Starting phenix.real_space_refine on Sun Mar 17 21:28:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3l_3434/03_2024/5m3l_3434_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3l_3434/03_2024/5m3l_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3l_3434/03_2024/5m3l_3434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3l_3434/03_2024/5m3l_3434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3l_3434/03_2024/5m3l_3434_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3l_3434/03_2024/5m3l_3434_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.520 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 Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "C ARG 56": "NH1" <-> "NH2" Residue "D ARG 55": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "E ARG 13": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 127": "NH1" <-> "NH2" Residue "G ARG 105": "NH1" <-> "NH2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 121": "NH1" <-> "NH2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 127": "NH1" <-> "NH2" Residue "L ARG 104": "NH1" <-> "NH2" Residue "L ARG 125": "NH1" <-> "NH2" Residue "M ARG 168": "NH1" <-> "NH2" Residue "N ARG 26": "NH1" <-> "NH2" Residue "N ARG 199": "NH1" <-> "NH2" Residue "O ARG 43": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 6} 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: {'GLN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 6} 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3} 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, 'HIS:plan': 2, 'ASP:plan': 8} 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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3} 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, 'ARG:plan': 1, 'ASP:plan': 4} 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, 'HIS:plan': 1, 'ASP:plan': 3} 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, 'HIS:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 5} 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: {'GLN:plan1': 1, 'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 8} 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, 'HIS:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} 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: 9.47, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.72 Conformation dependent library (CDL) restraints added in 3.6 seconds 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... running ksdssp... Secondary structure from input PDB file: 103 helices and 9 sheets defined 58.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 removed outlier: 3.649A pdb=" N VAL A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 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 47 through 51 removed outlier: 3.891A pdb=" N ALA A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 51' Processing helix chain 'A' and resid 66 through 83 removed outlier: 4.143A pdb=" N ARG A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 102 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) Processing helix chain 'A' and resid 109 through 121 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 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 132 through 145 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) removed outlier: 4.028A pdb=" N ARG A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 19 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 25 through 40 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 51 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) Processing helix chain 'B' and resid 59 through 77 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 82 through 97 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) Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.516A pdb=" N LYS B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 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 9 through 19 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 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 29 through 44 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 49 through 57 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 65 through 83 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 88 through 103 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) Processing helix chain 'C' and resid 110 through 126 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 Processing helix chain 'C' and resid 133 through 146 Processing helix chain 'D' and resid 11 through 25 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) Processing helix chain 'D' and resid 28 through 45 removed outlier: 3.748A pdb=" N VAL D 32 " --> pdb=" O HIS D 29 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA D 33 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU D 36 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TRP D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG D 40 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 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 66 through 83 removed outlier: 3.557A pdb=" N LEU D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 102 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) Processing helix chain 'D' and resid 108 through 126 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 132 through 146 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) removed outlier: 4.371A pdb=" N GLY D 145 " --> pdb=" O GLN D 141 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 23 removed outlier: 3.650A pdb=" N VAL E 22 " --> pdb=" O ILE E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 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 47 through 51 removed outlier: 3.886A pdb=" N ALA E 51 " --> pdb=" O PRO E 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 51' Processing helix chain 'E' and resid 66 through 83 removed outlier: 4.143A pdb=" N ARG E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU E 83 " --> pdb=" O LEU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 102 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) Processing helix chain 'E' and resid 109 through 121 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 132 through 146 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 6 through 19 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 25 through 40 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 51 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) Processing helix chain 'F' and resid 59 through 77 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 82 through 97 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) Processing helix chain 'F' and resid 105 through 120 removed outlier: 3.527A pdb=" N LYS F 110 " --> pdb=" O PHE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 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 9 through 19 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 22 through 24 No H-bonds generated for 'chain 'G' and resid 22 through 24' Processing helix chain 'G' and resid 29 through 44 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 49 through 57 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 65 through 83 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 88 through 103 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) Processing helix chain 'G' and resid 110 through 126 removed outlier: 3.916A pdb=" N GLY G 117 " --> pdb=" O LYS G 114 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE G 119 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA G 121 " --> pdb=" O GLU G 118 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU G 124 " --> pdb=" O ALA G 121 " (cutoff:3.500A) Proline residue: G 125 - end of helix Processing helix chain 'G' and resid 133 through 146 removed outlier: 3.500A pdb=" N LYS G 146 " --> pdb=" O GLY G 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 25 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) Processing helix chain 'H' and resid 28 through 45 removed outlier: 3.746A pdb=" N VAL H 32 " --> pdb=" O HIS H 29 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA H 33 " --> pdb=" O GLU H 30 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU H 36 " --> pdb=" O ALA H 33 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP H 39 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG H 40 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE H 43 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 55 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 66 through 82 removed outlier: 3.560A pdb=" N LEU H 77 " --> pdb=" O VAL H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 102 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) Processing helix chain 'H' and resid 108 through 126 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 132 through 146 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) removed outlier: 4.420A pdb=" N GLY H 145 " --> pdb=" O GLN H 141 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE H 146 " --> pdb=" O ILE H 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 23 removed outlier: 3.648A pdb=" N VAL I 22 " --> pdb=" O ILE I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 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 47 through 51 removed outlier: 3.890A pdb=" N ALA I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 47 through 51' Processing helix chain 'I' and resid 66 through 83 