (ttmm) cc_final: 0.8489 (tttm) REVERT: C 56 ARG cc_start: 0.7321 (tmm-80) cc_final: 0.7035 (tmm-80) REVERT: C 109 GLN cc_start: 0.6426 (mt0) cc_final: 0.6216 (mp10) REVERT: D 31 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7703 (ttm170) REVERT: D 36 LEU cc_start: 0.8532 (tt) cc_final: 0.8296 (tp) REVERT: D 62 TYR cc_start: 0.7934 (m-80) cc_final: 0.7407 (m-80) REVERT: D 72 ARG cc_start: 0.7632 (mtm180) cc_final: 0.7177 (mtm-85) REVERT: D 116 LYS cc_start: 0.7920 (tppt) cc_final: 0.7682 (tptt) REVERT: D 126 LEU cc_start: 0.8340 (mp) cc_final: 0.8116 (mp) REVERT: D 141 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7697 (tm-30) REVERT: E 45 HIS cc_start: 0.7382 (m90) cc_final: 0.6952 (m90) REVERT: E 67 LYS cc_start: 0.6222 (mtpt) cc_final: 0.5386 (mttt) REVERT: E 79 LEU cc_start: 0.8359 (tp) cc_final: 0.8135 (tp) REVERT: E 97 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7939 (tt) REVERT: E 113 ARG cc_start: 0.7059 (mmm-85) cc_final: 0.6724 (mmm-85) REVERT: E 121 ARG cc_start: 0.7210 (ttp-110) cc_final: 0.6843 (ttp-110) REVERT: F 123 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6225 (ptp-170) REVERT: G 38 LEU cc_start: 0.7131 (tt) cc_final: 0.6723 (mp) REVERT: G 103 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7690 (tm-30) REVERT: G 114 LYS cc_start: 0.7928 (tptm) cc_final: 0.7199 (mtpp) REVERT: G 124 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8652 (tp) REVERT: G 146 LYS cc_start: 0.8076 (tptp) cc_final: 0.6952 (mttm) REVERT: H 53 PHE cc_start: 0.8124 (m-10) cc_final: 0.7844 (m-10) REVERT: H 69 HIS cc_start: 0.8057 (t-90) cc_final: 0.7509 (t-90) REVERT: H 88 ASP cc_start: 0.7920 (p0) cc_final: 0.7477 (p0) REVERT: H 98 LYS cc_start: 0.7281 (tmtt) cc_final: 0.6181 (ttmm) REVERT: I 36 ARG cc_start: 0.7996 (ttp80) cc_final: 0.6895 (ttm170) REVERT: I 44 LYS cc_start: 0.7312 (tttm) cc_final: 0.7076 (tttm) REVERT: I 86 ASP cc_start: 0.8834 (t0) cc_final: 0.8588 (t70) REVERT: I 89 VAL cc_start: 0.8364 (t) cc_final: 0.8136 (t) REVERT: I 94 LEU cc_start: 0.8226 (tp) cc_final: 0.7990 (tp) REVERT: I 131 ASN cc_start: 0.8070 (t0) cc_final: 0.7743 (t0) REVERT: I 137 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7688 (ttm-80) REVERT: J 33 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8376 (mp) REVERT: J 114 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8194 (tp) REVERT: J 131 ASP cc_start: 0.7912 (t0) cc_final: 0.7589 (t0) REVERT: K 30 LYS cc_start: 0.6985 (ttmt) cc_final: 0.6402 (tppt) REVERT: K 110 LYS cc_start: 0.6909 (tttt) cc_final: 0.6214 (mptt) REVERT: K 146 LYS cc_start: 0.7731 (ttmm) cc_final: 0.7177 (mptt) REVERT: L 94 LEU cc_start: 0.8422 (mm) cc_final: 0.8077 (mt) REVERT: L 138 CYS cc_start: 0.7386 (m) cc_final: 0.7007 (m) REVERT: M 17 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8149 (mm-40) REVERT: M 88 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: M 184 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6588 (mmmt) REVERT: M 200 ASP cc_start: 0.7594 (t0) cc_final: 0.7267 (t70) REVERT: M 208 ILE cc_start: 0.8777 (mm) cc_final: 0.8543 (mm) REVERT: N 65 ARG cc_start: 0.7325 (tmm-80) cc_final: 0.6744 (ttp-170) REVERT: N 74 GLN cc_start: 0.8245 (pt0) cc_final: 0.7876 (pt0) REVERT: N 169 LYS cc_start: 0.8568 (mttt) cc_final: 0.7993 (ptmt) REVERT: N 216 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.7603 (p-80) REVERT: N 226 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8289 (mm-30) REVERT: O 30 HIS cc_start: 0.7716 (t70) cc_final: 0.7226 (t-90) REVERT: O 36 ASP cc_start: 0.7198 (t70) cc_final: 0.6552 (t0) REVERT: O 124 HIS cc_start: 0.8340 (p-80) cc_final: 0.7628 (p-80) REVERT: O 203 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6435 (p-80) REVERT: O 210 GLU cc_start: 0.7283 (tp30) cc_final: 0.6966 (tp30) outliers start: 87 outliers final: 65 residues processed: 658 average time/residue: 0.1722 time to fit residues: 164.0325 Evaluate side-chains 677 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 602 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 123 ARG Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 70 HIS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 184 LYS Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain N residue 208 HIS Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 216 HIS Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 203 HIS Chi-restraints excluded: chain O residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 184 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 117 optimal weight: 0.0030 chunk 36 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN E 96 HIS F 64 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS M 60 HIS O 68 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.144873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116434 restraints weight = 29159.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.119344 restraints weight = 17289.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.120941 restraints weight = 11855.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.121334 restraints weight = 9328.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.121516 restraints weight = 9040.672| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 19534 Z= 0.148 Angle : 0.700 13.158 26632 Z= 0.335 Chirality : 0.041 0.191 2876 Planarity : 0.004 0.046 3376 Dihedral : 8.287 88.920 2656 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.75 % Rotamer: Outliers : 5.01 % Allowed : 26.58 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.18), residues: 2364 helix: 0.67 (0.14), residues: 1353 sheet: -1.00 (0.36), residues: 204 loop : -0.75 (0.24), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 72 TYR 0.016 0.002 TYR F 20 PHE 0.040 0.002 PHE O 138 TRP 0.015 0.001 TRP G 19 HIS 0.012 0.001 HIS J 91 Details of bonding type rmsd covalent geometry : bond 0.00386 (19522) covalent geometry : angle 0.70030 (26632) hydrogen bonds : bond 0.04168 ( 945) hydrogen bonds : angle 4.53122 ( 2703) Misc. bond : bond 0.06661 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 609 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7620 (tpp80) cc_final: 0.7378 (tpp80) REVERT: A 62 GLU cc_start: 0.6948 (pm20) cc_final: 0.6453 (pm20) REVERT: A 82 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7981 (t0) REVERT: A 97 LEU cc_start: 0.8263 (tt) cc_final: 0.7821 (mt) REVERT: A 113 ARG cc_start: 0.6859 (ttp80) cc_final: 0.6341 (mmm-85) REVERT: A 137 ARG cc_start: 0.7493 (mmt-90) cc_final: 0.7234 (ttm-80) REVERT: B 89 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7980 (mt) REVERT: C 17 LYS cc_start: 0.9005 (ttmm) cc_final: 0.8496 (tttm) REVERT: C 56 ARG cc_start: 0.7337 (tmm-80) cc_final: 0.7045 (tmm-80) REVERT: D 31 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7727 (ttm170) REVERT: D 62 TYR cc_start: 0.7939 (m-80) cc_final: 0.7479 (m-80) REVERT: D 72 ARG cc_start: 0.7750 (mtm180) cc_final: 0.7259 (mtm-85) REVERT: D 116 LYS cc_start: 0.7885 (tppt) cc_final: 0.7648 (tptt) REVERT: D 126 LEU cc_start: 0.8353 (mp) cc_final: 0.8135 (mp) REVERT: D 141 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7683 (tm-30) REVERT: E 26 SER cc_start: 0.8083 (m) cc_final: 0.7871 (p) REVERT: E 45 HIS cc_start: 0.7450 (m90) cc_final: 0.6984 (m90) REVERT: E 67 LYS cc_start: 0.6189 (mtpt) cc_final: 0.5373 (mttt) REVERT: E 79 LEU cc_start: 0.8456 (tp) cc_final: 0.8231 (tp) REVERT: E 