Starting phenix.real_space_refine on Wed Mar 20 00:56:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shj_10199/03_2024/6shj_10199_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shj_10199/03_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_10199/03_2024/6shj_10199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shj_10199/03_2024/6shj_10199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shj_10199/03_2024/6shj_10199_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shj_10199/03_2024/6shj_10199_trim_updated.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= 0.001 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 14.67, per 1000 atoms: 0.57 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: 19.24 Conformation dependent library (CDL) restraints added in 3.7 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... running ksdssp... Secondary structure from input PDB file: 54 helices and 24 sheets defined 21.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 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) Processing sheet with id= A, first strand: chain 'D' and resid 98 through 100 removed outlier: 7.308A pdb=" N SER D 20 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLY D 70 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA D 22 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR D 135 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU D 23 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL D 137 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS D 167 " --> pdb=" O HIS D 257 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 167 through 171 Processing sheet with id= C, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.696A pdb=" N GLU D 191 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 317 through 319 Processing sheet with id= E, first strand: chain 'D' and resid 361 through 363 Processing sheet with id= F, first strand: chain 'D' and resid 365 through 367 removed outlier: 6.830A pdb=" N CYS D 382 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL D 415 " --> pdb=" O VAL D 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 98 through 103 removed outlier: 7.236A pdb=" N SER A 20 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLY A 70 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA A 22 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 72 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE A 24 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 135 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU A 23 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 137 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 168 through 171 Processing sheet with id= I, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= J, first strand: chain 'A' and resid 361 through 363 Processing sheet with id= K, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.635A pdb=" N CYS A 382 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 415 " --> pdb=" O VAL A 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 180 through 183 Processing sheet with id= M, first strand: chain 'B' and resid 98 through 100 removed outlier: 7.308A pdb=" N SER B 20 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N GLY B 70 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA B 22 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR B 135 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU B 23 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 137 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU B 25 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU B 139 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS B 167 " --> pdb=" O HIS B 257 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 167 through 171 Processing sheet with id= O, first strand: chain 'B' and resid 179 through 182 removed outlier: 3.696A pdb=" N GLU B 191 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= Q, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= R, first strand: chain 'B' and resid 365 through 367 removed outlier: 6.831A pdb=" N CYS B 382 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 415 " --> pdb=" O VAL B 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 98 through 103 removed outlier: 7.235A pdb=" N SER C 20 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N GLY C 70 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 22 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE C 72 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE C 24 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR C 135 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU C 23 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C 137 " --> pdb=" O LEU C 23 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 168 through 171 Processing sheet with id= U, first strand: chain 'C' and resid 317 through 319 Processing sheet with id= V, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= W, first strand: chain 'C' and resid 365 through 367 removed outlier: 6.635A pdb=" N CYS C 382 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 415 " --> pdb=" O VAL C 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'C' and resid 180 through 183 214 hydrogen bonds defined for protein. 