removed outlier: 4.144A pdb=" N ARG I 72 " --> pdb=" O SER I 68 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 102 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) Processing helix chain 'I' and resid 109 through 121 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 124 through 126 No H-bonds generated for 'chain 'I' and resid 124 through 126' Processing helix chain 'I' and resid 132 through 145 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) removed outlier: 4.021A pdb=" N ARG I 145 " --> pdb=" O ARG I 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 19 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 25 through 40 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 51 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) Processing helix chain 'J' and resid 59 through 77 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 82 through 97 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) Processing helix chain 'J' and resid 105 through 120 removed outlier: 3.518A pdb=" N LYS J 110 " --> pdb=" O PHE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 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 9 through 19 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 22 through 24 No H-bonds generated for 'chain 'K' and resid 22 through 24' Processing helix chain 'K' and resid 29 through 44 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 49 through 57 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 65 through 83 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 88 through 103 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) Processing helix chain 'K' and resid 110 through 126 removed outlier: 3.911A pdb=" N GLY K 117 " --> pdb=" O LYS K 114 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE K 119 " --> pdb=" O PHE K 116 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA K 121 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU K 124 " --> pdb=" O ALA K 121 " (cutoff:3.500A) Proline residue: K 125 - end of helix Processing helix chain 'K' and resid 133 through 146 removed outlier: 3.501A pdb=" N LYS K 146 " --> pdb=" O GLY K 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 25 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) Processing helix chain 'L' and resid 28 through 45 removed outlier: 3.745A pdb=" N VAL L 32 " --> pdb=" O HIS L 29 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA L 33 " --> pdb=" O GLU L 30 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU L 36 " --> pdb=" O ALA L 33 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP L 39 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG L 40 " --> pdb=" O GLU L 37 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE L 43 " --> pdb=" O ARG L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 55 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 66 through 82 removed outlier: 3.561A pdb=" N LEU L 77 " --> pdb=" O VAL L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 102 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) Processing helix chain 'L' and resid 108 through 126 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 132 through 146 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) removed outlier: 4.414A pdb=" N GLY L 145 " --> pdb=" O GLN L 141 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE L 146 " --> pdb=" O ILE L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 36 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 44 through 55 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 79 through 81 No H-bonds generated for 'chain 'M' and resid 79 through 81' Processing helix chain 'M' and resid 93 through 95 No H-bonds generated for 'chain 'M' and resid 93 through 95' Processing helix chain 'M' and resid 97 through 100 No H-bonds generated for 'chain 'M' and resid 97 through 100' Processing helix chain 'N' and resid 14 through 35 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 43 through 57 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 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 93 through 95 No H-bonds generated for 'chain 'N' and resid 93 through 95' Processing helix chain 'N' and resid 97 through 100 No H-bonds generated for 'chain 'N' and resid 97 through 100' Processing helix chain 'O' and resid 9 through 12 No H-bonds generated for 'chain 'O' and resid 9 through 12' Processing helix chain 'O' and resid 15 through 39 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 41 through 57 removed outlier: 3.688A pdb=" N LEU O 50 " --> pdb=" O LYS O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 81 No H-bonds generated for 'chain 'O' and resid 79 through 81' Processing sheet with id= A, 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= B, first strand: chain 'M' and resid 110 through 112 Processing sheet with id= C, first strand: chain 'M' and resid 205 through 209 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= D, first strand: chain 'N' and resid 66 through 68 Processing sheet with id= E, first strand: chain 'N' and resid 113 through 115 removed outlier: 3.783A pdb=" N HIS N 126 " --> pdb=" O SER N 115 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'N' and resid 147 through 153 Processing sheet with id= G, first strand: chain 'N' and resid 205 through 208 Processing sheet with id= H, first strand: chain 'O' and resid 66 through 68 Processing sheet with id= I, first strand: chain 'O' and resid 126 through 128 removed outlier: 6.557A pdb=" N GLU O 215 " --> pdb=" O CYS O 113 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE O 204 " --> pdb=" O CYS O 213 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG O 175 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU O 168 " --> pdb=" O THR O 177 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER O 131 " --> pdb=" O HIS O 145 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS O 147 " --> pdb=" O PHE O 129 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N PHE O 129 " --> pdb=" O HIS O 147 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU O 149 " --> pdb=" O LEU O 127 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU O 127 " --> pdb=" O GLU O 149 " (cutoff:3.500A) 795 hydrogen bonds defined for protein. 2142 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: 5.17 Time building geometry restraints manager: 7.38 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: 73.97 - 94.79: 42 94.79 - 115.61: 12526 115.61 - 136.42: 14040 136.42 - 157.24: 0 157.24 - 178.05: 24 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: 4840 2.83 - 3.52: 26748 3.52 - 4.21: 39071 4.21 - 4.90: 68135 Nonbonded interactions: 138805 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 2.520 nonbonded pdb=" O PRO I 124 " pdb=" N VAL I 126 " model vdw 1.784 2.520 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 138800 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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 151 or resid 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 145 or resid \ 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 151 or resid 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 151 or resid 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 151 or resid 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 147 or resid 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: 2.040 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: 0.020 Extract box with map and model: 10.050 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 47.730 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.150 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.570 ------------------------------------------------------------------------------- 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 : 0.013 0.216 19522 Z= 0.855 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 : 10.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.005 TRP F 34 HIS 0.016 0.003 HIS C 3 PHE 0.032 0.004 PHE M 215 TYR 0.041 0.005 TYR M 153 ARG 0.024 0.001 ARG I 137 *********************** 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 fitting. rotamer outliers: 11 poor density : 804 time to evaluate : 3.341 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: 0.7478 (ptp-170) REVERT: A 62 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7555 (pm20) REVERT: A 79 LEU cc_start: 0.8636 (tp) cc_final: 0.8081 (tp) REVERT: A 125 GLN cc_start: 0.8179 (mt0) cc_final: 0.7622 (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: 0.8255 (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: 0.7211 (tp30) REVERT: D 72 ARG cc_start: 0.7716 (mtm180) cc_final: 0.7333 (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: 0.7846 (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: 0.7570 (tp) REVERT: E 100 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7823 (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: 0.6701 (tttt) REVERT: F 41 VAL cc_start: 0.8687 (t) cc_final: 0.8359 (m) REVERT: F 95 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7636 (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: 0.8204 (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: 0.6717 (m-70) REVERT: G 115 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7679 (mmtp) REVERT: G 130 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.6050 (m-30) REVERT: G 146 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7745 (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: 0.7689 (m-70) REVERT: I 46 TYR cc_start: 0.7497 (m-80) cc_final: 0.7178 (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: 0.7269 (ttm170) REVERT: J 45 ARG cc_start: 0.6945 (mtt180) cc_final: 0.6544 (ttm110) REVERT: K 4 GLU cc_start: 0.5070 (tt0) cc_final: 0.3773 (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: 0.7425 (t-90) REVERT: K 92 ASP cc_start: 0.7845 (t70) cc_final: 0.7602 (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: 0.6620 (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: 0.7664 (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: 0.8415 (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: 0.7217 (mp0) REVERT: M 89 CYS cc_start: 0.7920 (m) cc_final: 0.7634 (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: 0.8259 (tm-30) REVERT: N 69 CYS cc_start: 0.8142 (m) cc_final: 0.7411 (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: 0.8634 (pm20) REVERT: N 77 ILE cc_start: 0.8773 (mt) cc_final: 0.8552 (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: 0.8342 (ttm110) REVERT: N 206 GLU cc_start: 0.8224 (mp0) cc_final: 0.7968 (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: 0.8278 (m-10) REVERT: O 83 CYS cc_start: 0.8532 (m) cc_final: 0.8043 (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: 0.7822 (t) 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: 0.7738 (tt0) REVERT: O 215 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7918 (mm-30) outliers start: 11 outliers final: 2 residues processed: 810 average time/residue: 0.3485 time to fit residues: 405.5404 Evaluate side-chains 639 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 636 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 195 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 110 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 82 ASN ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS D 117 HIS E 17 HIS E 75 ASN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS G 16 GLN G 70 HIS G 76 ASN ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 HIS ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 HIS ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN J 145 HIS K 76 ASN K 83 ASN L 27 HIS 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** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 19522 Z= 0.299 Angle : 0.774 12.095 26632 Z= 0.375 Chirality : 0.044 0.265 2876 Planarity : 0.005 0.151 3376 Dihedral : 9.096 89.365 2663 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.33 % Favored : 94.50 % Rotamer: Outliers : 4.37 % Allowed : 13.80 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.16), residues: 2364 helix: -1.41 (0.12), residues: 1310 sheet: -2.26 (0.32), residues: 192 loop : -1.51 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 34 HIS 0.010 0.001 HIS D 96 PHE 0.023 0.002 PHE L 132 TYR 0.016 0.002 TYR E 111 ARG 0.005 0.001 ARG H 31 *********************** 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 745 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 664 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8097 (m) cc_final: 0.7518 (p) REVERT: A 62 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7593 (pm20) REVERT: A 79 LEU cc_start: 0.8608 (tp) cc_final: 0.8075 (tp) REVERT: A 82 ASN cc_start: 0.8248 (m110) cc_final: 0.8036 (t0) REVERT: A 96 HIS cc_start: 0.7528 (t-90) cc_final: 0.7182 (t-170) REVERT: A 97 LEU cc_start: 0.8155 (tt) cc_final: 0.7766 (mp) REVERT: A 110 GLU cc_start: 0.8203 (tp30) cc_final: 0.7667 (tm-30) REVERT: A 113 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7281 (ttp80) REVERT: A 137 ARG cc_start: 0.7591 (mmt-90) cc_final: 0.7036 (mtt90) REVERT: B 50 ARG cc_start: 0.8674 (tpt170) cc_final: 0.8288 (mtt-85) REVERT: B 89 LEU cc_start: 0.8552 (tt) cc_final: 0.7994 (mt) REVERT: C 17 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8612 (ttpt) REVERT: C 103 GLU cc_start: 0.7696 (tp30) cc_final: 0.7336 (tp30) REVERT: D 13 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7723 (mp0) REVERT: D 27 HIS cc_start: 0.5999 (t-90) cc_final: 0.5366 (t-170) REVERT: D 31 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7650 (ttm170) REVERT: D 57 ARG cc_start: 0.7626 (mtp-110) cc_final: 0.6841 (tpt-90) REVERT: D 72 ARG cc_start: 0.7656 (mtm180) cc_final: 0.7276 (mtm-85) REVERT: D 126 LEU cc_start: 0.7955 (mp) cc_final: 0.7726 (mp) REVERT: D 137 ASP cc_start: 0.6780 (p0) cc_final: 0.6480 (p0) REVERT: D 138 CYS cc_start: 0.8856 (t) cc_final: 0.8556 (m) REVERT: D 141 GLN cc_start: 0.7566 (tt0) cc_final: 0.7331 (tm-30) REVERT: E 62 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6765 (pm20) REVERT: E 79 LEU cc_start: 0.8167 (tp) cc_final: 0.7960 (tp) REVERT: E 113 ARG cc_start: 0.7525 (mmm-85) cc_final: 0.7167 (mmm-85) REVERT: E 131 ASN cc_start: 0.7066 (t0) cc_final: 0.6664 (t0) REVERT: E 137 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.7014 (ttm110) REVERT: E 148 LYS cc_start: 0.6705 (tptp) cc_final: 0.6258 (tttt) REVERT: F 41 VAL cc_start: 0.8681 (t) cc_final: 0.8319 (m) REVERT: F 67 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7588 (mtm-85) REVERT: F 120 GLN cc_start: 0.8742 (tp40) cc_final: 0.8471 (tp-100) REVERT: F 134 ILE cc_start: 0.8283 (pp) cc_final: 0.7823 (mt) REVERT: G 17 LYS cc_start: 0.8399 (ttmm) cc_final: 0.8196 (tttp) REVERT: G 23 TRP cc_start: 0.7456 (m-90) cc_final: 0.6787 (m-90) REVERT: G 66 LYS cc_start: 0.7715 (tptt) cc_final: 0.7327 (tptm) REVERT: G 112 HIS cc_start: 0.7525 (m170) cc_final: 0.7153 (m170) REVERT: G 114 LYS cc_start: 0.7085 (tptm) cc_final: 0.6550 (mtpp) REVERT: G 146 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7791 (tptp) REVERT: H 129 HIS cc_start: 0.8096 (m-70) cc_final: 0.7576 (m170) REVERT: I 20 ASP cc_start: 0.8047 (t0) cc_final: 0.7670 (m-30) REVERT: J 34 TRP cc_start: 0.8206 (m100) cc_final: 0.7724 (m100) REVERT: J 43 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7456 (tm-30) REVERT: K 4 GLU cc_start: 0.4677 (tt0) cc_final: 0.4007 (tp30) REVERT: K 12 HIS cc_start: 0.7913 (p-80) cc_final: 0.6882 (p-80) REVERT: K 23 TRP cc_start: 0.7815 (m-90) cc_final: 0.7603 (m100) REVERT: K 42 LYS cc_start: 0.6890 (mtpp) cc_final: 0.6662 (mtpp) REVERT: K 92 ASP cc_start: 0.7951 (t70) cc_final: 0.7723 (t0) REVERT: K 146 LYS cc_start: 0.7935 (ttmm) cc_final: 0.7423 (mptt) REVERT: L 138 CYS cc_start: 0.7705 (t) cc_final: 0.7475 (m) REVERT: M 69 CYS cc_start: 0.8886 (m) cc_final: 0.8342 (m) REVERT: M 89 CYS cc_start: 0.7643 (m) cc_final: 0.7368 (m) REVERT: N 42 ASP cc_start: 0.8119 (p0) cc_final: 0.7888 (p0) REVERT: N 49 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8390 (tm-30) REVERT: N 69 CYS cc_start: 0.8015 (m) cc_final: 0.7600 (m) REVERT: N 73 GLU cc_start: 0.8514 (pm20) cc_final: 0.8190 (pm20) REVERT: N 131 THR cc_start: 0.8780 (t) cc_final: 0.8466 (p) REVERT: N 139 LYS cc_start: 0.7754 (pttm) cc_final: 0.7204 (ttmt) REVERT: N 169 LYS cc_start: 0.8638 (mttt) cc_final: 0.8296 (mtpt) REVERT: N 189 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6988 (p0) REVERT: N 226 GLU cc_start: 0.8033 (tp30) cc_final: 0.7615 (mm-30) REVERT: O 30 HIS cc_start: 0.7948 (t70) cc_final: 0.7711 (t-90) REVERT: O 56 GLU cc_start: 0.7781 (tt0) cc_final: 0.7528 (tt0) REVERT: O 83 CYS cc_start: 0.8522 (m) cc_final: 0.8079 (t) REVERT: O 133 SER cc_start: 0.8221 (m) cc_final: 0.7846 (t) REVERT: O 191 GLU cc_start: 0.8298 (tt0) cc_final: 0.7989 (tt0) REVERT: O 215 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8148 (mm-30) outliers start: 81 outliers final: 42 residues processed: 694 average time/residue: 0.3409 time to fit residues: 342.7918 Evaluate side-chains 623 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 580 time to evaluate : 1.924 ------------------------------------------------------------------------------- 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 C residue 29 SER 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 C residue 86 ASP Chi-restraints excluded: chain D residue 88 ASP 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 74 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain H residue 40 ARG 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 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 L residue 75 SER Chi-restraints excluded: chain L residue 142 ILE 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 147 LEU Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 189 ASP Chi-restraints excluded: chain N residue 216 HIS Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain O residue 177 THR 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 117 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 228 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS D 141 GLN E 69 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 16 GLN ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN I 93 HIS I 96 HIS J 64 HIS ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS ** L 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 19522 Z= 0.269 Angle : 0.689 9.078 26632 Z= 0.328 Chirality : 0.042 0.154 2876 Planarity : 0.005 0.104 3376 Dihedral : 8.578 86.552 2658 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.16 % Rotamer: Outliers : 5.61 % Allowed : 17.04 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2364 helix: -0.15 (0.14), residues: 1327 sheet: -1.48 (0.34), residues: 197 loop : -1.33 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 