113 ARG cc_start: 0.7084 (mmm-85) cc_final: 0.6727 (mmm-85) REVERT: E 121 ARG cc_start: 0.7221 (ttp-110) cc_final: 0.6756 (ttp-110) REVERT: F 120 GLN cc_start: 0.8851 (tp40) cc_final: 0.8518 (tp-100) REVERT: F 123 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6178 (ptp-170) REVERT: G 38 LEU cc_start: 0.7162 (tt) cc_final: 0.6688 (mp) REVERT: G 103 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7670 (tm-30) REVERT: G 114 LYS cc_start: 0.7948 (tptm) cc_final: 0.7242 (mtpp) REVERT: G 124 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8666 (tp) REVERT: G 146 LYS cc_start: 0.8052 (tptp) cc_final: 0.6975 (mttm) REVERT: H 69 HIS cc_start: 0.8084 (t-90) cc_final: 0.7513 (t-90) REVERT: H 88 ASP cc_start: 0.7974 (p0) cc_final: 0.7554 (p0) REVERT: H 98 LYS cc_start: 0.7219 (tmtt) cc_final: 0.6116 (ttmm) REVERT: I 36 ARG cc_start: 0.8003 (ttp80) cc_final: 0.6903 (ttm170) REVERT: I 44 LYS cc_start: 0.7305 (tttm) cc_final: 0.7057 (tttm) REVERT: I 94 LEU cc_start: 0.8390 (tp) cc_final: 0.8144 (tp) REVERT: I 131 ASN cc_start: 0.8167 (t0) cc_final: 0.7864 (t0) REVERT: I 137 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7624 (ttm-80) REVERT: J 16 TRP cc_start: 0.8055 (t-100) cc_final: 0.7833 (t-100) REVERT: J 33 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8390 (mp) REVERT: J 114 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8218 (tp) REVERT: J 131 ASP cc_start: 0.7894 (t0) cc_final: 0.7592 (t0) REVERT: K 30 LYS cc_start: 0.7001 (ttmt) cc_final: 0.6415 (tppt) REVERT: K 42 LYS cc_start: 0.7170 (mtpp) cc_final: 0.6937 (mtpp) REVERT: K 110 LYS cc_start: 0.6914 (tttt) cc_final: 0.6224 (mptt) REVERT: K 146 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7187 (mptt) REVERT: L 105 ASN cc_start: 0.8366 (p0) cc_final: 0.8034 (p0) REVERT: L 138 CYS cc_start: 0.7395 (m) cc_final: 0.6989 (m) REVERT: M 17 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8166 (mm-40) REVERT: M 88 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: M 184 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6684 (mmmt) REVERT: M 200 ASP cc_start: 0.7642 (t0) cc_final: 0.7292 (t70) REVERT: N 65 ARG cc_start: 0.7292 (tmm-80) cc_final: 0.6714 (ttp-170) REVERT: N 74 GLN cc_start: 0.8385 (pt0) cc_final: 0.7965 (pt0) REVERT: N 169 LYS cc_start: 0.8531 (mttt) cc_final: 0.8034 (ptmt) REVERT: N 216 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7544 (p-80) REVERT: N 226 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8310 (mm-30) REVERT: O 30 HIS cc_start: 0.7520 (t70) cc_final: 0.7100 (t-90) REVERT: O 36 ASP cc_start: 0.7292 (t70) cc_final: 0.6650 (t0) REVERT: O 124 HIS cc_start: 0.8310 (p-80) cc_final: 0.7591 (p-80) REVERT: O 203 HIS cc_start: 0.7167 (OUTLIER) cc_final: 0.6626 (p-80) REVERT: O 210 GLU cc_start: 0.7270 (tp30) cc_final: 0.6951 (tp30) outliers start: 93 outliers final: 74 residues processed: 644 average time/residue: 0.1659 time to fit residues: 156.7963 Evaluate side-chains 688 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 604 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 123 ARG Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 70 HIS Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 184 LYS Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain N residue 208 HIS Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 216 HIS Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 203 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 102 optimal weight: 8.9990 chunk 194 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 219 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 ASN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS M 36 ASN M 60 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.147762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.118175 restraints weight = 28850.