Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 20 07:36:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/10_2023/5a0q_2981_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/10_2023/5a0q_2981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/10_2023/5a0q_2981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/10_2023/5a0q_2981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/10_2023/5a0q_2981_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/10_2023/5a0q_2981_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 284 5.16 5 C 27550 2.51 5 N 7448 2.21 5 O 8166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 43448 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1860 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1674 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1535 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 3 Chain: "G" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1626 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 5, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1490 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 1 Chain: "J" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1374 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1512 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1480 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1453 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1428 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "O" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1860 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1674 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1535 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 3 Chain: "U" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1626 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 5, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "V" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "W" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1490 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 1 Chain: "X" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1374 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Y" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1512 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1480 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "a" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1453 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "b" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1428 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 1} Unresolved non-hydrogen planarities: 15 Chain: "V" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 1} Unresolved non-hydrogen planarities: 15 Chain: "W" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 22.07, per 1000 atoms: 0.51 Number of scatterers: 43448 At special positions: 0 Unit cell: (132.08, 171.6, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 284 16.00 O 8166 8.00 N 7448 7.00 C 27550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 54 " - pdb=" SG CYS M 61 " distance=2.01 Simple disulfide: pdb=" SG CYS a 54 " - pdb=" SG CYS a 61 " distance=2.01 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.28 Conformation dependent library (CDL) restraints added in 7.0 seconds 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 62 sheets defined 34.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'A' and resid 23 through 33 Processing helix chain 'A' and resid 84 through 104 removed outlier: 4.026A pdb=" N ARG A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.840A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.990A pdb=" N PHE A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 79 through 100 removed outlier: 3.788A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 removed outlier: 4.147A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 4.095A pdb=" N THR B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.760A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.679A pdb=" N ILE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY C 29 " --> pdb=" O MET C 25 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 removed outlier: 4.314A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.845A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 4.262A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 230 through 243 removed outlier: 3.719A pdb=" N GLU C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 removed outlier: 3.732A pdb=" N LYS D 27 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 removed outlier: 4.639A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 117 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 185 through 197 removed outlier: 4.060A pdb=" N LEU D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.591A pdb=" N LYS D 227 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL D 229 " --> pdb=" O GLU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 234 No H-bonds generated for 'chain 'D' and resid 231 through 234' Processing helix chain 'E' and resid 22 through 33 removed outlier: 3.937A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 103 removed outlier: 4.008A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 117 removed outlier: 3.775A pdb=" N VAL E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 184 removed outlier: 3.852A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 184 " --> pdb=" O SER E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 205 removed outlier: 3.513A pdb=" N SER E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN E 204 " --> pdb=" O ILE E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 235 removed outlier: 3.596A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 231 through 235' Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.777A pdb=" N GLU F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN F 31 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 98 removed outlier: 3.774A pdb=" N GLN F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 121 removed outlier: 4.206A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.904A pdb=" N LEU F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU F 173 " --> pdb=" O ARG F 169 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG F 174 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.681A pdb=" N ARG F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.847A pdb=" N ALA G 29 