34 HIS 0.006 0.001 HIS J 91 PHE 0.016 0.002 PHE F 106 TYR 0.014 0.002 TYR F 20 ARG 0.006 0.001 ARG I 121 *********************** 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 763 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 659 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8188 (m) cc_final: 0.7832 (t) REVERT: A 62 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7996 (pm20) REVERT: A 79 LEU cc_start: 0.8669 (tp) cc_final: 0.8230 (tp) REVERT: A 96 HIS cc_start: 0.7781 (t-90) cc_final: 0.7492 (t-170) REVERT: A 97 LEU cc_start: 0.8326 (tt) cc_final: 0.7879 (mt) REVERT: A 113 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7525 (ttp80) REVERT: A 137 ARG cc_start: 0.7701 (mmt-90) cc_final: 0.7070 (mtt90) REVERT: B 50 ARG cc_start: 0.8602 (tpt170) cc_final: 0.8207 (mtt-85) REVERT: B 89 LEU cc_start: 0.8645 (tt) cc_final: 0.8173 (mt) REVERT: C 17 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8653 (tttm) REVERT: C 103 GLU cc_start: 0.7739 (tp30) cc_final: 0.7519 (tp30) REVERT: D 13 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7495 (mp0) REVERT: D 27 HIS cc_start: 0.6488 (t-90) cc_final: 0.5998 (t-170) REVERT: D 72 ARG cc_start: 0.7666 (mtm180) cc_final: 0.7394 (mtm-85) REVERT: D 126 LEU cc_start: 0.7884 (mp) cc_final: 0.7666 (mp) REVERT: D 137 ASP cc_start: 0.6877 (p0) cc_final: 0.6561 (p0) REVERT: D 138 CYS cc_start: 0.9084 (t) cc_final: 0.8582 (m) REVERT: E 62 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6706 (pm20) REVERT: E 79 LEU cc_start: 0.8079 (tp) cc_final: 0.7859 (tp) REVERT: E 113 ARG cc_start: 0.7566 (mmm-85) cc_final: 0.7236 (mmm-85) REVERT: E 131 ASN cc_start: 0.7188 (t0) cc_final: 0.6594 (t0) REVERT: E 137 ARG cc_start: 0.7333 (ttp-110) cc_final: 0.7120 (ttm110) REVERT: E 148 LYS cc_start: 0.6739 (tptp) cc_final: 0.6249 (tttt) REVERT: F 123 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.6233 (ptp-170) REVERT: F 134 ILE cc_start: 0.8320 (pp) cc_final: 0.8106 (mt) REVERT: G 23 TRP cc_start: 0.7406 (m-90) cc_final: 0.6897 (m-90) REVERT: G 83 ASN cc_start: 0.8474 (m-40) cc_final: 0.8131 (m-40) REVERT: G 112 HIS cc_start: 0.7669 (m170) cc_final: 0.7285 (m170) REVERT: G 114 LYS cc_start: 0.7148 (tptm) cc_final: 0.6580 (mtpp) REVERT: G 146 LYS cc_start: 0.7857 (ttmm) cc_final: 0.7506 (tptp) REVERT: H 129 HIS cc_start: 0.7992 (m-70) cc_final: 0.7378 (m170) REVERT: I 20 ASP cc_start: 0.8124 (t0) cc_final: 0.7510 (m-30) REVERT: I 36 ARG cc_start: 0.7597 (ttp80) cc_final: 0.6564 (ttm170) REVERT: I 44 LYS cc_start: 0.7188 (tttm) cc_final: 0.6771 (tptt) REVERT: J 43 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7355 (tm-30) REVERT: K 4 GLU cc_start: 0.4730 (tt0) cc_final: 0.4239 (tp30) REVERT: K 6 CYS cc_start: 0.7127 (m) cc_final: 0.6877 (p) REVERT: K 12 HIS cc_start: 0.7933 (p-80) cc_final: 0.7006 (p-80) REVERT: K 30 LYS cc_start: 0.7042 (ttmt) cc_final: 0.6451 (tppt) REVERT: K 73 ARG cc_start: 0.7538 (ttm170) cc_final: 0.7234 (ttm170) REVERT: K 86 ASP cc_start: 0.6915 (p0) cc_final: 0.6670 (p0) REVERT: K 92 ASP cc_start: 0.8034 (t70) cc_final: 0.7808 (t0) REVERT: K 116 PHE cc_start: 0.6742 (t80) cc_final: 0.6413 (t80) REVERT: K 146 LYS cc_start: 0.7811 (ttmm) cc_final: 0.7239 (mptt) REVERT: L 138 CYS cc_start: 0.7594 (t) cc_final: 0.7298 (m) REVERT: M 106 HIS cc_start: 0.8284 (t-90) cc_final: 0.8000 (t-170) REVERT: M 200 ASP cc_start: 0.8452 (t0) cc_final: 0.8175 (t0) REVERT: N 46 PHE cc_start: 0.7624 (t80) cc_final: 0.7286 (t80) REVERT: N 139 LYS cc_start: 0.7735 (pttm) cc_final: 0.7245 (ttmt) REVERT: N 153 SER cc_start: 0.8193 (m) cc_final: 0.7447 (p) REVERT: N 169 LYS cc_start: 0.8649 (mttt) cc_final: 0.8062 (ptmt) REVERT: N 226 GLU cc_start: 0.8018 (tp30) cc_final: 0.7556 (mm-30) REVERT: O 30 HIS cc_start: 0.7760 (t70) cc_final: 0.7483 (t-90) REVERT: O 83 CYS cc_start: 0.8569 (m) cc_final: 0.8250 (t) REVERT: O 103 LYS cc_start: 0.7842 (tppp) cc_final: 0.7115 (ptpp) REVERT: O 133 SER cc_start: 0.8207 (m) cc_final: 0.7984 (t) REVERT: O 139 THR cc_start: 0.8904 (t) cc_final: 0.8329 (p) REVERT: O 191 GLU cc_start: 0.8255 (tt0) cc_final: 0.7963 (tt0) REVERT: O 215 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8402 (mm-30) outliers start: 104 outliers final: 68 residues processed: 701 average time/residue: 0.3400 time to fit residues: 346.2143 Evaluate side-chains 679 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 610 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL 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 107 ASP 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 80 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 123 ARG Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 71 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 J residue 46 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 102 HIS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 142 ILE 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 132 ILE Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 216 HIS Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain O residue 54 VAL 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 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 208 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 224 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 120 GLN C 76 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS M 65 HIS M 78 HIS N 202 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19522 Z= 0.328 Angle : 0.715 11.818 26632 Z= 0.340 Chirality : 0.042 0.248 2876 Planarity : 0.005 0.099 3376 Dihedral : 8.654 89.686 2656 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.54 % Favored : 94.33 % Rotamer: Outliers : 6.74 % Allowed : 19.19 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2364 helix: -0.05 (0.14), residues: 1327 sheet: -1.48 (0.34), residues: 204 loop : -1.12 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 19 HIS 0.035 0.001 HIS O 145 PHE 0.022 0.002 PHE F 106 TYR 0.014 0.002 TYR B 20 ARG 0.006 0.001 ARG J 18 *********************** 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 765 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 640 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.6362 (OUTLIER) cc_final: 0.5989 (m170) REVERT: A 26 SER cc_start: 0.8312 (m) cc_final: 0.8023 (t) REVERT: A 62 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7995 (pm20) REVERT: A 79 LEU cc_start: 0.8480 (tp) cc_final: 0.8015 (tp) REVERT: A 82 ASN cc_start: 0.8233 (t0) cc_final: 0.7923 (t0) REVERT: A 97 LEU cc_start: 0.8398 (tt) cc_final: 0.7948 (mt) REVERT: A 113 ARG cc_start: 0.8151 (ttp-170) cc_final: 0.7565 (ttp80) REVERT: A 137 ARG cc_start: 0.7713 (mmt-90) cc_final: 0.7046 (mtt90) REVERT: B 50 ARG cc_start: 0.8571 (tpt170) cc_final: 0.8191 (mtt-85) REVERT: B 89 LEU cc_start: 0.8643 (tt) cc_final: 0.8134 (mt) REVERT: C 17 LYS cc_start: 0.9105 (ttmm) cc_final: 0.8658 (tttm) REVERT: C 103 GLU cc_start: 0.7549 (tp30) cc_final: 0.7234 (tp30) REVERT: D 31 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7668 (ttm170) REVERT: D 72 ARG cc_start: 0.7732 (mtm180) cc_final: 0.7214 (mtm-85) REVERT: D 126 LEU cc_start: 0.7962 (mp) cc_final: 0.7751 (mp) REVERT: E 62 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6747 (pm20) REVERT: E 79 LEU cc_start: 0.8072 (tp) cc_final: 0.7842 (tp) REVERT: E 109 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6311 (ptmm) REVERT: E 113 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7280 (mmm-85) REVERT: E 131 ASN cc_start: 0.7213 (t0) cc_final: 0.6537 (t0) REVERT: F 95 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7555 (mt0) REVERT: F 120 GLN cc_start: 0.8820 (tp40) cc_final: 0.8479 (tp-100) REVERT: F 123 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6380 (ptp-170) REVERT: F 134 ILE cc_start: 0.8503 (pp) cc_final: 0.8247 (mt) REVERT: G 23 TRP cc_start: 0.7446 (m-90) cc_final: 0.7127 (m-90) REVERT: G 66 LYS cc_start: 0.7484 (tptt) cc_final: 0.7135 (tmtm) REVERT: G 83 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8156 (m-40) REVERT: G 112 HIS cc_start: 0.7817 (m170) cc_final: 0.7440 (m170) REVERT: G 114 LYS cc_start: 0.7206 (tptm) cc_final: 0.6659 (mtpp) REVERT: G 140 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6316 (mm) REVERT: H 129 HIS cc_start: 0.7764 (m-70) cc_final: 0.7429 (m-70) REVERT: I 36 ARG cc_start: 0.7646 (ttp80) cc_final: 0.6545 (ttm170) REVERT: J 43 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7399 (tm-30) REVERT: K 4 GLU cc_start: 0.4955 (tt0) cc_final: 0.4230 (tp30) REVERT: K 12 HIS cc_start: 0.7897 (p-80) cc_final: 0.7005 (p-80) REVERT: K 30 LYS cc_start: 0.6985 (ttmt) cc_final: 0.6479 (tppt) REVERT: K 86 ASP cc_start: 0.6857 (p0) cc_final: 0.6610 (p0) REVERT: K 92 ASP cc_start: 0.8024 (t70) cc_final: 0.7804 (t0) REVERT: K 110 LYS cc_start: 0.6174 (tttt) cc_final: 0.5807 (tmmt) REVERT: K 146 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7231 (mptt) REVERT: L 138 CYS cc_start: 0.7761 (t) cc_final: 0.7519 (m) REVERT: M 200 ASP cc_start: 0.8478 (t0) cc_final: 0.8157 (t0) REVERT: N 46 PHE cc_start: 0.7740 (t80) cc_final: 0.7409 (t80) REVERT: N 65 ARG cc_start: 0.8261 (tmm-80) cc_final: 0.7930 (ttp-170) REVERT: N 129 ARG cc_start: 0.7797 (ptt180) cc_final: 0.7531 (ptm160) REVERT: N 139 LYS cc_start: 0.7803 (pttm) cc_final: 0.7338 (ttmt) REVERT: N 169 LYS cc_start: 0.8581 (mttt) cc_final: 0.7991 (ptmt) REVERT: N 189 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7157 (p0) REVERT: N 226 GLU cc_start: 0.8132 (tp30) cc_final: 0.7722 (mm-30) REVERT: O 30 HIS cc_start: 0.7812 (t70) cc_final: 0.7509 (t-90) REVERT: O 83 CYS cc_start: 0.8577 (m) cc_final: 0.8174 (t) REVERT: O 139 THR cc_start: 0.8931 (t) cc_final: 0.8217 (p) REVERT: O 191 GLU cc_start: 0.8212 (tt0) cc_final: 0.7977 (tt0) REVERT: O 215 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8457 (mm-30) outliers start: 125 outliers final: 84 residues processed: 697 average time/residue: 0.3383 time to fit residues: 344.3434 Evaluate side-chains 703 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 613 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 119 PHE 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 76 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 72 LEU 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 132 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 94 LEU 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 71 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 123 ARG Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 105 ASN 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 71 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 91 GLN 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 33 ILE Chi-restraints excluded: chain K residue 70 HIS Chi-restraints excluded: chain K residue 102 HIS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 142 ILE 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 132 ILE Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain N residue 189 ASP Chi-restraints excluded: chain N residue 208 HIS Chi-restraints excluded: chain N residue 224 THR 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 176 LEU Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS D 69 HIS ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 HIS F 31 GLN ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 HIS L 117 HIS ** L 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS M 106 HIS N 126 HIS N 202 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19522 Z= 0.304 Angle : 0.688 9.666 26632 Z= 0.326 Chirality : 0.042 0.195 2876 Planarity : 0.004 0.074 3376 Dihedral : 8.603 87.943 2656 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.80 % Favored : 94.04 % Rotamer: Outliers : 7.28 % Allowed : 20.86 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.17), residues: 2364 helix: 0.01 (0.14), residues: 1332 sheet: -1.35 (0.34), residues: 209 loop : -1.13 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 34 HIS 0.012 0.001 HIS E 96 PHE 0.030 0.002 PHE K 116 TYR 0.015 0.002 TYR F 20 ARG 0.008 0.001 ARG J 18 *********************** 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 781 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 646 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.6377 (OUTLIER) cc_final: 0.5979 (m170) REVERT: A 26 SER cc_start: 0.8293 (m) cc_final: 0.8070 (t) REVERT: A 62 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7997 (pm20) REVERT: A 82 ASN cc_start: 0.8444 (t0) cc_final: 0.8079 (t0) REVERT: A 97 LEU cc_start: 0.8398 (tt) cc_final: 0.7951 (mt) REVERT: A 113 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.7373 (ttp80) REVERT: A 117 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7520 (mt-10) REVERT: A 137 ARG cc_start: 0.7716 (mmt-90) cc_final: 0.7218 (ttm-80) REVERT: A 148 LYS cc_start: 0.7297 (pttp) cc_final: 0.6882 (ptmt) REVERT: B 50 ARG cc_start: 0.8570 (tpt170) cc_final: 0.8188 (mtt-85) REVERT: B 89 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8096 (mt) REVERT: C 17 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8656 (tttm) REVERT: C 103 GLU cc_start: 0.7546 (tp30) cc_final: 0.7230 (tp30) REVERT: D 13 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7731 (mp0) REVERT: D 72 ARG cc_start: 0.7710 (mtm180) cc_final: 0.7222 (mtm-85) REVERT: E 20 ASP cc_start: 0.7498 (t0) cc_final: 0.7119 (t0) REVERT: E 62 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6786 (pm20) REVERT: E 79 LEU cc_start: 0.8117 (tp) cc_final: 0.7878 (tp) REVERT: E 113 ARG cc_start: 0.7645 (mmm-85) cc_final: 0.7273 (mmm-85) REVERT: E 131 ASN cc_start: 0.7222 (t0) cc_final: 0.6580 (t0) REVERT: F 95 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7653 (mt0) REVERT: F 120 GLN cc_start: 0.8811 (tp40) cc_final: 0.8525 (tp-100) REVERT: F 123 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6329 (ptp-170) REVERT: G 83 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8205 (m-40) REVERT: G 114 LYS cc_start: 0.7578 (tptm) cc_final: 0.6935 (mtpp) REVERT: H 71 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8405 (mm110) REVERT: I 36 ARG cc_start: 0.7755 (ttp80) cc_final: 0.6723 (ttm170) REVERT: J 43 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7461 (tm-30) REVERT: K 4 GLU cc_start: 0.5093 (tt0) cc_final: 0.4280 (tp30) REVERT: K 10 GLU cc_start: 0.7522 (tp30) cc_final: 0.7318 (tp30) REVERT: K 30 LYS cc_start: 0.6998 (ttmt) cc_final: 0.6504 (tppt) REVERT: K 92 ASP cc_start: 0.8020 (t70) cc_final: 0.7816 (t0) REVERT: K 110 LYS cc_start: 0.6117 (tttt) cc_final: 0.5762 (tmmt) REVERT: K 146 LYS cc_start: 0.7838 (ttmm) cc_final: 0.7215 (mptt) REVERT: L 94 LEU cc_start: 0.8422 (mm) cc_final: 0.8052 (mm) REVERT: L 138 CYS cc_start: 0.7697 (t) cc_final: 0.7407 (m) REVERT: M 200 ASP cc_start: 0.8587 (t0) cc_final: 0.8253 (t0) REVERT: N 46 PHE cc_start: 0.7691 (t80) cc_final: 0.7312 (t80) REVERT: N 65 ARG cc_start: 0.8264 (tmm-80) cc_final: 0.7894 (ttp-170) REVERT: N 74 GLN cc_start: 0.8343 (pt0) cc_final: 0.7978 (pt0) REVERT: N 129 ARG cc_start: 0.7665 (ptt180) cc_final: 0.7364 (ptp90) REVERT: N 139 LYS cc_start: 0.7743 (pttm) cc_final: 0.7333 (ttmt) REVERT: N 169 LYS cc_start: 0.8572 (mttt) cc_final: 0.8007 (ptmt) REVERT: N 189 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7109 (p0) REVERT: N 226 GLU cc_start: 0.8218 (tp30) cc_final: 0.7974 (mm-30) REVERT: O 30 HIS cc_start: 0.7863 (t70) cc_final: 0.7537 (t-90) REVERT: O 68 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8302 (tm-30) REVERT: O 83 CYS cc_start: 0.8514 (m) cc_final: 0.8122 (t) REVERT: O 139 THR cc_start: 0.8898 (t) cc_final: 0.8130 (p) REVERT: O 191 GLU cc_start: 0.8132 (tt0) cc_final: 0.7873 (tt0) REVERT: O 203 HIS cc_start: 0.7443 (OUTLIER) cc_final: 0.7115 (p-80) REVERT: O 215 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8337 (mm-30) outliers start: 135 outliers final: 97 residues processed: 703 average time/residue: 0.3155 time to fit residues: 321.4856 Evaluate side-chains 727 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 623 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 47 LEU 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 107 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 72 LEU 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 132 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 122 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 107 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 E residue 132 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 123 ARG Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain I residue 15 ILE 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 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 33 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 102 HIS 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 74 LEU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 47 ILE 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 147 LEU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain N residue 189 ASP Chi-restraints excluded: chain N residue 208 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 133 SER Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 203 HIS Chi-restraints excluded: chain O residue 204 ILE Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 131 optimal weight: 0.0050 chunk 55 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN C 12 HIS D 27 HIS ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS M 29 HIS M 60 HIS N 126 HIS O 145 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19522 Z= 0.201 Angle : 0.632 11.174 26632 Z= 0.299 Chirality : 0.039 0.171 2876 Planarity : 0.004 0.057 3376 Dihedral : 8.440 88.772 2656 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 5.34 % Allowed : 24.10 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2364 helix: 0.32 (0.14), residues: 1330 sheet: -1.04 (0.35), residues: 205 loop : -1.14 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 34 HIS 0.015 0.001 HIS E 96 PHE 0.019 0.001 PHE K 116 TYR 0.011 0.001 TYR F 20 ARG 0.008 0.000 ARG J 18 *********************** 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 746 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 647 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.6220 (m170) REVERT: A 62 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7972 (pm20) REVERT: A 82 ASN cc_start: 0.8519 (t160) cc_final: 0.8149 (t0) REVERT: A 96 HIS cc_start: 0.7850 (t-90) cc_final: 0.7533 (t-170) REVERT: A 117 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7252 (tm-30) REVERT: A 137 ARG cc_start: 0.7563 (mmt-90) cc_final: 0.7164 (ttm-80) REVERT: A 148 LYS cc_start: 0.7369 (pttp) cc_final: 0.6991 (ptmt) REVERT: B 50 ARG cc_start: 0.8608 (tpt170) cc_final: 0.8223 (mtt-85) REVERT: B 89 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8109 (mt) REVERT: B 107 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7732 (t70) REVERT: C 17 LYS cc_start: 0.9050 (ttmm) cc_final: 0.8574 (tttm) REVERT: C 103 GLU cc_start: 0.7482 (tp30) cc_final: 0.7124 (tp30) REVERT: D 72 ARG cc_start: 0.7582 (mtm180) cc_final: 0.7152 (mtm-85) REVERT: E 20 ASP cc_start: 0.7530 (t0) cc_final: 0.7140 (t0) REVERT: E 26 SER cc_start: 0.7708 (m) cc_final: 0.7494 (p) REVERT: E 62 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6752 (pm20) REVERT: E 113 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7277 (mmm-85) REVERT: E 131 ASN cc_start: 0.7210 (t0) cc_final: 0.6737 (t0) REVERT: F 95 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7566 (mt0) REVERT: F 120 GLN cc_start: 0.8769 (tp40) cc_final: 0.8495 (tp-100) REVERT: F 123 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6333 (ptp-170) REVERT: G 23 TRP cc_start: 0.7320 (m-90) cc_final: 0.6720 (m-90) REVERT: G 49 GLU cc_start: 0.7306 (tt0) cc_final: 0.6992 (tt0) REVERT: G 66 LYS cc_start: 0.7188 (tptt) cc_final: 0.6942 (tttm) REVERT: G 83 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8106 (m-40) REVERT: G 114 LYS cc_start: 0.7589 (tptm) cc_final: 0.6835 (mtpp) REVERT: G 131 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7707 (p90) REVERT: H 98 LYS cc_start: 0.6270 (tttp) cc_final: 0.5694 (ttmm) REVERT: I 36 ARG cc_start: 0.7738 (ttp80) cc_final: 0.6731 (ttm170) REVERT: J 34 TRP cc_start: 0.8072 (m100) cc_final: 0.7626 (m100) REVERT: J 55 ASP cc_start: 0.6673 (t0) cc_final: 0.6174 (t0) REVERT: K 4 GLU cc_start: 0.5211 (tt0) cc_final: 0.4442 (tp30) REVERT: K 30 LYS cc_start: 0.6954 (ttmt) cc_final: 0.6461 (tppt) REVERT: K 92 ASP cc_start: 0.8016 (t70) cc_final: 0.7816 (t0) REVERT: K 110 LYS cc_start: 0.6009 (tttt) cc_final: 0.5769 (tmmt) REVERT: K 146 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7267 (mptt) REVERT: L 84 LEU cc_start: 0.8140 (mt) cc_final: 0.7798 (tt) REVERT: L 138 CYS cc_start: 0.7766 (t) cc_final: 0.7167 (m) REVERT: M 200 ASP cc_start: 0.8660 (t0) cc_final: 0.8409 (t0) REVERT: N 74 GLN cc_start: 0.8282 (pt0) cc_final: 0.7961 (pt0) REVERT: N 129 ARG cc_start: 0.7680 (ptt180) cc_final: 0.7446 (ptp90) REVERT: N 139 LYS cc_start: 0.7519 (pttm) cc_final: 0.7112 (ttmt) REVERT: N 169 LYS cc_start: 0.8551 (mttt) cc_final: 0.7973 (ptmt) REVERT: N 189 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7125 (p0) REVERT: N 226 GLU cc_start: 0.8351 (tp30) cc_final: 0.8119 (mm-30) REVERT: O 30 HIS cc_start: 0.7797 (t70) cc_final: 0.7535 (t-90) REVERT: O 73 ASP cc_start: 0.8667 (p0) cc_final: 0.8379 (p0) REVERT: O 83 CYS cc_start: 0.8551 (m) cc_final: 0.7950 (t) REVERT: O 124 HIS cc_start: 0.8491 (p-80) cc_final: 0.8112 (p-80) REVERT: O 139 THR cc_start: 0.8848 (t) cc_final: 0.8365 (p) REVERT: O 176 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8431 (pp) REVERT: O 191 GLU cc_start: 0.8005 (tt0) cc_final: 0.7785 (tt0) REVERT: O 203 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6950 (p-80) REVERT: O 215 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8375 (mm-30) outliers start: 99 outliers final: 65 residues processed: 689 average time/residue: 0.3303 time to fit residues: 329.9385 Evaluate side-chains 705 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 631 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 17 HIS 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 119 PHE 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 89 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 107 VAL 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 123 ARG Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 131 TYR 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 70 SER Chi-restraints excluded: chain H residue 121 VAL 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 85 ASP Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 70 HIS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 102 HIS Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 59 GLU 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 147 LEU Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 189 ASP Chi-restraints excluded: chain N residue 224 THR 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 176 LEU Chi-restraints excluded: chain O residue 203 HIS Chi-restraints excluded: chain O residue 204 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 223 optimal weight: 0.0970 chunk 139 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN M 60 HIS N 126 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19522 Z= 0.264 Angle : 0.661 10.288 26632 Z= 0.312 Chirality : 0.041 0.252 2876 Planarity : 0.004 0.051 3376 Dihedral : 8.371 88.545 2656 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.37 % Favored : 94.46 % Rotamer: Outliers : 5.88 % Allowed : 24.15 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2364 helix: 0.32 (0.15), residues: 1336 sheet: -1.01 (0.35), residues: 209 loop : -1.10 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 34 HIS 0.010 0.001 HIS E 96 PHE 0.016 0.002 PHE K 116 TYR 0.012 0.001 TYR B 20 ARG 0.008 0.001 ARG J 18 *********************** 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 737 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 628 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7279 (tpp80) REVERT: A 17 HIS cc_start: 0.6608 (OUTLIER) cc_final: 0.6202 (m170) REVERT: A 62 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7975 (pm20) REVERT: A 82 ASN cc_start: 0.8442 (t160) cc_final: 0.8079 (t0) REVERT: A 117 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7266 (tm-30) REVERT: A 137 ARG cc_start: 0.7591 (mmt-90) cc_final: 0.7180 (ttm-80) REVERT: A 148 LYS cc_start: 0.7263 (pttp) cc_final: 0.6889 (ptmt) REVERT: B 50 ARG cc_start: 0.8647 (tpt170) cc_final: 0.8292 (mtt-85) REVERT: B 89 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8108 (mt) REVERT: C 17 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8636 (tttm) REVERT: C 103 GLU cc_start: 0.7514 (tp30) cc_final: 0.7178 (tp30) REVERT: D 72 ARG cc_start: 0.7661 (mtm180) cc_final: 0.7186 (mtm-85) REVERT: E 20 ASP cc_start: 0.7458 (t0) cc_final: 0.7091 (t0) REVERT: E 26 SER cc_start: 0.7727 (m) cc_final: 0.7517 (p) REVERT: E 62 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6778 (pm20) REVERT: E 109 LYS cc_start: 0.6434 (OUTLIER) cc_final: 0.6170 (ptmm) REVERT: E 131 ASN cc_start: 0.7281 (t0) cc_final: 0.6812 (t0) REVERT: F 95 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7597 (mt0) REVERT: F 120 GLN cc_start: 0.8778 (tp40) cc_final: 0.8492 (tp-100) REVERT: F 123 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6431 (ptp-170) REVERT: G 23 TRP cc_start: 0.7398 (m-90) cc_final: 0.6996 (m-90) REVERT: G 49 GLU cc_start: 0.7301 (tt0) cc_final: 0.6965 (tt0) REVERT: G 66 LYS cc_start: 0.7161 (tptt) cc_final: 0.6921 (tttm) REVERT: G 83 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8157 (m-40) REVERT: G 114 LYS cc_start: 0.7596 (tptm) cc_final: 0.6917 (mtpp) REVERT: G 131 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7761 (p90) REVERT: I 36 ARG cc_start: 0.7695 (ttp80) cc_final: 0.6756 (ttm170) REVERT: J 16 TRP cc_start: 0.8499 (t-100) cc_final: 0.7758 (t60) REVERT: J 34 TRP cc_start: 0.8124 (m100) cc_final: 0.7681 (m100) REVERT: J 55 ASP cc_start: 0.6624 (t0) cc_final: 0.6179 (t0) REVERT: J 73 ASP cc_start: 0.7884 (t70) cc_final: 0.7614 (t0) REVERT: K 4 GLU cc_start: 0.5271 (tt0) cc_final: 0.4504 (tp30) REVERT: K 10 GLU cc_start: 0.7621 (tp30) cc_final: 0.7117 (tp30) REVERT: K 30 LYS cc_start: 0.6994 (ttmt) cc_final: 0.6498 (tppt) REVERT: K 92 ASP cc_start: 0.7981 (t70) cc_final: 0.7772 (t0) REVERT: K 110 LYS cc_start: 0.6027 (tttt) cc_final: 0.5800 (tmmt) REVERT: K 146 LYS cc_start: 0.7794 (ttmm) cc_final: 0.7223 (mptt) REVERT: L 84 LEU cc_start: 0.8154 (mt) cc_final: 0.7810 (tt) REVERT: L 94 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7503 (mm) REVERT: L 138 CYS cc_start: 0.7850 (t) cc_final: 0.7194 (m) REVERT: M 88 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: M 200 ASP cc_start: 0.8639 (t0) cc_final: 0.8374 (t0) REVERT: N 74 GLN cc_start: 0.8363 (pt0) cc_final: 0.8030 (pt0) REVERT: N 129 ARG cc_start: 0.7642 (ptt180) cc_final: 0.7317 (ptp90) REVERT: N 139 LYS cc_start: 0.7619 (pttm) cc_final: 0.7183 (ttmt) REVERT: N 169 LYS cc_start: 0.8578 (mttt) cc_final: 0.8047 (ptmt) REVERT: N 189 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7078 (p0) REVERT: O 30 HIS cc_start: 0.7815 (t70) cc_final: 0.7558 (t-90) REVERT: O 32 GLU cc_start: 0.7272 (pt0) cc_final: 0.6966 (pt0) REVERT: O 73 ASP cc_start: 0.8609 (p0) cc_final: 0.8330 (p0) REVERT: O 83 CYS cc_start: 0.8554 (m) cc_final: 0.8150 (t) REVERT: O 124 HIS cc_start: 0.8516 (p-80) cc_final: 0.8101 (p-80) REVERT: O 139 THR cc_start: 0.8837 (t) cc_final: 0.8349 (p) REVERT: O 191 GLU cc_start: 0.8074 (tt0) cc_final: 0.7860 (tt0) REVERT: O 203 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.7080 (p-80) REVERT: O 215 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8431 (mm-30) outliers start: 109 outliers final: 82 residues processed: 671 average time/residue: 0.3330 time to fit residues: 324.7048 Evaluate side-chains 711 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 619 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 17 HIS 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 119 PHE 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 76 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 109 LYS 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 123 ARG Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 121 VAL 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 85 ASP 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 41 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain K residue 12 HIS 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 102 HIS Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain M residue 47 ILE 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 112 THR Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 189 ASP Chi-restraints excluded: chain N residue 208 HIS Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 203 HIS Chi-restraints excluded: chain O residue 204 ILE Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.3980 chunk 133 optimal weight: 0.0870 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 214 optimal weight: 0.0770 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 HIS M 106 HIS N 126 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19522 Z= 0.183 Angle : 0.639 11.193 26632 Z= 0.299 Chirality : 0.039 0.201 2876 Planarity : 0.004 0.054 3376 Dihedral : 8.229 89.800 2656 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.74 % Favored : 95.09 % Rotamer: Outliers : 3.99 % Allowed : 26.47 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 2364 helix: 0.59 (0.15), residues: 1316 sheet: -0.72 (0.37), residues: 202 loop : -1.21 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 19 HIS 0.012 0.001 HIS J 91 PHE 0.016 0.001 PHE H 34 TYR 0.009 0.001 TYR B 20 ARG 0.009 0.000 ARG L 40 *********************** 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 715 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 641 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.6430 (OUTLIER) cc_final: 0.6020 (m170) REVERT: A 62 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7994 (pm20) REVERT: A 82 ASN cc_start: 0.8487 (t160) cc_final: 0.8174 (t0) REVERT: A 96 HIS cc_start: 0.7785 (t-90) cc_final: 0.7408 (t-170) REVERT: A 117 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7219 (tm-30) REVERT: A 121 ARG cc_start: 0.6766 (mtp85) cc_final: 0.6558 (mtp85) REVERT: A 137 ARG cc_start: 0.7499 (mmt-90) cc_final: 0.7112 (mtm-85) REVERT: B 50 ARG cc_start: 0.8629 (tpt170) cc_final: 0.8270 (mtt-85) REVERT: B 89 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8061 (mt) REVERT: B 107 ASP cc_start: 0.8310 (t70) cc_final: 0.8105 (t70) REVERT: C 17 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8709 (tttm) REVERT: C 103 GLU cc_start: 0.7394 (tp30) cc_final: 0.7028 (tp30) REVERT: D 13 GLU cc_start: 0.7832 (mp0) cc_final: 0.7334 (mp0) REVERT: D 72 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7086 (mtm-85) REVERT: E 12 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7897 (mtt90) REVERT: E 20 ASP cc_start: 0.7516 (t0) cc_final: 0.7194 (t0) REVERT: E 62 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6848 (pm20) REVERT: E 113 ARG cc_start: 0.7550 (mmm-85) cc_final: 0.7295 (mmm-85) REVERT: F 48 PHE cc_start: 0.8771 (m-10) cc_final: 0.8515 (m-80) REVERT: F 120 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8263 (tp-100) REVERT: F 123 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6389 (ptp-170) REVERT: G 23 TRP cc_start: 0.7278 (m-90) cc_final: 0.6807 (m-90) REVERT: G 49 GLU cc_start: 0.7270 (tt0) cc_final: 0.6850 (tt0) REVERT: G 66 LYS cc_start: 0.7229 (tptt) cc_final: 0.6963 (tttm) REVERT: G 83 ASN cc_start: 0.8394 (m-40) cc_final: 0.8015 (m-40) REVERT: G 101 GLN cc_start: 0.8167 (tp-100) cc_final: 0.7905 (tt0) REVERT: G 112 HIS cc_start: 0.7860 (m170) cc_final: 0.7290 (m170) REVERT: G 114 LYS cc_start: 0.7597 (tptm) cc_final: 0.6903 (mtpp) REVERT: H 98 LYS cc_start: 0.6360 (tttp) cc_final: 0.5787 (ttmm) REVERT: I 36 ARG cc_start: 0.7547 (ttp80) cc_final: 0.6601 (ttm170) REVERT: J 34 TRP cc_start: 0.8091 (m100) cc_final: 0.7562 (m100) REVERT: K 4 GLU cc_start: 0.5396 (tt0) cc_final: 0.4270 (mm-30) REVERT: K 30 LYS cc_start: 0.6944 (ttmt) cc_final: 0.6480 (tppt) REVERT: K 92 ASP cc_start: 0.7947 (t70) cc_final: 0.7743 (t0) REVERT: K 110 LYS cc_start: 0.5975 (tttt) cc_final: 0.5757 (tmmt) REVERT: K 146 LYS cc_start: 0.7771 (ttmm) cc_final: 0.7210 (mptt) REVERT: L 36 LEU cc_start: 0.8367 (tt) cc_final: 0.8131 (tp) REVERT: L 84 LEU cc_start: 0.8070 (mt) cc_final: 0.7426 (tp) REVERT: L 94 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7440 (mm) REVERT: L 104 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.7401 (mtp85) REVERT: L 138 CYS cc_start: 0.7451 (t) cc_final: 0.6994 (m) REVERT: M 88 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: M 184 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6625 (mmmt) REVERT: M 200 ASP cc_start: 0.8735 (t0) cc_final: 0.8503 (t0) REVERT: N 74 GLN cc_start: 0.8288 (pt0) cc_final: 0.7957 (pt0) REVERT: N 139 LYS cc_start: 0.7622 (pttm) cc_final: 0.7216 (ttmt) REVERT: N 169 LYS cc_start: 0.8548 (mttt) cc_final: 0.7989 (ptmt) REVERT: N 189 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.7033 (p0) REVERT: O 30 HIS cc_start: 0.7703 (t70) cc_final: 0.7491 (t-90) REVERT: O 32 GLU cc_start: 0.7068 (pt0) cc_final: 0.6742 (pt0) REVERT: O 73 ASP cc_start: 0.8504 (p0) cc_final: 0.8024 (p0) REVERT: O 83 CYS cc_start: 0.8539 (m) cc_final: 0.7970 (t) REVERT: O 124 HIS cc_start: 0.8298 (p-80) cc_final: 0.7974 (p-80) REVERT: O 139 THR cc_start: 0.8867 (t) cc_final: 0.8510 (p) REVERT: O 176 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8397 (pp) REVERT: O 191 GLU cc_start: 0.8058 (tt0) cc_final: 0.7817 (tt0) REVERT: O 203 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.7020 (p-80) REVERT: O 215 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8365 (mm-30) outliers start: 74 outliers final: 50 residues processed: 673 average time/residue: 0.3325 time to fit residues: 324.0246 Evaluate side-chains 676 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 617 time to evaluate : 2.003 ------------------------------------------------------------------------------- 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 17 HIS Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 119 PHE 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 89 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 88 LEU 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 11 ASP 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 70 SER 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 85 ASP Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain K residue 12 HIS 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 102 HIS Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 184 LYS Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 189 ASP 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 133 SER Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 203 HIS Chi-restraints excluded: chain O residue 204 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 188 optimal weight: 0.0370 chunk 197 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 136 optimal weight: 0.0170 overall best weight: 0.9898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 HIS N 126 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19522 Z= 0.197 Angle : 0.639 9.600 26632 Z= 0.297 Chirality : 0.039 0.237 2876 Planarity : 0.004 0.070 3376 Dihedral : 8.150 89.802 2656 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 3.99 % Allowed : 27.17 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2364 helix: 0.73 (0.15), residues: 1301 sheet: -0.60 (0.38), residues: 202 loop : -1.22 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 23 HIS 0.010 0.001 HIS E 96 PHE 0.017 0.001 PHE E 112 TYR 0.009 0.001 TYR B 20 ARG 0.012 0.001 ARG A 104 *********************** 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 701 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 627 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.6511 (OUTLIER) cc_final: 0.6164 (m170) REVERT: A 62 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7972 (pm20) REVERT: A 82 ASN cc_start: 0.8484 (t160) cc_final: 0.8200 (t0) REVERT: A 117 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7142 (tm-30) REVERT: A 121 ARG cc_start: 0.6758 (mtp85) cc_final: 0.6553 (mtp85) REVERT: A 137 ARG cc_start: 0.7558 (mmt-90) cc_final: 0.7175 (mtm-85) REVERT: B 50 ARG cc_start: 0.8666 (tpt170) cc_final: 0.8302 (mtt-85) REVERT: B 89 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8066 (mt) REVERT: C 17 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8674 (tttm) REVERT: C 103 GLU cc_start: 0.7339 (tp30) cc_final: 0.6981 (tp30) REVERT: C 109 GLN cc_start: 0.7548 (mm-40) cc_final: 0.6579 (mp10) REVERT: E 20 ASP cc_start: 0.7508 (t0) cc_final: 0.7194 (t0) REVERT: E 62 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6858 (pm20) REVERT: F 48 PHE cc_start: 0.8773 (m-10) cc_final: 0.8522 (m-80) REVERT: F 120 GLN cc_start: 0.8760 (tp40) cc_final: 0.8254 (tp-100) REVERT: F 123 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6331 (ptp-170) REVERT: G 23 TRP cc_start: 0.7289 (m-90) cc_final: 0.6830 (m-90) REVERT: G 101 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7902 (tt0) REVERT: G 114 LYS cc_start: 0.7597 (tptm) cc_final: 0.6922 (mtpp) REVERT: H 69 HIS cc_start: 0.7794 (t-90) cc_final: 0.7334 (t-90) REVERT: H 98 LYS cc_start: 0.6382 (tttp) cc_final: 0.5831 (ttmm) REVERT: J 16 TRP cc_start: 0.8436 (t-100) cc_final: 0.7734 (t60) REVERT: J 34 TRP cc_start: 