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.122459 restraints weight = 17357.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.123827 restraints weight = 10030.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.124100 restraints weight = 8575.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.124511 restraints weight = 8280.759| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 19534 Z= 0.123 Angle : 0.677 13.842 26632 Z= 0.322 Chirality : 0.040 0.167 2876 Planarity : 0.004 0.069 3376 Dihedral : 8.207 88.494 2656 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.65 % Favored : 95.22 % Rotamer: Outliers : 4.20 % Allowed : 27.44 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2364 helix: 0.91 (0.14), residues: 1343 sheet: -0.87 (0.37), residues: 203 loop : -0.77 (0.24), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 104 TYR 0.014 0.001 TYR B 20 PHE 0.048 0.001 PHE O 138 TRP 0.018 0.001 TRP G 19 HIS 0.016 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00305 (19522) covalent geometry : angle 0.67669 (26632) hydrogen bonds : bond 0.03734 ( 945) hydrogen bonds : angle 4.36213 ( 2703) Misc. bond : bond 0.05803 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 621 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7504 (tpp80) cc_final: 0.7043 (tpp80) REVERT: A 60 GLU cc_start: 0.6439 (tp30) cc_final: 0.6134 (tp30) REVERT: A 62 GLU cc_start: 0.6906 (pm20) cc_final: 0.6295 (pm20) REVERT: A 82 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7882 (t0) REVERT: A 97 LEU cc_start: 0.8057 (tt) cc_final: 0.7506 (mt) REVERT: A 137 ARG cc_start: 0.7338 (mmt-90) cc_final: 0.7095 (ttm-80) REVERT: B 89 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7948 (mt) REVERT: C 17 LYS cc_start: 0.8979 (ttmm) cc_final: 0.8501 (tttm) REVERT: C 56 ARG cc_start: 0.7343 (tmm-80) cc_final: 0.7063 (tmm-80) REVERT: C 146 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8083 (tptp) REVERT: D 62 TYR cc_start: 0.7875 (m-80) cc_final: 0.7589 (m-80) REVERT: D 72 ARG cc_start: 0.7620 (mtm180) cc_final: 0.7125 (mtm-85) REVERT: D 126 LEU cc_start: 0.8461 (mp) cc_final: 0.8253 (mp) REVERT: D 141 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7681 (tm-30) REVERT: E 26 SER cc_start: 0.8017 (m) cc_final: 0.7795 (p) REVERT: E 45 HIS cc_start: 0.7478 (m90) cc_final: 0.7021 (m90) REVERT: E 67 LYS cc_start: 0.6083 (mtpt) cc_final: 0.5255 (mttt) REVERT: E 113 ARG cc_start: 0.7011 (mmm-85) cc_final: 0.6753 (mmm-85) REVERT: E 121 ARG cc_start: 0.7210 (ttp-110) cc_final: 0.6729 (ttp-110) REVERT: F 120 GLN cc_start: 0.8838 (tp40) cc_final: 0.8549 (tp-100) REVERT: F 123 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.6114 (ptp-170) REVERT: G 38 LEU cc_start: 0.7004 (tt) cc_final: 0.6634 (mp) REVERT: G 52 ASP cc_start: 0.7822 (t70) cc_final: 0.7617 (t0) REVERT: G 103 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7747 (tm-30) REVERT: G 114 LYS cc_start: 0.7959 (tptm) cc_final: 0.7200 (mtpp) REVERT: G 124 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8646 (tp) REVERT: G 146 LYS cc_start: 0.7980 (tptp) cc_final: 0.6978 (mttm) REVERT: H 69 HIS cc_start: 0.7978 (t-90) cc_final: 0.7534 (t-90) REVERT: H 88 ASP cc_start: 0.8009 (p0) cc_final: 0.7606 (p0) REVERT: H 98 LYS cc_start: 0.7167 (tmtt) cc_final: 0.6086 (ttmm) REVERT: I 36 ARG cc_start: 0.7936 (ttp80) cc_final: 0.6918 (ttm170) REVERT: I 86 ASP cc_start: 0.8847 (t0) cc_final: 0.8616 (t70) REVERT: I 94 LEU cc_start: 0.8340 (tp) cc_final: 0.8111 (tp) REVERT: I 112 PHE cc_start: 0.8088 (m-10) cc_final: 0.7874 (m-80) REVERT: I 131 ASN cc_start: 0.8119 (t0) cc_final: 0.7819 (t0) REVERT: I 137 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7634 (ttm-80) REVERT: J 33 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8347 (mp) REVERT: J 114 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8206 (tp) REVERT: J 131 ASP cc_start: 0.7880 (t0) cc_final: 0.7601 (t0) REVERT: K 30 LYS cc_start: 0.6983 (ttmt) cc_final: 0.6362 (tppt) REVERT: K 110 LYS cc_start: 0.6881 (tttt) cc_final: 0.6320 (tmmt) REVERT: K 146 LYS cc_start: 0.7714 (ttmm) cc_final: 0.7150 (mptt) REVERT: L 94 LEU cc_start: 0.8743 (mt) cc_final: 0.8144 (mm) REVERT: L 105 ASN cc_start: 0.8625 (p0) cc_final: 0.8274 (p0) REVERT: L 138 CYS cc_start: 0.7433 (m) cc_final: 0.7016 (m) REVERT: M 88 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: M 184 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6626 (mmmt) REVERT: M 200 ASP cc_start: 0.7596 (t0) cc_final: 0.7251 (t70) REVERT: N 74 GLN cc_start: 0.8343 (pt0) cc_final: 0.7970 (pt0) REVERT: N 131 THR cc_start: 0.8828 (t) cc_final: 0.8555 (p) REVERT: N 169 LYS cc_start: 0.8486 (mttt) cc_final: 0.7949 (ptmt) REVERT: N 226 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8343 (mm-30) REVERT: O 30 HIS cc_start: 0.7466 (t70) cc_final: 0.7040 (t-90) REVERT: O 36 ASP cc_start: 0.7313 (t70) cc_final: 0.6662 (t0) REVERT: O 124 HIS cc_start: 0.8156 (p-80) cc_final: 0.7443 (p-80) REVERT: O 203 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6815 (p-80) REVERT: O 210 GLU cc_start: 0.7269 (tp30) cc_final: 0.6950 (tp30) outliers start: 78 outliers final: 58 residues processed: 652 average time/residue: 0.1632 time to fit residues: 155.8713 Evaluate side-chains 668 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 600 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 123 ARG Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 70 HIS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 184 LYS Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 203 HIS Chi-restraints excluded: chain O residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 66 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 136 HIS ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS M 60 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.146144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.116235 restraints weight = 28943.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.120600 restraints weight = 17751.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.122664 restraints weight = 10026.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.123294 restraints weight = 7990.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.123707 restraints weight = 7632.913| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 19534 Z= 0.143 Angle : 0.700 13.231 26632 Z= 0.333 Chirality : 0.041 0.244 2876 Planarity : 0.005 0.063 3376 Dihedral : 8.163 88.037 2656 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.78 % Favored : 95.09 % Rotamer: Outliers : 4.31 % Allowed : 27.49 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2364 helix: 0.90 (0.14), residues: 1344 sheet: -0.80 (0.37), residues: 209 loop : -0.80 (0.24), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 104 TYR 0.016 0.001 TYR B 20 PHE 0.044 0.002 PHE O 138 TRP 0.014 0.001 TRP G 19 HIS 0.016 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00372 (19522) covalent geometry : angle 0.69973 (26632) hydrogen bonds : bond 0.03964 ( 945) hydrogen bonds : angle 4.40884 ( 2703) Misc. bond : bond 0.06394 ( 12) =============================================================================== Job complete usr+sys time: 4102.79 seconds wall clock time: 71 minutes 19.33 seconds (4279.33 seconds total)