Starting phenix.real_space_refine on Fri Aug 9 10:19:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shj_10199/08_2024/6shj_10199_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shj_10199/08_2024/6shj_10199.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/6shj_10199/08_2024/6shj_10199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shj_10199/08_2024/6shj_10199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shj_10199/08_2024/6shj_10199_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shj_10199/08_2024/6shj_10199_trim.cif" } 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= 0.001 sd= 0.129 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 82 5.16 5 C 8240 2.51 5 N 2310 2.21 5 O 2462 1.98 5 H 12832 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 219": "OD1" <-> "OD2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 430": "OE1" <-> "OE2" Residue "A ASP 35": "OD1" <-> "OD2" Residue "A ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 386": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 419": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 219": "OD1" <-> "OD2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 430": "OE1" <-> "OE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 142": "OD1" <-> "OD2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C ASP 243": "OD1" <-> "OD2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 386": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 419": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25934 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 6462 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 6420 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 416, 6420 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 6443 Chain: "A" Number of atoms: 6465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6465 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 6462 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 6420 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 416, 6420 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 6443 Chain: "C" Number of atoms: 6465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6465 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.76, per 1000 atoms: 0.65 Number of scatterers: 25934 At special positions: 0 Unit cell: (107.841, 107.841, 100.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 82 16.00 P 8 15.00 O 2462 8.00 N 2310 7.00 C 8240 6.00 H 12832 1.00 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: 20.70 Conformation dependent library (CDL) restraints added in 4.5 seconds 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3128 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 21.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'D' and resid 13 through 18 Proline residue: D 17 - end of helix No H-bonds generated for 'chain 'D' and resid 13 through 18' Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 54 through 63 removed outlier: 3.727A pdb=" N CYS D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 86 Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 125 through 131 removed outlier: 3.569A pdb=" N ARG D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR D 131 " --> pdb=" O ILE D 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 131' Processing helix chain 'D' and resid 150 through 159 removed outlier: 3.515A pdb=" N ILE D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 221 through 231 removed outlier: 3.554A pdb=" N GLU D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 251 removed outlier: 4.008A pdb=" N GLU D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 280 through 288 Processing helix chain 'D' and resid 419 through 425 removed outlier: 3.714A pdb=" N ARG D 423 " --> pdb=" O ARG D 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 18 No H-bonds generated for 'chain 'A' and resid 15 through 18' Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 53 through 63 removed outlier: 4.158A pdb=" N ALA A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 117 through 123 removed outlier: 4.094A pdb=" N THR A 122 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 123 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.774A pdb=" N TYR A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.643A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.850A pdb=" N ASN A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 419 through 425 removed outlier: 3.829A pdb=" N LYS A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 425 " --> pdb=" O MET A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 Proline residue: B 17 - end of helix No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.727A pdb=" N CYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 125 through 131 removed outlier: 3.569A pdb=" N ARG B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 131' Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.514A pdb=" N ILE B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 221 through 231 removed outlier: 3.554A pdb=" N GLU B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 removed outlier: 4.008A pdb=" N GLU B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 280 through 288 Processing helix chain 'B' and resid 419 through 425 removed outlier: 3.715A pdb=" N ARG B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 