0.8057 (m100) cc_final: 0.7548 (m100) REVERT: K 4 GLU cc_start: 0.5481 (tt0) cc_final: 0.4328 (mm-30) REVERT: K 30 LYS cc_start: 0.6942 (ttmt) cc_final: 0.6488 (tppt) REVERT: K 92 ASP cc_start: 0.7950 (t70) cc_final: 0.7734 (t0) REVERT: K 110 LYS cc_start: 0.6094 (tttt) cc_final: 0.5858 (ttpt) REVERT: K 146 LYS cc_start: 0.7791 (ttmm) cc_final: 0.7212 (mptt) REVERT: L 36 LEU cc_start: 0.8346 (tt) cc_final: 0.8134 (tp) REVERT: L 84 LEU cc_start: 0.8058 (mt) cc_final: 0.7391 (tp) REVERT: L 94 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7405 (mm) REVERT: L 104 ARG cc_start: 0.7666 (mtt-85) cc_final: 0.7415 (mtp85) REVERT: L 138 CYS cc_start: 0.7413 (t) cc_final: 0.6945 (m) REVERT: M 88 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: M 184 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6588 (mmmt) REVERT: N 74 GLN cc_start: 0.8307 (pt0) cc_final: 0.7972 (pt0) REVERT: N 139 LYS cc_start: 0.7622 (pttm) cc_final: 0.7235 (ttmt) REVERT: N 169 LYS cc_start: 0.8539 (mttt) cc_final: 0.7972 (ptmt) REVERT: N 189 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.7033 (p0) REVERT: O 30 HIS cc_start: 0.7672 (t70) cc_final: 0.7455 (t-90) REVERT: O 32 GLU cc_start: 0.7064 (pt0) cc_final: 0.6764 (pt0) REVERT: O 73 ASP cc_start: 0.8470 (p0) cc_final: 0.7998 (p0) REVERT: O 83 CYS cc_start: 0.8650 (m) cc_final: 0.8002 (t) REVERT: O 124 HIS cc_start: 0.8241 (p-80) cc_final: 0.7741 (p-80) REVERT: O 139 THR cc_start: 0.8880 (t) cc_final: 0.8527 (p) REVERT: O 176 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8427 (pp) REVERT: O 191 GLU cc_start: 0.8105 (tt0) cc_final: 0.7860 (tt0) REVERT: O 203 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6980 (p-80) REVERT: O 215 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8429 (mm-30) outliers start: 74 outliers final: 58 residues processed: 658 average time/residue: 0.3392 time to fit residues: 322.5968 Evaluate side-chains 679 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 612 time to evaluate : 1.670 ------------------------------------------------------------------------------- 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 17 HIS Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 119 PHE 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 89 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 88 LEU 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 11 ASP Chi-restraints excluded: chain G residue 96 ASP 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 105 ASN 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 85 ASP Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain K residue 12 HIS 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 102 HIS Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 184 LYS Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 173 ASN Chi-restraints excluded: chain N residue 189 ASP Chi-restraints excluded: chain N residue 208 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 131 SER Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 203 HIS Chi-restraints excluded: chain O residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 19522 Z= 0.367 Angle : 0.739 10.783 26632 Z= 0.352 Chirality : 0.043 0.223 2876 Planarity : 0.005 0.103 3376 Dihedral : 8.429 89.334 2656 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.37 % Favored : 94.46 % Rotamer: Outliers : 4.80 % Allowed : 26.36 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2364 helix: 0.23 (0.14), residues: 1330 sheet: -0.97 (0.36), residues: 205 loop : -1.07 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 135 HIS 0.010 0.001 HIS D 136 PHE 0.019 0.002 PHE B 106 TYR 0.018 0.002 TYR F 20 ARG 0.014 0.001 ARG A 104 ********************** 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 726 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 637 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.6179 (m170) REVERT: A 62 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7961 (pm20) REVERT: A 82 ASN cc_start: 0.8547 (t160) cc_final: 0.8226 (t0) REVERT: A 117 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7158 (tm-30) REVERT: A 137 ARG cc_start: 0.7591 (mmt-90) cc_final: 0.7137 (mtm-85) REVERT: A 148 LYS cc_start: 0.7138 (pttp) cc_final: 0.6775 (ptmt) REVERT: B 50 ARG cc_start: 0.8634 (tpt170) cc_final: 0.8351 (mtt-85) REVERT: B 89 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8096 (mt) REVERT: C 17 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8680 (tttm) REVERT: C 103 GLU cc_start: 0.7562 (tp30) cc_final: 0.7250 (tp30) REVERT: C 109 GLN cc_start: 0.7481 (mm-40) cc_final: 0.6521 (mp10) REVERT: C 132 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8051 (p0) REVERT: D 141 GLN cc_start: 0.7157 (tm-30) cc_final: 0.6893 (tm-30) REVERT: E 20 ASP cc_start: 0.7390 (t0) cc_final: 0.7034 (t0) REVERT: E 62 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6915 (pm20) REVERT: E 81 ILE cc_start: 0.7968 (mt) cc_final: 0.7747 (mt) REVERT: F 95 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7681 (mt0) REVERT: F 120 GLN cc_start: 0.8827 (tp40) cc_final: 0.8299 (tp-100) REVERT: F 123 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6462 (ptp-170) REVERT: G 103 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7161 (tm-30) REVERT: G 114 LYS cc_start: 0.7609 (tptm) cc_final: 0.6899 (mtpp) REVERT: G 137 LYS cc_start: 0.7591 (tptm) cc_final: 0.7290 (mttt) REVERT: H 69 HIS cc_start: 0.7715 (t-90) cc_final: 0.7300 (t-90) REVERT: I 36 ARG cc_start: 0.7725 (ttp80) cc_final: 0.6840 (ttm170) REVERT: J 16 TRP cc_start: 0.8478 (t-100) cc_final: 0.7809 (t60) REVERT: J 34 TRP cc_start: 0.8072 (m100) cc_final: 0.7645 (m100) REVERT: K 4 GLU cc_start: 0.5687 (tt0) cc_final: 0.4452 (mm-30) REVERT: K 30 LYS cc_start: 0.7015 (ttmt) cc_final: 0.6523 (tppt) REVERT: K 110 LYS cc_start: 0.6107 (tttt) cc_final: 0.5841 (tmmt) REVERT: K 146 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7141 (mptt) REVERT: M 40 HIS cc_start: 0.7275 (t70) cc_final: 0.7017 (t70) REVERT: M 207 LYS cc_start: 0.7978 (ptpt) cc_final: 0.7750 (ptpp) REVERT: N 46 PHE cc_start: 0.7774 (t80) cc_final: 0.7403 (t80) REVERT: N 74 GLN cc_start: 0.8519 (pt0) cc_final: 0.8201 (pt0) REVERT: N 139 LYS cc_start: 0.7648 (pttm) cc_final: 0.7255 (ttmt) REVERT: N 169 LYS cc_start: 0.8557 (mttt) cc_final: 0.8024 (ptmt) REVERT: O 30 HIS cc_start: 0.7839 (t70) cc_final: 0.7536 (t-90) REVERT: O 32 GLU cc_start: 0.7306 (pt0) cc_final: 0.6986 (pt0) REVERT: O 73 ASP cc_start: 0.8518 (p0) cc_final: 0.8043 (p0) REVERT: O 83 CYS cc_start: 0.8602 (m) cc_final: 0.7893 (t) REVERT: O 124 HIS cc_start: 0.8566 (p-80) cc_final: 0.7879 (p-80) REVERT: O 139 THR cc_start: 0.8903 (t) cc_final: 0.8369 (p) REVERT: O 191 GLU cc_start: 0.8251 (tt0) cc_final: 0.8030 (tt0) REVERT: O 203 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.7033 (p-80) REVERT: O 215 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8248 (mm-30) outliers start: 89 outliers final: 70 residues processed: 676 average time/residue: 0.3123 time to fit residues: 304.5845 Evaluate side-chains 685 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 610 time to evaluate : 1.990 ------------------------------------------------------------------------------- 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 17 HIS 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 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 76 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 72 LEU 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 132 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 123 ARG 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 49 ILE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 105 ASN 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 J residue 41 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain K residue 12 HIS 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 102 HIS Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 208 HIS Chi-restraints excluded: chain N residue 214 THR 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 131 SER Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 203 HIS Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 184 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 161 optimal weight: 0.0670 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 HIS M 60 HIS N 202 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.145002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.115629 restraints weight = 29293.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.119275 restraints weight = 17619.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.121133 restraints weight = 10568.583| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19522 Z= 0.274 Angle : 0.692 10.152 26632 Z= 0.327 Chirality : 0.042 0.228 2876 Planarity : 0.005 0.113 3376 Dihedral : 8.357 88.244 2656 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 4.04 % Allowed : 27.33 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2364 helix: 0.30 (0.15), residues: 1323 sheet: -0.97 (0.36), residues: 211 loop : -1.18 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 34 HIS 0.010 0.001 HIS E 96 PHE 0.026 0.002 PHE D 132 TYR 0.014 0.002 TYR F 20 ARG 0.013 0.001 ARG A 104 =============================================================================== Job complete usr+sys time: 5458.98 seconds wall clock time: 97 minutes 51.54 seconds (5871.54 seconds total)