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU G 31 " --> pdb=" O MET G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 102 removed outlier: 4.122A pdb=" N SER G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.893A pdb=" N ASP G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR G 122 " --> pdb=" O TYR G 118 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR G 123 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU G 124 " --> pdb=" O HIS G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 178 Processing helix chain 'G' and resid 181 through 183 No H-bonds generated for 'chain 'G' and resid 181 through 183' Processing helix chain 'G' and resid 186 through 200 removed outlier: 4.550A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 236 Processing helix chain 'H' and resid 49 through 54 removed outlier: 3.764A pdb=" N ALA H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 70 removed outlier: 3.537A pdb=" N ILE H 68 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 89 Processing helix chain 'H' and resid 132 through 139 removed outlier: 4.360A pdb=" N GLY H 137 " --> pdb=" O TYR H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 166 removed outlier: 4.225A pdb=" N LEU H 153 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN H 154 " --> pdb=" O GLU H 150 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU H 162 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 89 Processing helix chain 'I' and resid 131 through 141 removed outlier: 3.808A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 165 removed outlier: 3.542A pdb=" N SER I 156 " --> pdb=" O LYS I 152 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU I 157 " --> pdb=" O ASN I 153 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA I 158 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 76 removed outlier: 3.577A pdb=" N TYR J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 95 Processing helix chain 'J' and resid 146 through 149 No H-bonds generated for 'chain 'J' and resid 146 through 149' Processing helix chain 'J' and resid 159 through 176 removed outlier: 4.025A pdb=" N GLU J 164 " --> pdb=" O ASP J 160 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG J 176 " --> pdb=" O ASN J 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 71 removed outlier: 3.612A pdb=" N THR K 53 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN K 55 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE K 56 " --> pdb=" O THR K 53 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU K 58 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS K 62 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN K 65 " --> pdb=" O LYS K 62 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR K 67 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN K 71 " --> pdb=" O LYS K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 92 Processing helix chain 'K' and resid 135 through 146 removed outlier: 3.696A pdb=" N THR K 139 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU K 140 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER K 141 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU K 143 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP K 144 " --> pdb=" O SER K 141 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR K 146 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 169 removed outlier: 3.541A pdb=" N VAL K 157 " --> pdb=" O ARG K 153 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU K 158 " --> pdb=" O GLU K 154 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN K 168 " --> pdb=" O LEU K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 69 removed outlier: 3.577A pdb=" N SER L 53 " --> pdb=" O ALA L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 90 removed outlier: 3.550A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 removed outlier: 3.980A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG L 141 " --> pdb=" O GLY L 137 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY L 142 " --> pdb=" O VAL L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 164 Processing helix chain 'M' and resid 58 through 78 removed outlier: 3.579A pdb=" N THR M 63 " --> pdb=" O GLY M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 97 removed outlier: 4.160A pdb=" N SER M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 153 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 168 through 185 removed outlier: 3.824A pdb=" N VAL M 178 " --> pdb=" O LEU M 174 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 76 removed outlier: 3.829A pdb=" N LEU N 76 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 101 Processing helix chain 'N' and resid 146 through 154 removed outlier: 3.905A pdb=" N VAL N 153 " --> pdb=" O LEU N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 172 removed outlier: 3.729A pdb=" N ARG N 166 " --> pdb=" O GLN N 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 33 Processing helix chain 'O' and resid 84 through 104 removed outlier: 4.026A pdb=" N ARG O 88 " --> pdb=" O THR O 84 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN O 90 " --> pdb=" O ASP O 86 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 127 removed outlier: 3.841A pdb=" N VAL O 124 " --> pdb=" O ASP O 120 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR O 126 " --> pdb=" O SER O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 181 removed outlier: 3.990A pdb=" N PHE O 178 " --> pdb=" O GLU O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 205 Processing helix chain 'P' and resid 19 through 29 Processing helix chain 'P' and resid 79 through 100 removed outlier: 3.788A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS P 87 " --> pdb=" O ARG P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 121 removed outlier: 4.148A pdb=" N TYR P 120 " --> pdb=" O VAL P 116 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR P 121 " --> pdb=" O MET P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 175 removed outlier: 4.093A pdb=" N THR P 171 " --> pdb=" O VAL P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 196 removed outlier: 3.760A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU P 196 " --> pdb=" O LEU P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 225 No H-bonds generated for 'chain 'P' and resid 222 through 225' Processing helix chain 'Q' and resid 19 through 30 removed outlier: 3.679A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY Q 29 " --> pdb=" O MET Q 25 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 101 removed outlier: 4.314A pdb=" N VAL Q 85 " --> pdb=" O SER Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 123 removed outlier: 3.845A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 178 removed outlier: 4.262A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 200 Processing helix chain 'Q' and resid 230 through 243 removed outlier: 3.719A pdb=" N GLU Q 242 " --> pdb=" O LYS Q 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 28 removed outlier: 3.732A pdb=" N LYS R 27 " --> pdb=" O GLN R 23 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS R 28 " --> pdb=" O GLU R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 97 removed outlier: 4.639A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG R 86 " --> pdb=" O ILE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 117 Processing helix chain 'R' and resid 165 through 173 Processing helix chain 'R' and resid 185 through 197 removed outlier: 4.060A pdb=" N LEU R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 229 removed outlier: 3.590A pdb=" N LYS R 227 " --> pdb=" O GLU R 224 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL R 229 " --> pdb=" O GLU R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 234 No H-bonds generated for 'chain 'R' and resid 231 through 234' Processing helix chain 'S' and resid 22 through 33 removed outlier: 3.937A pdb=" N LYS S 32 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 103 removed outlier: 4.008A pdb=" N LYS S 86 " --> pdb=" O ILE S 82 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 117 removed outlier: 3.775A pdb=" N VAL S 116 " --> pdb=" O VAL S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 184 removed outlier: 3.852A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL S 184 " --> pdb=" O SER S 180 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 205 removed outlier: 3.512A pdb=" N SER S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS S 203 " --> pdb=" O LEU S 199 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN S 204 " --> pdb=" O ILE S 200 " (cutoff:3.500A) Processing helix chain 'S' and resid 231 through 235 removed outlier: 3.596A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 231 through 235' Processing helix chain 'T' and resid 20 through 31 removed outlier: 3.777A pdb=" N GLU T 27 " --> pdb=" O GLU T 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN T 31 " --> pdb=" O GLU T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 98 removed outlier: 3.774A pdb=" N GLN T 90 " --> pdb=" O ASN T 86 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER T 95 " --> pdb=" O GLU T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 121 removed outlier: 4.207A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix Processing helix chain 'T' and resid 165 through 174 removed outlier: 3.904A pdb=" N LEU T 172 " --> pdb=" O ALA T 168 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG T 174 " --> pdb=" O THR T 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 184 through 195 removed outlier: 3.681A pdb=" N ARG T 193 " --> pdb=" O LYS T 189 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 29 removed outlier: 3.848A pdb=" N ALA U 29 " --> pdb=" O TYR U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 102 removed outlier: 4.122A pdb=" N SER U 86 " --> pdb=" O ALA U 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 124 removed outlier: 3.893A pdb=" N ASP U 113 " --> pdb=" O LYS U 109 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR U 122 " --> pdb=" O TYR U 118 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR U 123 " --> pdb=" O VAL U 119 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU U 124 " --> pdb=" O HIS U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 178 Processing helix chain 'U' and resid 181 through 183 No H-bonds generated for 'chain 'U' and resid 181 through 183' Processing helix chain 'U' and resid 186 through 200 removed outlier: 4.550A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA U 194 " --> pdb=" O VAL U 190 " (cutoff:3.500A) Processing helix chain 'U' and resid 229 through 236 Processing helix chain 'V' and resid 49 through 54 removed outlier: 3.764A pdb=" N ALA V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 70 removed outlier: 3.537A pdb=" N ILE V 68 " --> pdb=" O GLY V 64 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU V 69 " --> pdb=" O PHE V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 89 Processing helix chain 'V' and resid 132 through 139 removed outlier: 4.360A pdb=" N GLY V 137 " --> pdb=" O TYR V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 166 removed outlier: 4.225A pdb=" N LEU V 153 " --> pdb=" O LYS V 149 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN V 154 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA V 161 " --> pdb=" O ALA V 157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU V 162 " --> pdb=" O ASN V 158 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG V 166 " --> pdb=" O LEU V 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 70 Processing helix chain 'W' and resid 76 through 89 Processing helix chain 'W' and resid 131 through 141 removed outlier: 3.808A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 165 removed outlier: 3.542A pdb=" N SER W 156 " --> pdb=" O LYS W 152 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU W 157 " --> pdb=" O ASN W 153 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA W 158 " --> pdb=" O LEU W 154 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 76 removed outlier: 3.576A pdb=" N TYR X 73 " --> pdb=" O ARG X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 95 Processing helix chain 'X' and resid 146 through 149 No H-bonds generated for 'chain 'X' and resid 146 through 149' Processing helix chain 'X' and resid 159 through 176 removed outlier: 4.025A pdb=" N GLU X 164 " --> pdb=" O ASP X 160 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG X 176 " --> pdb=" O ASN X 172 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 71 removed outlier: 3.613A pdb=" N THR Y 53 " --> pdb=" O ALA Y 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN Y 55 " --> pdb=" O ASP Y 52 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE Y 56 " --> pdb=" O THR Y 53 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU Y 58 " --> pdb=" O GLN Y 55 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS Y 62 " --> pdb=" O TYR Y 59 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN Y 65 " --> pdb=" O LYS Y 62 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR Y 67 " --> pdb=" O VAL Y 64 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN Y 71 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 92 Processing helix chain 'Y' and resid 135 through 146 removed outlier: 3.697A pdb=" N THR Y 139 " --> pdb=" O ALA Y 136 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU Y 140 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER Y 141 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU Y 143 " --> pdb=" O LEU Y 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP Y 144 " --> pdb=" O SER Y 141 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR Y 146 " --> pdb=" O LEU Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 169 removed outlier: 3.541A pdb=" N VAL Y 157 " --> pdb=" O ARG Y 153 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU Y 158 " --> pdb=" O GLU Y 154 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS Y 163 " --> pdb=" O LEU Y 159 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU Y 165 " --> pdb=" O ARG Y 161 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU Y 166 " --> pdb=" O LYS Y 162 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU Y 167 " --> pdb=" O CYS Y 163 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN Y 168 " --> pdb=" O LEU Y 164 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 69 removed outlier: 3.577A pdb=" N SER Z 53 " --> pdb=" O ALA Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 90 removed outlier: 3.550A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 142 removed outlier: 3.980A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG Z 141 " --> pdb=" O GLY Z 137 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY Z 142 " --> pdb=" O VAL Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 164 Processing helix chain 'a' and resid 58 through 78 removed outlier: 3.579A pdb=" N THR a 63 " --> pdb=" O GLY a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 97 removed outlier: 4.160A pdb=" N SER a 93 " --> pdb=" O ALA a 89 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR a 94 " --> pdb=" O ALA a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 153 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 168 through 185 removed outlier: 3.823A pdb=" N VAL a 178 " --> pdb=" O LEU a 174 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE a 179 " --> pdb=" O VAL a 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 76 removed outlier: 3.829A pdb=" N LEU b 76 " --> pdb=" O ILE b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 101 Processing helix chain 'b' and resid 146 through 154 removed outlier: 3.905A pdb=" N VAL b 153 " --> pdb=" O LEU b 149 " (cutoff:3.500A) Processing helix chain 'b' and resid 162 through 172 removed outlier: 3.729A pdb=" N ARG b 166 " --> pdb=" O GLN b 162 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 167 through 169 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.678A pdb=" N GLY A 142 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N CYS A 78 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS A 71 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N MET A 80 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 69 " --> pdb=" O MET A 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 159 through 162 Processing sheet with id= D, first strand: chain 'B' and resid 154 through 156 removed outlier: 3.784A pdb=" N THR B 68 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 73 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= F, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= G, first strand: chain 'D' and resid 158 through 161 Processing sheet with id= H, first strand: chain 'D' and resid 69 through 74 removed outlier: 3.569A pdb=" N ILE D 133 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 167 through 170 removed outlier: 3.757A pdb=" N ARG E 168 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL E 50 " --> pdb=" O GLU E 216 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 67 through 69 Processing sheet with id= K, first strand: chain 'F' and resid 159 through 161 removed outlier: 3.728A pdb=" N VAL F 215 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 63 through 65 removed outlier: 4.713A pdb=" N ILE F 144 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN F 146 " --> pdb=" O PHE F 154 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 45 through 49 Processing sheet with id= N, first strand: chain 'G' and resid 74 through 78 Processing sheet with id= O, first strand: chain 'H' and resid 125 through 128 Processing sheet with id= P, first strand: chain 'H' and resid 45 through 47 Processing sheet with id= Q, first strand: chain 'I' and resid 124 through 127 removed outlier: 4.005A pdb=" N LEU I 175 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU I 186 " --> pdb=" O LEU I 175 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 42 through 46 removed outlier: 3.659A pdb=" N ASP I 104 " --> pdb=" O GLY I 107 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER I 118 " --> pdb=" O TYR I 114 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.232A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 10 through 14 Processing sheet with id= U, first strand: chain 'J' and resid 49 through 54 Processing sheet with id= V, first strand: chain 'J' and resid 27 through 29 removed outlier: 3.759A pdb=" N PHE J 27 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR J 35 " --> pdb=" O PHE J 27 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE J 29 " --> pdb=" O MET J 33 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N MET J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'K' and resid 129 through 132 Processing sheet with id= X, first strand: chain 'K' and resid 113 through 118 removed outlier: 3.715A pdb=" N ILE K 42 " --> pdb=" O SER K 39 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU K 44 " --> pdb=" O LYS K 37 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS K 37 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS K 46 " --> pdb=" O MET K 35 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET K 35 " --> pdb=" O CYS K 46 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= Z, first strand: chain 'L' and resid 98 through 103 Processing sheet with id= AA, first