53 through 63 removed outlier: 4.158A pdb=" N ALA C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'C' and resid 117 through 123 removed outlier: 4.094A pdb=" N THR C 122 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN C 123 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.773A pdb=" N TYR C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.643A pdb=" N ALA C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.850A pdb=" N ASN C 287 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 406 Processing helix chain 'C' and resid 419 through 425 removed outlier: 3.830A pdb=" N LYS C 424 " --> pdb=" O GLU C 420 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU C 425 " --> pdb=" O MET C 421 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.77 Time building geometry restraints manager: 21.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.91: 2914 0.91 - 1.14: 9880 1.14 - 1.36: 4496 1.36 - 1.58: 8780 1.58 - 1.81: 136 Bond restraints: 26206 Sorted by residual: bond pdb=" CE1 PHE C 91 " pdb=" HE1 PHE C 91 " ideal model delta sigma weight residual 0.930 1.155 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" CE1 PHE A 91 " pdb=" HE1 PHE A 91 " ideal model delta sigma weight residual 0.930 1.155 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" ND2 ASN C 96 " pdb="HD22 ASN C 96 " ideal model delta sigma weight residual 0.860 1.070 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" ND2 ASN A 96 " pdb="HD22 ASN A 96 " ideal model delta sigma weight residual 0.860 1.069 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C5 FBP A 501 " pdb=" O5 FBP A 501 " ideal model delta sigma weight residual 1.608 1.407 0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 26201 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.66: 496 105.66 - 113.29: 30639 113.29 - 120.92: 9613 120.92 - 128.55: 6423 128.55 - 136.19: 139 Bond angle restraints: 47310 Sorted by residual: angle pdb=" N HIS A 78 " pdb=" CA HIS A 78 " pdb=" C HIS A 78 " ideal model delta sigma weight residual 113.97 102.99 10.98 1.28e+00 6.10e-01 7.36e+01 angle pdb=" N HIS C 78 " pdb=" CA HIS C 78 " pdb=" C HIS C 78 " ideal model delta sigma weight residual 113.97 103.00 10.97 1.28e+00 6.10e-01 7.35e+01 angle pdb=" C TYR A 75 " pdb=" N GLN A 76 " pdb=" CA GLN A 76 " ideal model delta sigma weight residual 121.54 136.19 -14.65 1.91e+00 2.74e-01 5.88e+01 angle pdb=" C TYR C 75 " pdb=" N GLN C 76 " pdb=" CA GLN C 76 " ideal model delta sigma weight residual 121.54 136.14 -14.60 1.91e+00 2.74e-01 5.84e+01 angle pdb=" C TYR C 75 " pdb=" CA TYR C 75 " pdb=" CB TYR C 75 " ideal model delta sigma weight residual 110.19 123.90 -13.71 2.18e+00 2.10e-01 3.96e+01 ... (remaining 47305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 10805 16.53 - 33.06: 1180 33.06 - 49.58: 325 49.58 - 66.11: 110 66.11 - 82.64: 14 Dihedral angle restraints: 12434 sinusoidal: 6834 harmonic: 5600 Sorted by residual: dihedral pdb=" CG PHE A 91 " pdb=" CD1 PHE A 91 " pdb=" CE1 PHE A 91 " pdb=" HE1 PHE A 91 " ideal model delta harmonic sigma weight residual 180.00 133.77 46.23 0 5.00e+00 4.00e-02 8.55e+01 dihedral pdb=" CG PHE C 91 " pdb=" CD1 PHE C 91 " pdb=" CE1 PHE C 91 " pdb=" HE1 PHE C 91 " ideal model delta harmonic sigma weight residual 180.00 133.81 46.19 0 5.00e+00 4.00e-02 8.54e+01 dihedral pdb=" CG HIS D 83 " pdb=" ND1 HIS D 83 " pdb=" CE1 HIS D 83 " pdb=" HE1 HIS D 83 " ideal model delta harmonic sigma weight residual 180.00 139.11 40.89 0 5.00e+00 4.00e-02 6.69e+01 ... (remaining 12431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1856 0.116 - 0.232: 126 0.232 - 0.348: 24 0.348 - 0.465: 0 0.465 - 0.581: 6 Chirality restraints: 2012 Sorted by residual: chirality pdb=" CA ARG B 232 " pdb=" N ARG B 232 " pdb=" C ARG B 232 " pdb=" CB ARG B 232 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CA ARG D 232 " pdb=" N ARG D 232 " pdb=" C ARG D 232 " pdb=" CB ARG D 232 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.41e+00 chirality pdb=" CA TYR A 75 " pdb=" N TYR A 75 " pdb=" C TYR A 75 " pdb=" CB TYR A 75 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.73e+00 ... (remaining 2009 not shown) Planarity restraints: 3940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 91 " 0.053 2.00e-02 2.50e+03 1.62e-01 7.85e+02 pdb=" CG PHE A 91 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE A 91 " -0.140 2.00e-02 2.50e+03 pdb=" CD2 PHE A 91 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 91 " -0.228 2.00e-02 2.50e+03 pdb=" CE2 PHE A 91 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 91 " -0.088 2.00e-02 2.50e+03 pdb=" HD1 PHE A 91 " -0.110 2.00e-02 2.50e+03 pdb=" HD2 PHE A 91 " 0.084 2.00e-02 2.50e+03 pdb=" HE1 PHE A 91 " 0.450 2.00e-02 2.50e+03 pdb=" HE2 PHE A 91 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 91 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 91 " -0.053 2.00e-02 2.50e+03 1.62e-01 7.85e+02 pdb=" CG PHE C 91 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE C 91 " 0.140 2.00e-02 2.50e+03 pdb=" CD2 PHE C 91 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE C 91 " 0.228 2.00e-02 2.50e+03 pdb=" CE2 PHE C 91 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE C 91 " 0.088 2.00e-02 2.50e+03 pdb=" HD1 PHE C 91 " 0.110 2.00e-02 2.50e+03 pdb=" HD2 PHE C 91 " -0.084 2.00e-02 2.50e+03 pdb=" HE1 PHE C 91 " -0.450 2.00e-02 2.50e+03 pdb=" HE2 PHE C 91 " 0.009 2.00e-02 2.50e+03 pdb=" HZ PHE C 91 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 96 " -0.122 2.00e-02 2.50e+03 2.04e-01 6.24e+02 pdb=" CG ASN C 96 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN C 96 " 0.146 2.00e-02 2.50e+03 pdb=" ND2 ASN C 96 " -0.304 2.00e-02 2.50e+03 pdb="HD21 ASN C 96 " -0.102 2.00e-02 2.50e+03 pdb="HD22 ASN C 96 " 0.328 2.00e-02 2.50e+03 ... (remaining 3937 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1650 2.19 - 2.79: 52958 2.79 - 3.39: 70899 3.39 - 4.00: 97597 4.00 - 4.60: 152816 Nonbonded interactions: 375920 Sorted by model distance: nonbonded pdb=" O GLN A 76 " pdb="HE21 GLN A 76 " model vdw 1.585 2.450 nonbonded pdb=" O GLN C 76 " pdb="HE21 GLN C 76 " model vdw 1.585 2.450 nonbonded pdb=" O ASN C 60 " pdb=" HG SER C 64 " model vdw 1.677 2.450 nonbonded pdb=" O ASN A 60 " pdb=" HG SER A 64 " model vdw 1.678 2.450 nonbonded pdb=" HZ2 LYS C 146 " pdb=" O ASP C 298 " model vdw 1.686 2.450 ... (remaining 375915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 13 or resid 15 through 28 or resid 30 through 1 \ 05 or (resid 106 through 107 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or (resid 115 and (name N or name CA or name C or nam \ e O or name CB or name HA )) or resid 116 through 431 or resid 501)) selection = (chain 'B' and (resid 10 through 13 or resid 15 through 28 or resid 30 through 9 \ 2 or (resid 93 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 94 through 107 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB or name HA )) or resid 116 through 431 or resid 501)) selection = (chain 'C' and (resid 10 through 13 or resid 15 through 28 or resid 30 through 1 \ 05 or (resid 106 through 107 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or (resid 115 and (name N or name CA or name C or nam \ e O or name CB or name HA )) or resid 116 through 431 or resid 501)) selection = (chain 'D' and (resid 10 through 13 or resid 15 through 28 or resid 30 through 9 \ 2 or (resid 93 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 94 through 107 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB or name HA )) or resid 116 through 431 or resid 501)) } 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=0.50 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.390 Extract box with map and model: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 88.800 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.120 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 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 : 0.010 0.201 13374 Z= 0.634 Angle : 1.036 14.648 18150 Z= 0.602 Chirality : 0.074 0.581 2012 Planarity : 0.011 0.072 2364 Dihedral : 14.699 82.640 5078 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.98 % Favored : 92.90 % Rotamer: Outliers : 3.58 % Allowed : 7.15 % Favored : 89.27 % Cbeta Deviations : 0.38 % 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: -4.39 (0.16), residues: 1652 helix: -3.63 (0.17), residues: 404 sheet: -3.63 (0.25), residues: 256 loop : -2.43 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.008 TRP A 274 HIS 0.045 0.009 HIS C 238 PHE 0.096 0.011 PHE C 218 TYR 0.079 0.009 TYR B 224 ARG 0.082 0.008 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 291 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7044 (mp0) REVERT: D 134 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: D 375 ARG cc_start: 0.6869 (ttm-80) cc_final: 0.6416 (ttm110) REVERT: D 421 MET cc_start: 0.7609 (mtt) cc_final: 0.7332 (mtt) REVERT: D 430 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6874 (mm-30) REVERT: A 18 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7889 (mt) REVERT: A 78 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.7085 (t70) REVERT: A 100 ASP cc_start: 0.6875 (t0) cc_final: 0.6113 (t70) REVERT: A 134 GLU cc_start: 0.6565 (tp30) cc_final: 0.6078 (mm-30) REVERT: A 174 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8772 (pt0) REVERT: A 213 MET cc_start: 0.8206 (mtp) cc_final: 0.7982 (mtp) REVERT: A 408 TYR cc_start: 0.6469 (t80) cc_final: 0.6258 (t80) REVERT: A 430 GLU cc_start: 0.7071 (tt0) cc_final: 0.6518 (tm-30) REVERT: B 100 ASP cc_start: 0.7040 (t70) cc_final: 0.6688 (t70) REVERT: B 298 ASP cc_start: 0.7699 (t0) cc_final: 0.7379 (t0) REVERT: B 328 MET cc_start: 0.6161 (mtm) cc_final: 0.5954 (mtp) REVERT: B 394 MET cc_start: 0.7270 (ttm) cc_final: 0.6630 (ttm) REVERT: B 421 MET cc_start: 0.7418 (mtt) cc_final: 0.7217 (mtt) REVERT: B 430 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: C 18 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7660 (mt) REVERT: C 78 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7317 (t70) REVERT: C 100 ASP cc_start: 0.6939 (t0) cc_final: 0.5950 (t70) REVERT: C 242 LYS cc_start: 0.8183 (mttt) cc_final: 0.7979 (mtpp) REVERT: C 352 SER cc_start: 0.6392 (OUTLIER) cc_final: 0.6123 (p) REVERT: C 428 LYS cc_start: 0.7811 (tptt) cc_final: 0.7602 (tppt) REVERT: C 430 GLU cc_start: 0.6800 (tt0) cc_final: 0.6394 (tm-30) outliers start: 46 outliers final: 29 residues processed: 329 average time/residue: 0.7227 time to fit residues: 321.2896 Evaluate side-chains 222 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 406 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 128 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: