Starting phenix.real_space_refine (version: dev) on Thu Feb 23 02:01:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3l_3434/02_2023/5m3l_3434_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3l_3434/02_2023/5m3l_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_3434/02_2023/5m3l_3434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3l_3434/02_2023/5m3l_3434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3l_3434/02_2023/5m3l_3434_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3l_3434/02_2023/5m3l_3434_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.520 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 10.72, per 1000 atoms: 0.56 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: 7.83 Conformation dependent library (CDL) restraints added in 2.9 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: 1.32 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: 5.24 Time building geometry restraints manager: 8.48 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 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. 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.760 Check model and map are aligned: 0.280 Process input model: 48.400 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 10.28 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.40 % Favored : 91.46 % Rotamer Outliers : 0.59 % 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 *********************** 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 : 2.164 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 outliers start: 11 outliers final: 2 residues processed: 810 average time/residue: 0.3542 time to fit residues: 414.0423 Evaluate side-chains 623 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 621 time to evaluate : 2.161 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1680 time to fit residues: 3.8550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 70 optimal weight: 0.0980 chunk 110 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 210 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** A 125 GLN B 64 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS E 17 HIS E 69 HIS E 75 ASN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN F 64 HIS F 93 GLN F 120 GLN G 16 GLN G 76 ASN H 69 HIS ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 HIS ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN J 145 HIS K 3 HIS K 76 ASN L 27 HIS ** L 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 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 M 127 HIS N 17 ASN ** O 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 19522 Z= 0.310 Angle : 0.796 12.462 26632 Z= 0.382 Chirality : 0.045 0.221 2876 Planarity : 0.006 0.153 3376 Dihedral : 9.113 89.780 2656 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer Outliers : 4.69 % 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: -2.41 (0.16), residues: 2364 helix: -1.37 (0.12), residues: 1310 sheet: -2.30 (0.32), residues: 192 loop : -1.49 (0.22), residues: 862 *********************** 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 748 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 661 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 48 residues processed: 688 average time/residue: 0.3282 time to fit residues: 328.9135 Evaluate side-chains 626 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 578 time to evaluate : 2.169 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.1849 time to fit residues: 19.3638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.0870 chunk 65 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 211 optimal weight: 0.0770 chunk 228 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 overall best weight: 2.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 93 HIS ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN D 96 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN F 120 GLN G 16 GLN G 112 HIS ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 HIS I 96 HIS J 64 HIS K 83 ASN L 27 HIS ** L 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 GLN M 29 HIS ** M 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS M 124 ASN N 202 ASN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 145 HIS O 206 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 19522 Z= 0.252 Angle : 0.696 9.156 26632 Z= 0.330 Chirality : 0.041 0.170 2876 Planarity : 0.005 0.119 3376 Dihedral : 8.594 87.324 2656 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.29 % Favored : 94.59 % Rotamer Outliers : 3.23 % 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: -1.09 (0.17), residues: 2364 helix: -0.18 (0.14), residues: 1320 sheet: -1.51 (0.34), residues: 194 loop : -1.21 (0.23), residues: 850 *********************** 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 692 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 632 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 36 residues processed: 656 average time/residue: 0.3423 time to fit residues: 327.1917 Evaluate side-chains 625 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 589 time to evaluate : 2.168 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2082 time to fit residues: 15.9527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 9.9990 chunk 158 optimal weight: 0.7980 chunk 109 optimal weight: 0.1980 chunk 23 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN C 76 ASN D 96 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN G 76 ASN H 120 HIS I 75 ASN L 27 HIS ** L 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 GLN M 29 HIS M 65 HIS M 78 HIS M 106 HIS N 45 HIS N 86 HIS N 126 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 19522 Z= 0.315 Angle : 0.716 10.937 26632 Z= 0.339 Chirality : 0.042 0.158 2876 Planarity : 0.005 0.101 3376 Dihedral : 8.646 89.625 2656 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.58 % Favored : 94.29 % Rotamer Outliers : 4.80 % 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: -0.87 (0.18), residues: 2364 helix: -0.03 (0.14), residues: 1330 sheet: -1.35 (0.34), residues: 206 loop : -1.05 (0.23), residues: 828 *********************** 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 719 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 630 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 53 residues processed: 668 average time/residue: 0.3563 time to fit residues: 344.3666 Evaluate side-chains 642 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 589 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.1901 time to fit residues: 21.5435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 46 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN L 117 HIS ** L 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS M 106 HIS N 126 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5517 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= 0.261 Angle : 0.674 9.887 26632 Z= 0.320 Chirality : 0.041 0.215 2876 Planarity : 0.004 0.076 3376 Dihedral : 8.534 89.587 2656 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer Outliers : 3.07 % 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: -0.60 (0.18), residues: 2364 helix: 0.19 (0.14), residues: 1327 sheet: -1.16 (0.34), residues: 208 loop : -0.97 (0.23), residues: 829 *********************** 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 678 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 621 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 26 residues processed: 643 average time/residue: 0.3401 time to fit residues: 318.1030 Evaluate side-chains 616 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 590 time to evaluate : 2.236 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1974 time to fit residues: 12.2312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 131 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 0.0010 chunk 117 optimal weight: 6.