strand: chain 'M' and resid 135 through 138 Processing sheet with id= AB, first strand: chain 'M' and resid 52 through 55 Processing sheet with id= AC, first strand: chain 'M' and resid 197 through 199 Processing sheet with id= AD, first strand: chain 'N' and resid 136 through 138 removed outlier: 3.674A pdb=" N ALA N 23 " --> pdb=" O LEU N 12 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 42 through 44 Processing sheet with id= AF, first strand: chain 'O' and resid 167 through 169 Processing sheet with id= AG, first strand: chain 'O' and resid 160 through 162 removed outlier: 3.678A pdb=" N GLY O 142 " --> pdb=" O GLN O 150 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N CYS O 78 " --> pdb=" O LYS O 71 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS O 71 " --> pdb=" O CYS O 78 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N MET O 80 " --> pdb=" O LEU O 69 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU O 69 " --> pdb=" O MET O 80 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'P' and resid 159 through 162 Processing sheet with id= AI, first strand: chain 'P' and resid 154 through 156 removed outlier: 3.784A pdb=" N THR P 68 " --> pdb=" O ILE P 71 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU P 73 " --> pdb=" O PRO P 66 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id= AK, first strand: chain 'Q' and resid 72 through 76 Processing sheet with id= AL, first strand: chain 'R' and resid 158 through 161 Processing sheet with id= AM, first strand: chain 'R' and resid 69 through 74 removed outlier: 3.569A pdb=" N ILE R 133 " --> pdb=" O TYR R 145 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'S' and resid 167 through 170 removed outlier: 3.757A pdb=" N ARG S 168 " --> pdb=" O GLY S 39 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL S 50 " --> pdb=" O GLU S 216 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'S' and resid 67 through 69 Processing sheet with id= AP, first strand: chain 'T' and resid 159 through 161 removed outlier: 3.729A pdb=" N VAL T 215 " --> pdb=" O ALA T 44 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'T' and resid 63 through 65 removed outlier: 4.713A pdb=" N ILE T 144 " --> pdb=" O CYS T 156 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS T 156 " --> pdb=" O ILE T 144 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN T 146 " --> pdb=" O PHE T 154 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'U' and resid 45 through 49 Processing sheet with id= AS, first strand: chain 'U' and resid 74 through 78 Processing sheet with id= AT, first strand: chain 'V' and resid 126 through 128 Processing sheet with id= AU, first strand: chain 'V' and resid 45 through 47 Processing sheet with id= AV, first strand: chain 'W' and resid 124 through 127 removed outlier: 4.005A pdb=" N LEU W 175 " --> pdb=" O LEU W 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU W 186 " --> pdb=" O LEU W 175 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'W' and resid 42 through 46 removed outlier: 3.659A pdb=" N ASP W 104 " --> pdb=" O GLY W 107 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER W 118 " --> pdb=" O TYR W 114 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.232A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'X' and resid 10 through 14 Processing sheet with id= AZ, first strand: chain 'X' and resid 49 through 54 Processing sheet with id= BA, first strand: chain 'X' and resid 27 through 29 removed outlier: 3.759A pdb=" N PHE X 27 " --> pdb=" O THR X 35 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR X 35 " --> pdb=" O PHE X 27 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE X 29 " --> pdb=" O MET X 33 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N MET X 33 " --> pdb=" O ILE X 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id= BC, first strand: chain 'Y' and resid 113 through 118 removed outlier: 3.715A pdb=" N ILE Y 42 " --> pdb=" O SER Y 39 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU Y 44 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS Y 37 " --> pdb=" O LEU Y 44 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS Y 46 " --> pdb=" O MET Y 35 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET Y 35 " --> pdb=" O CYS Y 46 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'Z' and resid 5 through 8 Processing sheet with id= BE, first strand: chain 'Z' and resid 98 through 103 Processing sheet with id= BF, first strand: chain 'a' and resid 135 through 138 Processing sheet with id= BG, first strand: chain 'a' and resid 52 through 55 Processing sheet with id= BH, first strand: chain 'a' and resid 197 through 199 Processing sheet with id= BI, first strand: chain 'b' and resid 136 through 138 removed outlier: 3.674A pdb=" N ALA b 23 " --> pdb=" O LEU b 12 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'b' and resid 42 through 44 1835 hydrogen bonds defined for protein. 5058 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: 15.15 Time building geometry restraints manager: 19.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9099 1.33 - 1.46: 15127 1.46 - 1.59: 19485 1.59 - 1.72: 13 1.72 - 1.85: 450 Bond restraints: 44174 Sorted by residual: bond pdb=" C THR V 1 " pdb=" N THR V 2 " ideal model delta sigma weight residual 1.331 1.782 -0.451 1.30e-02 5.92e+03 1.20e+03 bond pdb=" C THR H 1 " pdb=" N THR H 2 " ideal model delta sigma weight residual 1.331 1.782 -0.451 1.30e-02 5.92e+03 1.20e+03 bond pdb=" C THR L 1 " pdb=" N THR L 2 " ideal model delta sigma weight residual 1.331 1.485 -0.154 1.37e-02 5.33e+03 1.27e+02 bond pdb=" C THR Z 1 " pdb=" N THR Z 2 " ideal model delta sigma weight residual 1.331 1.485 -0.154 1.37e-02 5.33e+03 1.27e+02 bond pdb=" N PRO I 123 " pdb=" CD PRO I 123 " ideal model delta sigma weight residual 1.473 1.367 0.106 1.40e-02 5.10e+03 5.72e+01 ... (remaining 44169 not shown) Histogram of bond angle deviations from ideal: 87.13 - 100.02: 177 100.02 - 112.91: 21518 112.91 - 125.79: 37045 125.79 - 138.68: 875 138.68 - 151.57: 7 Bond angle restraints: 59622 Sorted by residual: angle pdb=" N GLY T 17 " pdb=" CA GLY T 17 " pdb=" C GLY T 17 " ideal model delta sigma weight residual 113.18 151.57 -38.39 2.37e+00 1.78e-01 2.62e+02 angle pdb=" N SER E 172 " pdb=" CA SER E 172 " pdb=" C SER E 172 " ideal model delta sigma weight residual 111.14 125.87 -14.73 1.08e+00 8.57e-01 1.86e+02 angle pdb=" N SER S 172 " pdb=" CA SER S 172 " pdb=" C SER S 172 " ideal model delta sigma weight residual 111.14 125.81 -14.67 1.08e+00 8.57e-01 1.84e+02 angle pdb=" N SER Q 153 " pdb=" CA SER Q 153 " pdb=" C SER Q 153 " ideal model delta sigma weight residual 108.79 89.26 19.53 1.53e+00 4.27e-01 1.63e+02 angle pdb=" N SER C 153 " pdb=" CA SER C 153 " pdb=" C SER C 153 " ideal model delta sigma weight residual 108.79 89.28 19.51 1.53e+00 4.27e-01 1.63e+02 ... (remaining 59617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 23958 17.60 - 35.20: 1866 35.20 - 52.80: 391 52.80 - 70.41: 213 70.41 - 88.01: 72 Dihedral angle restraints: 26500 sinusoidal: 10464 harmonic: 16036 Sorted by residual: dihedral pdb=" CA GLU M 18 " pdb=" C GLU M 18 " pdb=" N ASP M 19 " pdb=" CA ASP M 19 " ideal model delta harmonic sigma weight residual 180.00 -137.66 -42.34 0 5.00e+00 4.00e-02 7.17e+01 dihedral pdb=" CA GLU a 18 " pdb=" C GLU a 18 " pdb=" N ASP a 19 " pdb=" CA ASP a 19 " ideal model delta harmonic sigma weight residual -180.00 -137.66 -42.34 0 5.00e+00 4.00e-02 7.17e+01 dihedral pdb=" C GLN V 7 " pdb=" N GLN V 7 " pdb=" CA GLN V 7 " pdb=" CB GLN V 7 " ideal model delta harmonic sigma weight residual -122.60 -103.78 -18.82 0 2.50e+00 1.60e-01 5.67e+01 ... (remaining 26497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 5441 0.144 - 0.288: 1168 0.288 - 0.433: 102 0.433 - 0.577: 20 0.577 - 0.721: 1 Chirality restraints: 6732 Sorted by residual: chirality pdb=" CA PHE H 8 " pdb=" N PHE H 8 " pdb=" C PHE H 8 " pdb=" CB PHE H 8 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA MET W 135 " pdb=" N MET W 135 " pdb=" C MET W 135 " pdb=" CB MET W 135 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" CA MET I 135 " pdb=" N MET I 135 " pdb=" C MET I 135 " pdb=" CB MET I 135 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 ... (remaining 6729 not shown) Planarity restraints: 7614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 KNM W 300 " 0.005 2.00e-02 2.50e+03 2.67e-01 8.94e+02 pdb=" C8 KNM W 300 " -0.068 2.00e-02 2.50e+03 pdb=" C9 KNM W 300 " 0.312 2.00e-02 2.50e+03 pdb=" N2 KNM W 300 " -0.460 2.00e-02 2.50e+03 pdb=" O3 KNM W 300 " 0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 KNM I 300 " -0.005 2.00e-02 2.50e+03 2.67e-01 8.93e+02 pdb=" C8 KNM I 300 " 0.068 2.00e-02 2.50e+03 pdb=" C9 KNM I 300 " -0.311 2.00e-02 2.50e+03 pdb=" N2 KNM I 300 " 0.460 2.00e-02 2.50e+03 pdb=" O3 KNM I 300 " -0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 KNM H 300 " -0.191 2.00e-02 2.50e+03 2.47e-01 7.65e+02 pdb=" C8 KNM H 300 " 0.082 2.00e-02 2.50e+03 pdb=" C9 KNM H 300 " -0.298 2.00e-02 2.50e+03 pdb=" N2 KNM H 300 " 0.417 2.00e-02 2.50e+03 pdb=" O3 KNM H 300 " -0.010 2.00e-02 2.50e+03 ... (remaining 7611 not shown) Histogram of nonbonded interaction distances: 0.70 - 1.54: 10 1.54 - 2.38: 310 2.38 - 3.22: 43722 3.22 - 4.06: 113497 4.06 - 4.90: 213285 Warning: very small nonbonded interaction distances. Nonbonded interactions: 370824 Sorted by model distance: nonbonded pdb=" O SER Y 23 " pdb=" OD1 ASN Y 24 " model vdw 0.702 3.040 nonbonded pdb=" O SER K 23 " pdb=" OD1 ASN K 24 " model vdw 0.702 3.040 nonbonded pdb=" O VAL X 137 " pdb=" OH TYR X 146 " model vdw 0.977 2.440 nonbonded pdb=" O VAL J 137 " pdb=" OH TYR J 146 " model vdw 0.977 2.440 nonbonded pdb=" NH1 ARG J 26 " pdb=" CB MET J 33 " model vdw 1.392 3.520 ... (remaining 370819 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' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.040 Extract box with map and model: 6.440 Check model and map are aligned: 0.610 Set scattering table: 0.350 Process input model: 110.370 Find NCS groups from input model: 4.190 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 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 : 0.019 0.451 44174 Z= 1.266 Angle : 2.216 38.391 59622 Z= 1.459 Chirality : 0.115 0.721 6732 Planarity : 0.019 0.267 7614 Dihedral : 15.416 88.008 16238 Min Nonbonded Distance : 0.702 Molprobity Statistics. All-atom Clashscore : 33.75 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.46 % Favored : 95.14 % Rotamer: Outliers : 1.99 % Allowed : 9.50 % Favored : 88.51 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.18 (0.09), residues: 5432 helix: -2.12 (0.08), residues: 1892 sheet: -2.40 (0.13), residues: 1204 loop : -1.71 (0.12), residues: 2336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1964 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1872 time to evaluate : 5.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR J 196 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR X 196 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 92 outliers final: 30 residues processed: 1930 average time/residue: 0.6199 time to fit residues: 1890.5352 Evaluate side-chains 1421 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1391 time to evaluate : 4.795 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 2 residues processed: 30 average time/residue: 0.4032 time to fit residues: 29.7432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 459 optimal weight: 5.9990 chunk 412 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 426 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 317 optimal weight: 4.9990 chunk 494 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 68 HIS A 90 GLN A 123 GLN A 127 GLN B 62 HIS B 87 HIS ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 30 HIS C 69 ASN C 142 HIS C 166 ASN D 23 GLN D 54 GLN E 178 GLN E 211 ASN E 224 GLN F 20 HIS ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 117 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN H 110 GLN H 154 GLN ** I 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 ASN J 187 HIS K 63 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN M 131 GLN N 104 ASN N 108 ASN N 147 GLN O 33 ASN O 68 HIS O 90 GLN O 123 GLN O 127 GLN P 62 HIS P 87 HIS ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN Q 30 HIS Q 69 ASN Q 142 HIS Q 166 ASN R 23 GLN R 54 GLN R 175 ASN S 178 GLN S 211 ASN S 224 GLN T 20 HIS ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 HIS T 117 GLN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN V 110 GLN V 154 GLN ** W 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 156 ASN X 187 HIS Y 55 GLN Y 63 ASN ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN a 131 GLN b 108 ASN b 147 GLN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 44174 Z= 0.350 Angle : 0.855 16.216 59622 Z= 0.454 Chirality : 0.050 0.253 6732 Planarity : 0.007 0.077 7614 Dihedral : 7.175 55.425 6118 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 5.88 % Allowed : 17.39 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.29 (0.10), residues: 5432 helix: -0.92 (0.10), residues: 1890 sheet: -2.11 (0.13), residues: 1272 loop : -1.47 (0.12), residues: 2270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1764 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1493 time to evaluate : 5.310 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR J 196 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR X 196 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 271 outliers final: 152 residues processed: 1652 average time/residue: 0.5875 time to fit residues: 1543.3851 Evaluate side-chains 1472 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1320 time to evaluate : 4.814 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 152 outliers final: 4 residues processed: 152 average time/residue: 0.3831 time to fit residues: 117.1315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 274 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 411 optimal weight: 0.5980 chunk 336 optimal weight: 8.9990 chunk 136 optimal weight: 0.9980 chunk 494 optimal weight: 6.9990 chunk 534 optimal weight: 6.9990 chunk 440 optimal weight: 10.0000 chunk 490 optimal weight: 8.9990 chunk 168 optimal weight: 8.9990 chunk 397 optimal weight: 3.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN N 104 ASN ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 166 GLN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN W 57 GLN ** W 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 55 GLN ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN b 104 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 44174 Z= 0.303 Angle : 0.762 14.186 59622 Z= 0.402 Chirality : 0.048 0.194 6732 Planarity : 0.006 0.061 7614 Dihedral : 6.798 58.985 6118 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 4.38 % Allowed : 20.95 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.04 (0.11), residues: 5432 helix: -0.61 (0.11), residues: 1910 sheet: -1.95 (0.13), residues: 1242 loop : -1.48 (0.12), residues: 2280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1600 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1398 time to evaluate : 5.028 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR J 196 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR X 196 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 202 outliers final: 100 residues processed: 1532 average time/residue: 0.5934 time to fit residues: 1448.0735 Evaluate side-chains 1386 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1286 time to evaluate : 4.803 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 100 outliers final: 3 residues processed: 100 average time/residue: 0.3865 time to fit residues: 79.2231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 488 optimal weight: 4.9990 chunk 372 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 54 optimal weight: 0.0170 chunk 236 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 496 optimal weight: 8.9990 chunk 525 optimal weight: 0.9990 chunk 259 optimal weight: 5.9990 chunk 470 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 123 GLN A 127 GLN B 108 GLN B 168 ASN C 102 GLN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN G 22 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN N 104 ASN O 75 ASN ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 GLN P 168 ASN Q 102 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 HIS ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 166 GLN U 22 GLN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN b 104 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 44174 Z= 0.226 Angle : 0.694 14.278 59622 Z= 0.362 Chirality : 0.046 0.226 6732 Planarity : 0.005 0.055 7614 Dihedral : 6.447 59.338 6118 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 2.99 % Allowed : 23.53 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.77 (0.11), residues: 5432 helix: -0.31 (0.11), residues: 1916 sheet: -1.88 (0.13), residues: 1248 loop : -1.35 (0.13), residues: 2268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1517 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1379 time to evaluate : 4.519 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 81 residues processed: 1455 average time/residue: 0.5897 time to fit residues: 1357.8812 Evaluate side-chains 1369 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1288 time to evaluate : 4.928 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. outliers start: 81 outliers final: 4 residues processed: 81 average time/residue: 0.3954 time to fit residues: 66.2068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 437 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 391 optimal weight: 20.0000 chunk 216 optimal weight: 7.9990 chunk 448 optimal weight: 5.9990 chunk 363 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 chunk 471 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN G 110 HIS G 221 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN ** R 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 166 GLN U 221 ASN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN V 62 GLN ** V 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 44174 Z= 0.451 Angle : 0.880 14.769 59622 Z= 0.458 Chirality : 0.053 0.270 6732 Planarity : 0.007 0.081 7614 Dihedral : 7.031 54.121 6118 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.89 % Favored : 93.98 % Rotamer: Outliers : 4.79 % Allowed : 23.87 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.11), residues: 5432 helix: -0.88 (0.11), residues: 1904 sheet: -1.89 (0.13), residues: 1276 loop : -1.62 (0.12), residues: 2252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1489 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1268 time to evaluate : 5.033 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 221 outliers final: 120 residues processed: 1423 average time/residue: 0.5964 time to fit residues: 1346.7742 Evaluate side-chains 1335 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1215 time to evaluate : 5.010 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. outliers start: 120 outliers final: 4 residues processed: 120 average time/residue: 0.4009 time to fit residues: 96.4788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 176 optimal weight: 4.9990 chunk 473 optimal weight: 9.9990 chunk 103 optimal weight: 40.0000 chunk 308 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 526 optimal weight: 0.8980 chunk 436 optimal weight: 9.9990 chunk 243 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 276 optimal weight: 0.0370 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN E 104 ASN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 GLN ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 44174 Z= 0.216 Angle : 0.690 14.297 59622 Z= 0.359 Chirality : 0.046 0.329 6732 Planarity : 0.005 0.063 7614 Dihedral : 6.344 52.466 6118 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.85 % Favored : 96.02 % Rotamer: Outliers : 2.93 % Allowed : 25.46 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.76 (0.11), residues: 5432 helix: -0.40 (0.11), residues: 1924 sheet: -1.66 (0.13), residues: 1248 loop : -1.39 (0.13), residues: 2260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1498 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1363 time to evaluate : 5.045 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 58 residues processed: 1436 average time/residue: 0.6003 time to fit residues: 1371.3091 Evaluate side-chains 1292 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1234 time to evaluate : 4.643 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. outliers start: 58 outliers final: 4 residues processed: 58 average time/residue: 0.4130 time to fit residues: 49.9805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 507 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 299 optimal weight: 6.9990 chunk 384 optimal weight: 8.9990 chunk 297 optimal weight: 6.9990 chunk 443 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 524 optimal weight: 20.0000 chunk 328 optimal weight: 0.6980 chunk 319 optimal weight: 0.6980 chunk 242 optimal weight: 20.0000 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN E 104 ASN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 GLN S 104 ASN ** S 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 44174 Z= 0.292 Angle : 0.740 14.074 59622 Z= 0.384 Chirality : 0.048 0.234 6732 Planarity : 0.005 0.087 7614 Dihedral : 6.338 49.635 6118 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.10 % Favored : 94.77 % Rotamer: Outliers : 2.80 % Allowed : 27.17 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.75 (0.11), residues: 5432 helix: -0.36 (0.11), residues: 1902 sheet: -1.61 (0.13), residues: 1266 loop : -1.43 (0.13), residues: 2264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1242 time to evaluate : 4.917 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 129 outliers final: 80 residues processed: 1314 average time/residue: 0.6027 time to fit residues: 1256.5696 Evaluate side-chains 1287 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1207 time to evaluate : 4.890 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. outliers start: 80 outliers final: 4 residues processed: 80 average time/residue: 0.3878 time to fit residues: 65.6557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 324 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 313 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 333 optimal weight: 1.9990 chunk 357 optimal weight: 6.9990 chunk 259 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 412 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN D 23 GLN E 104 ASN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 155 ASN R 23 GLN S 104 ASN ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 117 GLN ** T 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 44174 Z= 0.213 Angle : 0.692 14.025 59622 Z= 0.358 Chirality : 0.046 0.243 6732 Planarity : 0.005 0.079 7614 Dihedral : 6.061 56.164 6118 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 1.54 % Allowed : 27.67 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.11), residues: 5432 helix: -0.12 (0.11), residues: 1902 sheet: -1.38 (0.14), residues: 1246 loop : -1.30 (0.13), residues: 2284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1289 time to evaluate : 5.093 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 37 residues processed: 1320 average time/residue: 0.5077 time to fit residues: 1064.5248 Evaluate side-chains 1249 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1212 time to evaluate : 3.539 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. outliers start: 37 outliers final: 4 residues processed: 37 average time/residue: 0.2813 time to fit residues: 24.3021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 476 optimal weight: 0.4980 chunk 502 optimal weight: 4.9990 chunk 458 optimal weight: 0.5980 chunk 488 optimal weight: 7.9990 chunk 294 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 383 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 441 optimal weight: 9.9990 chunk 462 optimal weight: 8.9990 chunk 486 optimal weight: 8.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN J 71 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS V 53 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 ASN a 77 HIS ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 44174 Z= 0.256 Angle : 0.725 13.691 59622 Z= 0.375 Chirality : 0.047 0.258 6732 Planarity : 0.005 0.095 7614 Dihedral : 6.105 50.360 6118 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.66 % Favored : 95.21 % Rotamer: Outliers : 1.26 % Allowed : 28.40 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.42 (0.11), residues: 5432 helix: -0.18 (0.11), residues: 1914 sheet: -1.33 (0.14), residues: 1262 loop : -1.21 (0.13), residues: 2256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1226 time to evaluate : 4.371 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 58 outliers final: 43 residues processed: 1247 average time/residue: 0.5087 time to fit residues: 1009.7517 Evaluate side-chains 1236 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1193 time to evaluate : 4.634 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. outliers start: 43 outliers final: 4 residues processed: 43 average time/residue: 0.3965 time to fit residues: 38.6217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 320 optimal weight: 0.9990 chunk 516 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 541 optimal weight: 5.9990 chunk 498 optimal weight: 9.9990 chunk 431 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 333 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: