Starting phenix.real_space_refine on Wed Mar 20 04:14:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eqg_31265/03_2024/7eqg_31265_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eqg_31265/03_2024/7eqg_31265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eqg_31265/03_2024/7eqg_31265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eqg_31265/03_2024/7eqg_31265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eqg_31265/03_2024/7eqg_31265_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eqg_31265/03_2024/7eqg_31265_neut.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 130 5.49 5 S 41 5.16 5 C 16072 2.51 5 N 4814 2.21 5 O 5244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 7": "OE1" <-> "OE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G GLU 283": "OE1" <-> "OE2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "H PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 230": "OE1" <-> "OE2" Residue "H GLU 283": "OE1" <-> "OE2" Residue "I GLU 38": "OE1" <-> "OE2" Residue "I ARG 250": "NH1" <-> "NH2" Residue "I GLU 316": "OE1" <-> "OE2" Residue "I GLU 321": "OE1" <-> "OE2" Residue "I GLU 338": "OE1" <-> "OE2" Residue "L ARG 39": "NH1" <-> "NH2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "L ARG 68": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L GLU 77": "OE1" <-> "OE2" Residue "L ARG 80": "NH1" <-> "NH2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L ARG 119": "NH1" <-> "NH2" Residue "L GLU 126": "OE1" <-> "OE2" Residue "L ARG 156": "NH1" <-> "NH2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "P TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q GLU 53": "OE1" <-> "OE2" Residue "Q TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26301 Number of models: 1 Model: "" Number of chains: 17 Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2360 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2516 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2544 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2548 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2560 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 566 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 571 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1429 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "M" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1226 Classifications: {'RNA': 58} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 19, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 32, 'rna3p': 25} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 907 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "P" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 568 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 570 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 567 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1893 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 17, 'TRANS': 245} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 131 Chain: "O" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 549 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1, ' DC:plan2': 3, ' DA:plan2': 1, ' DC:plan': 3, ' DA:plan': 1} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 14.65, per 1000 atoms: 0.56 Number of scatterers: 26301 At special positions: 0 Unit cell: (162.8, 136.4, 167.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 130 15.00 O 5244 8.00 N 4814 7.00 C 16072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.84 Conformation dependent library (CDL) restraints added in 4.4 seconds 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5768 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 39 sheets defined 28.4% alpha, 18.3% beta 29 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 7.73 Creating SS restraints... Processing helix chain 'C' and resid 33 through 48 removed outlier: 4.090A pdb=" N PHE C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.591A pdb=" N GLN C 133 " --> pdb=" O GLN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'C' and resid 189 through 201 removed outlier: 3.880A pdb=" N LEU C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.634A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.520A pdb=" N GLY D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 264 removed outlier: 3.549A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 removed outlier: 3.569A pdb=" N LEU D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.674A pdb=" N GLN D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 36 removed outlier: 3.576A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 129 removed outlier: 3.672A pdb=" N ASP E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.601A pdb=" N ALA E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 removed outlier: 3.766A pdb=" N VAL E 153 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 205 removed outlier: 3.659A pdb=" N ALA E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY E 202 " --> pdb=" O LEU E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 266 removed outlier: 3.628A pdb=" N ILE E 260 " --> pdb=" O HIS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 314 removed outlier: 3.692A pdb=" N LEU E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.546A pdb=" N GLY E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 Processing helix chain 'F' and resid 112 through 129 removed outlier: 3.679A pdb=" N GLN F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR F 125 " --> pdb=" O THR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.746A pdb=" N GLY F 202 " --> pdb=" O LEU F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.701A pdb=" N ILE F 260 " --> pdb=" O HIS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 63 through 71 removed outlier: 3.799A pdb=" N LEU G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.849A pdb=" N LYS G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 144 removed outlier: 3.579A pdb=" N HIS G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 204 removed outlier: 3.751A pdb=" N GLU G 197 " --> pdb=" O ASP G 193 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 266 removed outlier: 3.979A pdb=" N THR G 266 " --> pdb=" O ASN G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 278 removed outlier: 4.051A