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 112 HIS H 93 GLN L 96 HIS L 136 HIS M 60 HIS N 126 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19522 Z= 0.194 Angle : 0.641 9.876 26632 Z= 0.301 Chirality : 0.039 0.184 2876 Planarity : 0.004 0.065 3376 Dihedral : 8.384 89.595 2656 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.82 % Favored : 95.01 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: -0.27 (0.18), residues: 2364 helix: 0.61 (0.15), residues: 1284 sheet: -0.92 (0.35), residues: 205 loop : -1.07 (0.23), residues: 875 *********************** 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 658 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 614 time to evaluate : 2.408 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 21 residues processed: 632 average time/residue: 0.3278 time to fit residues: 306.1753 Evaluate side-chains 605 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 584 time to evaluate : 2.266 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1720 time to fit residues: 9.9022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 223 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN M 40 HIS M 56 ASN M 60 HIS N 61 HIS N 74 GLN N 126 HIS O 124 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5961 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= 0.231 Angle : 0.660 11.424 26632 Z= 0.310 Chirality : 0.040 0.256 2876 Planarity : 0.004 0.049 3376 Dihedral : 8.294 89.790 2656 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.08 % Favored : 94.75 % Rotamer Outliers : 2.48 % 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: -0.32 (0.18), residues: 2364 helix: 0.49 (0.15), residues: 1315 sheet: -0.75 (0.36), residues: 205 loop : -1.07 (0.23), residues: 844 *********************** 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 660 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 614 time to evaluate : 2.194 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 31 residues processed: 629 average time/residue: 0.3378 time to fit residues: 312.1000 Evaluate side-chains 629 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 598 time to evaluate : 2.325 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1970 time to fit residues: 14.2665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.6980 chunk 133 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 214 optimal weight: 0.1980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN M 60 HIS N 61 HIS N 126 HIS O 124 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 19522 Z= 0.212 Angle : 0.658 10.149 26632 Z= 0.308 Chirality : 0.040 0.224 2876 Planarity : 0.004 0.048 3376 Dihedral : 8.229 89.897 2656 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.99 % Favored : 94.84 % Rotamer Outliers : 1.35 % 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: -0.22 (0.18), residues: 2364 helix: 0.62 (0.15), residues: 1283 sheet: -0.64 (0.36), residues: 203 loop : -1.07 (0.22), residues: 878 *********************** 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 628 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 603 time to evaluate : 2.316 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 612 average time/residue: 0.3298 time to fit residues: 297.8837 Evaluate side-chains 608 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 591 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2062 time to fit residues: 8.9654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 214 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN M 60 HIS N 61 HIS N 126 HIS O 124 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.004 0.066 19522 Z= 0.254 Angle : 0.671 10.364 26632 Z= 0.318 Chirality : 0.040 0.204 2876 Planarity : 0.004 0.051 3376 Dihedral : 8.226 89.557 2656 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.20 % Favored : 94.63 % Rotamer Outliers : 1.46 % 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: -0.34 (0.18), residues: 2364 helix: 0.50 (0.15), residues: 1314 sheet: -0.76 (0.36), residues: 205 loop : -1.11 (0.22), residues: 845 *********************** 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 628 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 601 time to evaluate : 2.231 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 611 average time/residue: 0.3265 time to fit residues: 294.5622 Evaluate side-chains 612 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 593 time to evaluate : 2.457 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1727 time to fit residues: 9.5030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 231 optimal weight: 0.0770 chunk 212 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN G 112 HIS H 93 GLN M 60 HIS M 106 HIS N 61 HIS N 126 HIS O 124 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 19522 Z= 0.195 Angle : 0.652 10.294 26632 Z= 0.308 Chirality : 0.039 0.189 2876 Planarity : 0.004 0.047 3376 Dihedral : 8.160 89.569 2656 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer Outliers : 0.38 % 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: -0.14 (0.18), residues: 2364 helix: 0.74 (0.15), residues: 1278 sheet: -0.57 (0.37), residues: 203 loop : -1.12 (0.22), residues: 883 ********************** 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 615 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 608 time to evaluate : 2.400 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 610 average time/residue: 0.3307 time to fit residues: 299.2327 Evaluate side-chains 592 residues out of total 2071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 588 time to evaluate : 2.228 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1692 time to fit residues: 4.4415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 23 optimal weight: 0.0030 chunk 33 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS F 64 HIS ** F 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 HIS G 100 HIS ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 HIS N 126 HIS O 124 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.145793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.117328 restraints weight = 29215.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.120114 restraints weight = 17124.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.121680 restraints weight = 11891.998| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.6463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 19522 Z= 0.264 Angle : 0.684 10.267 26632 Z= 0.326 Chirality : 0.041 0.188 2876 Planarity : 0.004 0.052 3376 Dihedral : 8.159 88.708 2656 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.33 % Favored : 94.50 % Rotamer Outliers : 0.97 % 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: -0.26 (0.18), residues: 2364 helix: 0.54 (0.15), residues: 1315 sheet: -0.62 (0.36), residues: 202 loop : -1.08 (0.22), residues: 847 =============================================================================== Job complete usr+sys time: 5254.93 seconds wall clock time: 94 minutes 28.78 seconds (5668.78 seconds total)