pdb=" N LEU G 277 " --> pdb=" O GLU G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 removed outlier: 3.517A pdb=" N LEU G 313 " --> pdb=" O ASP G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 58 through 62 removed outlier: 4.177A pdb=" N ARG H 62 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 72 removed outlier: 4.394A pdb=" N ALA H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 190 through 205 removed outlier: 3.728A pdb=" N ALA H 194 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU H 198 " --> pdb=" O ALA H 194 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 264 removed outlier: 3.562A pdb=" N ILE H 260 " --> pdb=" O HIS H 256 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU H 264 " --> pdb=" O ILE H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'I' and resid 63 through 72 removed outlier: 3.750A pdb=" N LEU I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN I 72 " --> pdb=" O ASP I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 129 Processing helix chain 'I' and resid 133 through 144 Processing helix chain 'I' and resid 190 through 204 Processing helix chain 'I' and resid 256 through 264 Processing helix chain 'I' and resid 274 through 278 removed outlier: 3.750A pdb=" N GLY I 278 " --> pdb=" O ASP I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 313 removed outlier: 3.648A pdb=" N LEU I 307 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 333 removed outlier: 3.874A pdb=" N TYR I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 53 Processing helix chain 'J' and resid 72 through 76 removed outlier: 3.968A pdb=" N ARG J 76 " --> pdb=" O GLU J 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 Processing helix chain 'L' and resid 16 through 34 removed outlier: 3.538A pdb=" N LEU L 20 " --> pdb=" O PRO L 16 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL L 23 " --> pdb=" O GLN L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 73 removed outlier: 3.566A pdb=" N ARG L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 77 removed outlier: 3.572A pdb=" N GLU L 77 " --> pdb=" O PRO L 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 74 through 77' Processing helix chain 'L' and resid 108 through 119 removed outlier: 3.910A pdb=" N LEU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG L 119 " --> pdb=" O ARG L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 131 removed outlier: 3.535A pdb=" N LYS L 129 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE L 131 " --> pdb=" O ALA L 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 54 Processing helix chain 'Q' and resid 39 through 55 Processing helix chain 'Q' and resid 72 through 77 removed outlier: 3.811A pdb=" N ARG Q 76 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL Q 77 " --> pdb=" O GLN Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 53 Processing helix chain 'B' and resid 13 through 33 removed outlier: 3.663A pdb=" N ILE B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 removed outlier: 3.897A pdb=" N THR B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 59 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.937A pdb=" N PHE B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 138 through 144 removed outlier: 3.833A pdb=" N VAL B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 162 Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 210 through 221 removed outlier: 4.172A pdb=" N ALA B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.545A pdb=" N ASN B 250 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 Processing sheet with id=AA1, first strand: chain 'C' and resid 56 through 61 removed outlier: 4.934A pdb=" N GLY C 58 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 112 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 110 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 56 through 61 removed outlier: 4.934A pdb=" N GLY C 58 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 112 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 110 " --> pdb=" O GLY C 60 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA C 103 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLN C 18 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 105 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER C 16 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL C 107 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ARG C 14 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 109 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 12 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AA4, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'C' and resid 185 through 188 Processing sheet with id=AA6, first strand: chain 'C' and resid 255 through 257 Processing sheet with id=AA7, first strand: chain 'C' and resid 304 through 306 Processing sheet with id=AA8, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.826A pdb=" N GLY D 334 " --> pdb=" O PHE D 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.532A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL D 158 " --> pdb=" O ASP D 177 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP D 177 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL D 160 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG D 175 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE D 162 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR D 173 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS D 164 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.532A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 48 Processing sheet with id=AB3, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.770A pdb=" N ALA E 108 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 20 removed outlier: 4.036A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL E 158 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP E 177 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE E 162 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AB6, first strand: chain 'E' and resid 44 through 51 removed outlier: 4.563A pdb=" N ALA E 82 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 12 through 14 removed outlier: 3.594A pdb=" N GLY F 334 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 170 through 177 removed outlier: 3.896A pdb=" N ARG F 172 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA F 157 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 94 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 24 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 44 through 51 Processing sheet with id=AC1, first strand: chain 'G' and resid 169 through 177 removed outlier: 5.038A pdb=" N VAL G 170 " --> pdb=" O ARG G 166 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ARG G 166 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 51 Processing sheet with id=AC3, first strand: chain 'H' and resid 13 through 14 removed outlier: 3.924A pdb=" N GLY H 334 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.978A pdb=" N VAL H 209 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG H 172 " --> pdb=" O HIS H 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AC6, first strand: chain 'H' and resid 45 through 48 removed outlier: 4.329A pdb=" N ALA H 82 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL H 225 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 287 through 288 Processing sheet with id=AC8, first strand: chain 'I' and resid 108 through 109 removed outlier: 3.639A pdb=" N ALA I 108 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 19 through 20 removed outlier: 4.286A pdb=" N LEU I 210 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG I 172 " --> pdb=" O HIS I 164 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AD2, first strand: chain 'I' and resid 44 through 51 Processing sheet with id=AD3, first strand: chain 'I' and resid 266 through 268 Processing sheet with id=AD4, first strand: chain 'I' and resid 287 through 288 removed outlier: 3.892A pdb=" N LYS I 293 " --> pdb=" O VAL I 288 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 28 through 35 removed outlier: 5.125A pdb=" N MET J 29 " --> pdb=" O ARG J 25 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG J 25 " --> pdb=" O MET J 29 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG J 33 " --> pdb=" O VAL J 21 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL J 21 " --> pdb=" O ARG J 33 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG J 35 " --> pdb=" O TYR J 19 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR J 19 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR J 5 " --> pdb=" O VAL J 60 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU J 62 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL J 7 " --> pdb=" O LEU J 62 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 29 through 37 removed outlier: 3.565A pdb=" N VAL K 31 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL K 21 " --> pdb=" O ARG K 33 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG K 35 " --> pdb=" O TYR K 19 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR K 19 " --> pdb=" O ARG K 35 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 7 through 8 removed outlier: 3.544A pdb=" N LEU L 58 " --> pdb=" O ILE L 7 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 100 through 103 removed outlier: 4.213A pdb=" N PHE L 158 " --> pdb=" O VAL L 103 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 28 through 37 removed outlier: 5.713A pdb=" N VAL P 30 " --> pdb=" O ARG P 25 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ARG P 25 " --> pdb=" O VAL P 30 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY P 32 " --> pdb=" O VAL P 23 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL P 23 " --> pdb=" O GLY P 32 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR P 19 " --> pdb=" O ALA P 36 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR P 5 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU P 62 " --> pdb=" O THR P 5 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL P 7 " --> pdb=" O LEU P 62 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 28 through 35 removed outlier: 5.179A pdb=" N VAL Q 30 " --> pdb=" O ARG Q 25 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG Q 25 " --> pdb=" O VAL Q 30 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLY Q 32 " --> pdb=" O VAL Q 23 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL Q 23 " --> pdb=" O GLY Q 32 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR Q 5 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU Q 62 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL Q 7 " --> pdb=" O LEU Q 62 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 31 through 35 removed outlier: 5.854A pdb=" N GLY R 32 " --> pdb=" O VAL R 23 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL R 23 " --> pdb=" O GLY R 32 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR R 5 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU R 62 " --> pdb=" O THR R 5 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL R 7 " --> pdb=" O LEU R 62 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 180 through 181 859 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 8.59 Time building geometry restraints manager: 10.79 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: 5292 1.33 - 1.45: 6733 1.45 - 1.57: 14713 1.57 - 1.69: 258 1.69 - 1.81: 74 Bond restraints: 27070 Sorted by residual: bond pdb=" C LEU C 263 " pdb=" N PRO C 264 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.08e-02 8.57e+03 1.45e+01 bond pdb=" N VAL Q 77 " pdb=" CA VAL Q 77 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.05e+01 bond pdb=" N VAL Q 60 " pdb=" CA VAL Q 60 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.69e+00 bond pdb=" N LEU E 148 " pdb=" CA LEU E 148 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.28e-02 6.10e+03 8.48e+00 bond pdb=" N ILE Q 61 " pdb=" CA ILE Q 61 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.29e+00 ... (remaining 27065 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.84: 1201 105.84 - 112.95: 14498 112.95 - 120.06: 9451 120.06 - 127.16: 11631 127.16 - 134.27: 546 Bond angle restraints: 37327 Sorted by residual: angle pdb=" C LEU B 268 " pdb=" N PRO B 269 " pdb=" CA PRO B 269 " ideal model delta sigma weight residual 119.66 126.39 -6.73 7.20e-01 1.93e+00 8.74e+01 angle pdb=" O3' G M 48 " pdb=" C3' G M 48 " pdb=" C2' G M 48 " ideal model delta sigma weight residual 109.50 119.42 -9.92 1.50e+00 4.44e-01 4.38e+01 angle pdb=" C4' G M 48 " pdb=" C3' G M 48 " pdb=" O3' G M 48 " ideal model delta sigma weight residual 109.40 117.98 -8.58 1.50e+00 4.44e-01 3.27e+01 angle pdb=" N LYS G 235 " pdb=" CA LYS G 235 " pdb=" C LYS G 235 " ideal model delta sigma weight residual 109.76 100.84 8.92 1.59e+00 3.96e-01 3.15e+01 angle pdb=" N ARG B 258 " pdb=" CA ARG B 258 " pdb=" C ARG B 258 " ideal model delta sigma weight residual 108.90 100.59 8.31 1.63e+00 3.76e-01 2.60e+01 ... (remaining 37322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 15432 35.90 - 71.79: 702 71.79 - 107.69: 55 107.69 - 143.59: 4 143.59 - 179.49: 7 Dihedral angle restraints: 16200 sinusoidal: 7256 harmonic: 8944 Sorted by residual: dihedral pdb=" O4' C M 49 " pdb=" C1' C M 49 " pdb=" N1 C M 49 " pdb=" C2 C M 49 " ideal model delta sinusoidal sigma weight residual 200.00 49.78 150.22 1 1.50e+01 4.44e-03 7.97e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual -128.00 49.49 -177.49 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual -128.00 45.45 -173.45 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 16197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4117 0.128 - 0.257: 117 0.257 - 0.385: 2 0.385 - 0.514: 0 0.514 - 0.642: 1 Chirality restraints: 4237 Sorted by residual: chirality pdb=" C3' G M 48 " pdb=" C4' G M 48 " pdb=" O3' G M 48 " pdb=" C2' G M 48 " both_signs ideal model delta sigma weight residual False -2.74 -2.10 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA LEU G 18 " pdb=" N LEU G 18 " pdb=" C LEU G 18 " pdb=" CB LEU G 18 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB THR E 266 " pdb=" CA THR E 266 " pdb=" OG1 THR E 266 " pdb=" CG2 THR E 266 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4234 not shown) Planarity restraints: 4453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 56 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO K 57 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO K 57 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 57 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 71 " -0.053 5.00e-02 4.00e+02 7.89e-02 9.97e+00 pdb=" N PRO B 72 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 25 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO C 26 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " 0.043 5.00e-02 4.00e+02 ... (remaining 4450 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 47 2.41 - 3.03: 13299 3.03 - 3.66: 36837 3.66 - 4.28: 55906 4.28 - 4.90: 96035 Nonbonded interactions: 202124 Sorted by model distance: nonbonded pdb=" N2 G M 48 " pdb=" N1 A M 55 " model vdw 1.791 2.560 nonbonded pdb=" O GLU L 110 " pdb=" CD ARG L 114 " model vdw 1.898 3.440 nonbonded pdb=" O2' U M 47 " pdb=" OP2 G M 48 " model vdw 1.957 2.440 nonbonded pdb=" NH2 ARG L 115 " pdb=" O2' G M 48 " model vdw 1.959 2.520 nonbonded pdb=" O ASN D 144 " pdb=" OD1 ASN D 144 " model vdw 2.062 3.040 ... (remaining 202119 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 'D' and (resid 6 through 32 or (resid 33 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 146 or (resid 147 throug \ h 152 and (name N or name CA or name C or name O or name CB )) or resid 153 thro \ ugh 236 or (resid 237 through 239 and (name N or name CA or name C or name O or \ name CB )) or resid 240 through 242 or (resid 243 and (name N or name CA or name \ C or name O or name CB )) or resid 244 through 272 or (resid 273 through 275 an \ d (name N or name CA or name C or name O or name CB )) or resid 276 through 300 \ or (resid 301 through 302 and (name N or name CA or name C or name O or name CB \ )) or resid 303 through 338)) selection = (chain 'E' and (resid 6 through 29 or (resid 30 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 49 or resid 76 through 1 \ 46 or (resid 147 through 152 and (name N or name CA or name C or name O or name \ CB )) or resid 153 through 236 or (resid 237 through 239 and (name N or name CA \ or name C or name O or name CB )) or resid 240 through 242 or (resid 243 and (na \ me N or name CA or name C or name O or name CB )) or resid 244 through 338)) selection = (chain 'F' and (resid 6 through 29 or (resid 30 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 49 or resid 76 through 1 \ 46 or (resid 147 through 152 and (name N or name CA or name C or name O or name \ CB )) or resid 153 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB )) or resid 185 through 236 or (resid 237 through 239 and (na \ me N or name CA or name C or name O or name CB )) or resid 240 through 272 or (r \ esid 273 through 275 and (name N or name CA or name C or name O or name CB )) or \ resid 276 or (resid 277 and (name N or name CA or name C or name O or name CB ) \ ) or resid 278 through 300 or (resid 301 through 302 and (name N or name CA or n \ ame C or name O or name CB )) or resid 303 through 338)) selection = (chain 'G' and (resid 6 through 29 or (resid 30 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 49 or resid 76 through 1 \ 83 or (resid 184 and (name N or name CA or name C or name O or name CB )) or res \ id 185 through 237 or (resid 238 through 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 242 or (resid 243 and (name N or name \ CA or name C or name O or name CB )) or resid 244 through 271 or (resid 272 thr \ ough 275 and (name N or name CA or name C or name O or name CB )) or resid 276 t \ hrough 300 or (resid 301 through 302 and (name N or name CA or name C or name O \ or name CB )) or resid 303 through 338)) selection = (chain 'H' and (resid 6 through 29 or (resid 30 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 49 or resid 76 through 1 \ 46 or (resid 147 through 152 and (name N or name CA or name C or name O or name \ CB )) or resid 153 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB )) or resid 185 through 236 or (resid 237 through 239 and (na \ me N or name CA or name C or name O or name CB )) or resid 240 through 242 or (r \ esid 243 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 276 or (resid 277 and (name N or name CA or name C or name O or name CB ) \ ) or resid 278 through 300 or (resid 301 through 302 and (name N or name CA or n \ ame C or name O or name CB )) or resid 303 through 338)) selection = (chain 'I' and (resid 6 through 29 or (resid 30 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 49 or resid 76 through 1 \ 46 or (resid 147 through 152 and (name N or name CA or name C or name O or name \ CB )) or resid 153 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB )) or resid 185 through 236 or (resid 237 through 239 and (na \ me N or name CA or name C or name O or name CB )) or resid 240 through 242 or (r \ esid 243 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 271 or (resid 272 through 275 and (name N or name CA or name C or name O \ or name CB )) or resid 276 through 300 or (resid 301 through 302 and (name N or \ name CA or name C or name O or name CB )) or resid 303 through 338)) } ncs_group { reference = (chain 'J' and (resid 2 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 78)) selection = (chain 'K' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 55 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 78)) selection = (chain 'P' and resid 2 through 78) selection = (chain 'Q' and (resid 2 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 75 or (resid 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 78)) selection = (chain 'R' and (resid 2 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 75 or (resid 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 78)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.570 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 71.430 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.090 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27070 Z= 0.333 Angle : 0.828 11.145 37327 Z= 0.484 Chirality : 0.053 0.642 4237 Planarity : 0.006 0.081 4453 Dihedral : 18.848 179.486 10432 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.13 % Favored : 92.84 % Rotamer: Outliers : 0.68 % Allowed : 13.83 % Favored : 85.49 % 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: -3.71 (0.12), residues: 3086 helix: -2.58 (0.12), residues: 835 sheet: -0.13 (0.21), residues: 553 loop : -3.37 (0.11), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 30 HIS 0.007 0.001 HIS H 324 PHE 0.018 0.002 PHE G 95 TYR 0.020 0.002 TYR G 271 ARG 0.005 0.001 ARG G 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 353 time to evaluate : 2.762 Fit side-chains revert: symmetry clash REVERT: C 268 ARG cc_start: 0.5852 (ttt90) cc_final: 0.5146 (tpt90) REVERT: D 285 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: E 330 LEU cc_start: 0.8556 (pp) cc_final: 0.8026 (mt) REVERT: G 19 ASP cc_start: 0.6013 (t0) cc_final: 0.5774 (t0) REVERT: G 25 MET cc_start: 0.8350 (mtt) cc_final: 0.8076 (mtt) REVERT: L 117 MET cc_start: 0.6429 (mtm) cc_final: 0.6090 (mtm) REVERT: R 48 MET cc_start: 0.8829 (mmm) cc_final: 0.8545 (tpt) REVERT: R 66 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8317 (mttt) REVERT: B 203 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7462 (m-70) REVERT: B 222 ARG cc_start: 0.4115 (tpt170) cc_final: 0.3355 (ptp90) outliers start: 16 outliers final: 9 residues processed: 367 average time/residue: 0.4908 time to fit residues: 259.3835 Evaluate side-chains 265 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 254 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain L residue 114 ARG Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 286 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 45 GLN C 69 GLN C 114 HIS C 168 GLN C 173 GLN C 194 GLN C 282 ASN D 77 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN E 83 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN F 110 ASN ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 GLN G 83 ASN G 164 HIS G 223 GLN G 241 GLN H 32 GLN H 110 ASN H 262 ASN I 310 ASN J 65 ASN P 58 ASN B 172 HIS B 255 ASN B 273 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27070 Z= 0.273 Angle : 0.629 12.395 37327 Z= 0.331 Chirality : 0.043 0.284 4237 Planarity : 0.005 0.061 4453 Dihedral : 19.413 174.081 5126 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.03 % Favored : 92.94 % Rotamer: Outliers : 2.60 % Allowed : 16.26 % Favored : 81.14 % 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: -2.50 (0.14), residues: 3086 helix: -0.64 (0.17), residues: 835 sheet: 0.18 (0.22), residues: 555 loop : -3.01 (0.12), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 30 HIS 0.007 0.001 HIS C 196 PHE 0.015 0.002 PHE H 95 TYR 0.021 0.002 TYR H 285 ARG 0.005 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 262 time to evaluate : 2.640 Fit side-chains REVERT: C 111 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8107 (pp) REVERT: C 147 TRP cc_start: 0.7114 (t60) cc_final: 0.6908 (t60) REVERT: C 298 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6534 (mp) REVERT: E 330 LEU cc_start: 0.8535 (pp) cc_final: 0.7924 (mt) REVERT: F 76 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8667 (mt) REVERT: G 25 MET cc_start: 0.8309 (mtt) cc_final: 0.8039 (mtt) REVERT: L 117 MET cc_start: 0.6379 (mtm) cc_final: 0.5947 (mtm) REVERT: R 66 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8343 (mttt) REVERT: B 222 ARG cc_start: 0.4220 (tpt170) cc_final: 0.3562 (ptp90) REVERT: B 259 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.5769 (m-80) outliers start: 61 outliers final: 33 residues processed: 307 average time/residue: 0.4464 time to fit residues: 204.6640 Evaluate side-chains 283 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 246 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 chunk 255 optimal weight: 40.0000 chunk 284 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 HIS D 77 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 HIS G 223 GLN R 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 27070 Z= 0.300 Angle : 0.635 12.879 37327 Z= 0.334 Chirality : 0.044 0.309 4237 Planarity : 0.005 0.072 4453 Dihedral : 19.236 174.589 5110 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.74 % Favored : 92.22 % Rotamer: Outliers : 2.86 % Allowed : 18.74 % Favored : 78.40 % 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: -2.05 (0.14), residues: 3086 helix: -0.02 (0.18), residues: 842 sheet: 0.39 (0.22), residues: 551 loop : -2.84 (0.13), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 30 HIS 0.007 0.001 HIS C 196 PHE 0.015 0.002 PHE H 95 TYR 0.020 0.002 TYR H 285 ARG 0.003 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 243 time to evaluate : 2.531 Fit side-chains REVERT: C 111 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8129 (pp) REVERT: C 180 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7122 (pp) REVERT: E 80 ASP cc_start: 0.7724 (m-30) cc_final: 0.7377 (m-30) REVERT: E 330 LEU cc_start: 0.8560 (pp) cc_final: 0.7952 (mt) REVERT: F 76 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8719 (mt) REVERT: F 128 GLU cc_start: 0.7807 (pp20) cc_final: 0.7033 (pp20) REVERT: F 129 GLN cc_start: 0.7331 (mt0) cc_final: 0.6992 (mt0) REVERT: R 66 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8350 (mttt) REVERT: B 222 ARG cc_start: 0.4045 (tpt170) cc_final: 0.3624 (ptp90) REVERT: B 259 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.5980 (m-80) outliers start: 67 outliers final: 44 residues processed: 293 average time/residue: 0.4192 time to fit residues: 184.9008 Evaluate side-chains 282 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 234 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 259 TYR Chi-restraints excluded: chain B residue 262 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 272 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN I 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 27070 Z= 0.322 Angle : 0.648 13.286 37327 Z= 0.340 Chirality : 0.044 0.318 4237 Planarity : 0.005 0.072 4453 Dihedral : 19.193 176.046 5110 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.97 % Favored : 92.00 % Rotamer: Outliers : 3.24 % Allowed : 19.72 % Favored : 77.04 % 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: -1.89 (0.14), residues: 3086 helix: 0.21 (0.18), residues: 842 sheet: 0.36 (0.22), residues: 551 loop : -2.75 (0.13), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 30 HIS 0.006 0.001 HIS G 256 PHE 0.015 0.002 PHE G 95 TYR 0.020 0.002 TYR H 285 ARG 0.006 0.000 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 237 time to evaluate : 2.939 Fit side-chains REVERT: C 111 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8052 (pp) REVERT: C 180 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7163 (pp) REVERT: C 277 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8223 (mp) REVERT: E 80 ASP cc_start: 0.7740 (m-30) cc_final: 0.7394 (m-30) REVERT: E 120 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7320 (tm-30) REVERT: E 330 LEU cc_start: 0.8587 (pp) cc_final: 0.7938 (mt) REVERT: F 76 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8735 (mt) REVERT: F 128 GLU cc_start: 0.7825 (pp20) cc_final: 0.7018 (pp20) REVERT: F 129 GLN cc_start: 0.7408 (mt0) cc_final: 0.6976 (mt0) REVERT: Q 24 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: R 66 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8348 (mttt) REVERT: B 222 ARG cc_start: 0.4055 (tpt170) cc_final: 0.3617 (ptp90) REVERT: B 259 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6362 (m-80) outliers start: 76 outliers final: 50 residues processed: 298 average time/residue: 0.4200 time to fit residues: 190.5398 Evaluate side-chains 286 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 230 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 0.2980 chunk 273 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 HIS ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN B 177 GLN B 200 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27070 Z= 0.189 Angle : 0.559 11.337 37327 Z= 0.295 Chirality : 0.041 0.203 4237 Planarity : 0.004 0.074 4453 Dihedral : 19.039 179.713 5108 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.74 % Favored : 93.23 % Rotamer: Outliers : 2.77 % Allowed : 20.70 % Favored : 76.53 % 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: -1.52 (0.15), residues: 3086 helix: 0.62 (0.18), residues: 842 sheet: 0.57 (0.23), residues: 547 loop : -2.57 (0.13), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 174 HIS 0.004 0.001 HIS H 324 PHE 0.012 0.001 PHE H 147 TYR 0.016 0.001 TYR H 285 ARG 0.007 0.000 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 253 time to evaluate : 2.923 Fit side-chains REVERT: C 111 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7912 (pp) REVERT: C 180 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7067 (pp) REVERT: C 240 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6195 (tt0) REVERT: C 277 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8051 (mp) REVERT: E 80 ASP cc_start: 0.7566 (m-30) cc_final: 0.7219 (m-30) REVERT: E 330 LEU cc_start: 0.8106 (pp) cc_final: 0.7798 (mt) REVERT: F 338 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6711 (tm-30) REVERT: G 271 TYR cc_start: 0.8207 (p90) cc_final: 0.7859 (p90) REVERT: Q 24 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: R 66 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8349 (mttt) REVERT: B 222 ARG cc_start: 0.4017 (tpt170) cc_final: 0.3531 (ptp90) REVERT: B 259 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6090 (m-80) outliers start: 65 outliers final: 38 residues processed: 303 average time/residue: 0.4655 time to fit residues: 214.9928 Evaluate side-chains 284 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 239 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 22 ASP Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 304 optimal weight: 0.9980 chunk 253 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 HIS D 77 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 77 GLN G 241 GLN ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 27070 Z= 0.370 Angle : 0.663 12.647 37327 Z= 0.348 Chirality : 0.045 0.340 4237 Planarity : 0.005 0.071 4453 Dihedral : 19.095 177.850 5108 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.52 % Favored : 91.45 % Rotamer: Outliers : 3.71 % Allowed : 20.49 % Favored : 75.80 % 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: -1.66 (0.15), residues: 3086 helix: 0.42 (0.18), residues: 844 sheet: 0.47 (0.22), residues: 551 loop : -2.61 (0.13), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 30 HIS 0.008 0.001 HIS C 196 PHE 0.016 0.002 PHE E 336 TYR 0.020 0.002 TYR H 285 ARG 0.006 0.000 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 235 time to evaluate : 2.592 Fit side-chains REVERT: C 111 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8029 (pp) REVERT: C 180 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7223 (pp) REVERT: C 240 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6304 (tt0) REVERT: E 80 ASP cc_start: 0.7646 (m-30) cc_final: 0.7295 (m-30) REVERT: E 120 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7360 (tm-30) REVERT: E 330 LEU cc_start: 0.8610 (pp) cc_final: 0.7997 (mt) REVERT: F 76 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8748 (mt) REVERT: F 128 GLU cc_start: 0.7884 (pp20) cc_final: 0.7015 (pp20) REVERT: F 129 GLN cc_start: 0.7433 (mt0) cc_final: 0.7006 (mt0) REVERT: F 148 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7695 (mt) REVERT: F 338 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: G 271 TYR cc_start: 0.8350 (p90) cc_final: 0.7971 (p90) REVERT: P 35 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7999 (mtt180) REVERT: Q 24 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: B 222 ARG cc_start: 0.3968 (tpt170) cc_final: 0.3546 (ptp90) REVERT: B 259 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6323 (m-80) outliers start: 87 outliers final: 61 residues processed: 303 average time/residue: 0.4470 time to fit residues: 203.0176 Evaluate side-chains 303 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 233 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 22 ASP Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 222 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 256 optimal weight: 30.0000 chunk 170 optimal weight: 0.9980 chunk 303 optimal weight: 0.3980 chunk 190 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN G 223 GLN G 324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27070 Z= 0.192 Angle : 0.563 11.439 37327 Z= 0.297 Chirality : 0.041 0.209 4237 Planarity : 0.004 0.074 4453 Dihedral : 18.977 179.459 5108 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.55 % Favored : 93.42 % Rotamer: Outliers : 2.86 % Allowed : 21.04 % Favored : 76.10 % 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: -1.38 (0.15), residues: 3086 helix: 0.75 (0.18), residues: 843 sheet: 0.63 (0.23), residues: 547 loop : -2.48 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 174 HIS 0.004 0.001 HIS H 324 PHE 0.012 0.001 PHE H 147 TYR 0.016 0.001 TYR H 285 ARG 0.007 0.000 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 244 time to evaluate : 2.885 Fit side-chains REVERT: C 111 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7968 (pp) REVERT: C 180 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7095 (pp) REVERT: C 240 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6190 (tt0) REVERT: E 80 ASP cc_start: 0.7564 (m-30) cc_final: 0.7223 (m-30) REVERT: E 120 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7346 (tm-30) REVERT: E 330 LEU cc_start: 0.8213 (pp) cc_final: 0.7919 (mt) REVERT: F 76 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8619 (mt) REVERT: F 338 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: G 271 TYR cc_start: 0.8224 (p90) cc_final: 0.7901 (p90) REVERT: J 28 LYS cc_start: 0.8014 (pttt) cc_final: 0.7546 (ptpp) REVERT: L 51 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.5468 (ptt-90) REVERT: P 35 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8003 (mtt180) REVERT: Q 24 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: R 66 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8333 (mttt) REVERT: B 222 ARG cc_start: 0.4151 (tpt170) cc_final: 0.3718 (ptp90) REVERT: B 259 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6111 (m-80) outliers start: 67 outliers final: 48 residues processed: 298 average time/residue: 0.4396 time to fit residues: 198.0748 Evaluate side-chains 292 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 235 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27070 Z= 0.229 Angle : 0.581 11.641 37327 Z= 0.306 Chirality : 0.042 0.238 4237 Planarity : 0.004 0.070 4453 Dihedral : 18.964 179.646 5108 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.58 % Favored : 92.38 % Rotamer: Outliers : 2.99 % Allowed : 21.17 % Favored : 75.84 % 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: -1.31 (0.15), residues: 3086 helix: 0.79 (0.18), residues: 845 sheet: 0.68 (0.22), residues: 551 loop : -2.44 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 30 HIS 0.005 0.001 HIS G 256 PHE 0.013 0.001 PHE H 147 TYR 0.017 0.002 TYR H 285 ARG 0.007 0.000 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 240 time to evaluate : 2.725 Fit side-chains REVERT: C 111 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7997 (pp) REVERT: C 180 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7134 (pp) REVERT: C 240 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.6129 (tt0) REVERT: E 80 ASP cc_start: 0.7648 (m-30) cc_final: 0.7311 (m-30) REVERT: E 120 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7382 (tm-30) REVERT: E 330 LEU cc_start: 0.8273 (pp) cc_final: 0.7971 (mt) REVERT: F 76 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8652 (mt) REVERT: F 128 GLU cc_start: 0.7837 (pp20) cc_final: 0.7018 (pp20) REVERT: F 129 GLN cc_start: 0.7285 (mt0) cc_final: 0.6903 (mt0) REVERT: F 338 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: G 271 TYR cc_start: 0.8204 (p90) cc_final: 0.7873 (p90) REVERT: H 270 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.6736 (m-90) REVERT: J 28 LYS cc_start: 0.8023 (pttt) cc_final: 0.7555 (ptpp) REVERT: L 51 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.5571 (ptt-90) REVERT: P 35 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8009 (mtt180) REVERT: Q 24 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: R 66 LYS cc_start: 0.8578 (mtmm) cc_final: 0.8302 (mttt) REVERT: B 222 ARG cc_start: 0.4146 (tpt170) cc_final: 0.3709 (ptp90) REVERT: B 259 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6216 (m-80) outliers start: 70 outliers final: 52 residues processed: 297 average time/residue: 0.4280 time to fit residues: 192.1244 Evaluate side-chains 299 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 237 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 22 ASP Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 270 TRP Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 282 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 chunk 267 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN D 77 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 27070 Z= 0.374 Angle : 0.679 12.750 37327 Z= 0.355 Chirality : 0.046 0.349 4237 Planarity : 0.005 0.067 4453 Dihedral : 19.087 178.108 5108 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.88 % Favored : 91.09 % Rotamer: Outliers : 3.20 % Allowed : 21.13 % Favored : 75.67 % 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: -1.56 (0.15), residues: 3086 helix: 0.47 (0.18), residues: 852 sheet: 0.49 (0.22), residues: 560 loop : -2.55 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 30 HIS 0.007 0.001 HIS G 256 PHE 0.017 0.002 PHE E 336 TYR 0.022 0.002 TYR H 285 ARG 0.008 0.000 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 240 time to evaluate : 2.896 Fit side-chains revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8105 (pp) REVERT: C 180 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7176 (pp) REVERT: C 240 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6322 (tt0) REVERT: E 80 ASP cc_start: 0.7634 (m-30) cc_final: 0.7291 (m-30) REVERT: E 120 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7366 (tm-30) REVERT: E 330 LEU cc_start: 0.8652 (pp) cc_final: 0.8024 (mt) REVERT: F 76 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8770 (mt) REVERT: F 128 GLU cc_start: 0.7882 (pp20) cc_final: 0.7052 (pp20) REVERT: F 129 GLN cc_start: 0.7457 (mt0) cc_final: 0.7004 (mt0) REVERT: F 338 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: G 271 TYR cc_start: 0.8357 (p90) cc_final: 0.7978 (p90) REVERT: H 124 THR cc_start: 0.8232 (t) cc_final: 0.8022 (p) REVERT: H 270 TRP cc_start: 0.8121 (OUTLIER) cc_final: 0.6941 (m-90) REVERT: I 309 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: J 28 LYS cc_start: 0.8054 (pttt) cc_final: 0.7591 (ptpp) REVERT: K 25 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.6890 (ttp-170) REVERT: L 51 ARG cc_start: 0.5825 (OUTLIER) cc_final: 0.5464 (ptt-90) REVERT: P 35 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8020 (mtt180) REVERT: Q 24 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: R 66 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8320 (mttt) REVERT: B 222 ARG cc_start: 0.3952 (tpt170) cc_final: 0.3464 (ptp90) REVERT: B 259 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6255 (m-80) outliers start: 75 outliers final: 56 residues processed: 303 average time/residue: 0.4431 time to fit residues: 200.5178 Evaluate side-chains 304 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 236 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 270 TRP Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 6.9990 chunk 299 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 313 optimal weight: 20.0000 chunk 288 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 193 optimal weight: 0.0010 chunk 153 optimal weight: 3.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 27070 Z= 0.430 Angle : 0.720 13.855 37327 Z= 0.377 Chirality : 0.047 0.382 4237 Planarity : 0.005 0.067 4453 Dihedral : 19.186 176.764 5108 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.43 % Favored : 90.54 % Rotamer: Outliers : 3.03 % Allowed : 21.21 % Favored : 75.76 % 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: -1.77 (0.14), residues: 3086 helix: 0.25 (0.18), residues: 851 sheet: 0.38 (0.22), residues: 561 loop : -2.64 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 30 HIS 0.009 0.001 HIS G 256 PHE 0.019 0.002 PHE E 336 TYR 0.022 0.002 TYR H 285 ARG 0.008 0.001 ARG E 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 243 time to evaluate : 2.598 Fit side-chains REVERT: C 111 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8131 (pp) REVERT: C 180 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7208 (pp) REVERT: C 240 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6476 (tt0) REVERT: E 80 ASP cc_start: 0.7645 (m-30) cc_final: 0.7299 (m-30) REVERT: E 120 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7362 (tm-30) REVERT: F 76 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8817 (mt) REVERT: F 128 GLU cc_start: 0.7871 (pp20) cc_final: 0.7168 (pp20) REVERT: F 129 GLN cc_start: 0.7655 (mt0) cc_final: 0.7133 (mt0) REVERT: F 338 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: G 271 TYR cc_start: 0.8442 (p90) cc_final: 0.8080 (p90) REVERT: H 124 THR cc_start: 0.8268 (t) cc_final: 0.8068 (p) REVERT: H 270 TRP cc_start: 0.8146 (OUTLIER) cc_final: 0.7032 (m-90) REVERT: I 309 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: K 25 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.6931 (ttp-170) REVERT: P 35 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8021 (mtt180) REVERT: Q 24 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7461 (tp30) REVERT: R 66 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8321 (mttt) REVERT: B 222 ARG cc_start: 0.3974 (tpt170) cc_final: 0.3462 (ptp90) REVERT: B 259 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6366 (m-80) outliers start: 71 outliers final: 57 residues processed: 301 average time/residue: 0.4327 time to fit residues: 195.0874 Evaluate side-chains 307 residues out of total 2511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 239 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 22 ASP Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 270 TRP Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 250 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 257 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN J 65 ASN R 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135593 restraints weight = 35301.538| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.52 r_work: 0.3295 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27070 Z= 0.177 Angle : 0.565 11.645 37327 Z= 0.298 Chirality : 0.041 0.232 4237 Planarity : 0.004 0.067 4453 Dihedral : 19.017 179.167 5108 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.64 % Favored : 93.32 % Rotamer: Outliers : 2.82 % Allowed : 21.77 % Favored : 75.42 % 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: -1.31 (0.15), residues: 3086 helix: 0.81 (0.18), residues: 841 sheet: 0.64 (0.22), residues: 550 loop : -2.43 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 147 HIS 0.004 0.001 HIS H 324 PHE 0.012 0.001 PHE H 147 TYR 0.013 0.001 TYR G 271 ARG 0.008 0.000 ARG E 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5188.50 seconds wall clock time: 94 minutes 0.96 seconds (5640.96 seconds total)