606 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: 9.40 Time building geometry restraints manager: 20.01 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: 1570 2.19 - 2.79: 52938 2.79 - 3.39: 70799 3.39 - 4.00: 97381 4.00 - 4.60: 152732 Nonbonded interactions: 375420 Sorted by model distance: nonbonded pdb=" O GLN A 76 " pdb="HE21 GLN A 76 " model vdw 1.585 1.850 nonbonded pdb=" O GLN C 76 " pdb="HE21 GLN C 76 " model vdw 1.585 1.850 nonbonded pdb=" O ASN C 60 " pdb=" HG SER C 64 " model vdw 1.677 1.850 nonbonded pdb=" O ASN A 60 " pdb=" HG SER A 64 " model vdw 1.678 1.850 nonbonded pdb=" HZ2 LYS C 146 " pdb=" O ASP C 298 " model vdw 1.686 1.850 ... (remaining 375415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 0.430 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: 0.360 Extract box with map and model: 3.130 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 84.730 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.660 ------------------------------------------------------------------------------- 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= 0.651 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 : 1.895 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: 0.7076 time to fit residues: 312.9190 Evaluate side-chains 222 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 2.081 ------------------------------------------------------------------------------- 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: 0.8980 chunk 124 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN A 78 HIS A 429 GLN B 147 GLN B 303 ASN B 429 GLN C 265 GLN C 303 ASN C 310 ASN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13374 Z= 0.167 Angle : 0.563 6.002 18150 Z= 0.293 Chirality : 0.045 0.148 2012 Planarity : 0.006 0.069 2364 Dihedral : 10.151 71.618 2059 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.29 % Allowed : 13.66 % Favored : 83.05 % 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: -3.53 (0.18), residues: 1652 helix: -2.78 (0.20), residues: 412 sheet: -3.06 (0.29), residues: 212 loop : -2.04 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 284 HIS 0.005 0.001 HIS B 78 PHE 0.008 0.001 PHE B 218 TYR 0.025 0.001 TYR C 75 ARG 0.005 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 2 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 241 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 1.830 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: D 134 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6835 (mt-10) REVERT: D 250 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7960 (mm-30) REVERT: D 302 ARG cc_start: 0.7453 (ptm-80) cc_final: 0.6952 (mmt-90) REVERT: D 421 MET cc_start: 0.7331 (mtt) cc_final: 0.6944 (mtt) REVERT: D 430 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6907 (mm-30) REVERT: A 18 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7915 (mt) REVERT: A 39 LYS cc_start: 0.7991 (tppp) cc_final: 0.7774 (tppp) REVERT: A 78 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.7090 (t70) REVERT: A 100 ASP cc_start: 0.6916 (t0) cc_final: 0.6427 (t0) REVERT: A 134 GLU cc_start: 0.6651 (tp30) cc_final: 0.6174 (mm-30) REVERT: A 135 TYR cc_start: 0.6919 (m-80) cc_final: 0.6645 (m-80) REVERT: A 174 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8681 (pt0) REVERT: A 399 ASN cc_start: 0.7587 (t0) cc_final: 0.7317 (t0) REVERT: A 430 GLU cc_start: 0.7012 (tt0) cc_final: 0.6609 (tm-30) REVERT: B 93 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7053 (mp0) REVERT: B 298 ASP cc_start: 0.7670 (t0) cc_final: 0.7280 (t0) REVERT: B 328 MET cc_start: 0.6074 (mtm) cc_final: 0.5848 (mtp) REVERT: B 394 MET cc_start: 0.7087 (ttm) cc_final: 0.6494 (ttm) REVERT: B 421 MET cc_start: 0.7229 (mtt) cc_final: 0.6932 (mtt) REVERT: B 430 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: C 18 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7567 (mt) REVERT: C 32 ARG cc_start: 0.7596 (mtm-85) cc_final: 0.7387 (mtm180) REVERT: C 39 LYS cc_start: 0.7828 (tppp) cc_final: 0.7619 (tppp) REVERT: C 100 ASP cc_start: 0.6867 (t0) cc_final: 0.6116 (t0) REVERT: C 378 ARG cc_start: 0.6270 (mtm-85) cc_final: 0.6046 (mtm180) REVERT: C 421 MET cc_start: 0.7196 (ttm) cc_final: 0.6395 (mtp) REVERT: C 430 GLU cc_start: 0.6515 (tt0) cc_final: 0.6242 (tm-30) outliers start: 42 outliers final: 29 residues processed: 225 average time/residue: 0.6929 time to fit residues: 216.9700 Evaluate side-chains 220 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 1.958 ------------------------------------------------------------------------------- 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 190 ILE Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 418 THR 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 164 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 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 235 ASN 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 80 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN D 303 ASN A 331 ASN B 76 GLN B 265 GLN B 303 ASN C 303 ASN C 331 ASN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5636 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13374 Z= 0.274 Angle : 0.543 5.006 18150 Z= 0.284 Chirality : 0.046 0.178 2012 Planarity : 0.005 0.044 2364 Dihedral : 8.908 65.151 2039 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.43 % Allowed : 14.23 % Favored : 82.33 % 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: -3.12 (0.18), residues: 1652 helix: -2.17 (0.23), residues: 402 sheet: -2.90 (0.29), residues: 232 loop : -1.85 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 88 HIS 0.004 0.001 HIS C 78 PHE 0.013 0.001 PHE A 259 TYR 0.025 0.001 TYR C 75 ARG 0.003 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 3 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 236 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 192 time to evaluate : 2.194 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: D 93 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7131 (mp0) REVERT: D 100 ASP cc_start: 0.6816 (t70) cc_final: 0.6608 (t70) REVERT: D 123 GLN cc_start: 0.7020 (mm-40) cc_final: 0.6646 (mt0) REVERT: D 134 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6851 (mt-10) REVERT: D 190 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8038 (pt) REVERT: D 250 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7985 (mm-30) REVERT: D 421 MET cc_start: 0.7239 (mtt) cc_final: 0.6942 (mtt) REVERT: D 430 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7021 (mm-30) REVERT: A 18 LEU cc_start: 0.8247 (mp) cc_final: 0.7923 (mt) REVERT: A 100 ASP cc_start: 0.7001 (t0) cc_final: 0.6371 (t0) REVERT: A 108 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.6933 (mtm) REVERT: A 134 GLU cc_start: 0.6731 (tp30) cc_final: 0.6370 (mm-30) REVERT: A 151 ARG cc_start: 0.5551 (OUTLIER) cc_final: 0.5192 (tpp80) REVERT: A 174 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8658 (pt0) REVERT: A 213 MET cc_start: 0.8377 (mtp) cc_final: 0.8128 (mtp) REVERT: A 355 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.5852 (ttt90) REVERT: A 430 GLU cc_start: 0.6963 (tt0) cc_final: 0.6653 (tm-30) REVERT: B 93 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7082 (mp0) REVERT: B 134 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6532 (mt-10) REVERT: B 253 LEU cc_start: 0.7793 (mt) cc_final: 0.7565 (mp) REVERT: B 298 ASP cc_start: 0.7741 (t0) cc_final: 0.7361 (t0) REVERT: B 328 MET cc_start: 0.6154 (mtm) cc_final: 0.5921 (mtp) REVERT: B 430 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: C 100 ASP cc_start: 0.7060 (t0) cc_final: 0.6375 (t0) REVERT: C 108 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6827 (mtm) REVERT: C 430 GLU cc_start: 0.6538 (tt0) cc_final: 0.6290 (tm-30) outliers start: 44 outliers final: 27 residues processed: 223 average time/residue: 0.6992 time to fit residues: 211.5549 Evaluate side-chains 210 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 20 SER 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 164 THR Chi-restraints excluded: chain C residue 225 GLU 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 424 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN D 265 GLN D 303 ASN ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13374 Z= 0.160 Angle : 0.494 4.858 18150 Z= 0.255 Chirality : 0.044 0.139 2012 Planarity : 0.004 0.041 2364 Dihedral : 8.151 59.537 2025 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.93 % Allowed : 15.45 % Favored : 81.62 % 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: -2.80 (0.19), residues: 1652 helix: -1.93 (0.24), residues: 414 sheet: -2.59 (0.31), residues: 222 loop : -1.67 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 284 HIS 0.003 0.001 HIS A 78 PHE 0.008 0.001 PHE C 259 TYR 0.022 0.001 TYR C 75 ARG 0.003 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 4 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 224 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 1.907 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: D 93 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7111 (mp0) REVERT: D 123 GLN cc_start: 0.7013 (mm-40) cc_final: 0.6635 (mt0) REVERT: D 134 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6687 (mt-10) REVERT: D 250 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8005 (mm-30) REVERT: D 421 MET cc_start: 0.7285 (mtt) cc_final: 0.6834 (mtt) REVERT: D 430 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6931 (mm-30) REVERT: A 108 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7352 (mtm) REVERT: A 134 GLU cc_start: 0.6712 (tp30) cc_final: 0.6381 (mm-30) REVERT: A 151 ARG cc_start: 0.5541 (OUTLIER) cc_final: 0.5195 (tpp80) REVERT: A 174 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8615 (pt0) REVERT: A 213 MET cc_start: 0.8364 (mtp) cc_final: 0.8112 (mtp) REVERT: A 355 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.5736 (ttt90) REVERT: A 430 GLU cc_start: 0.6909 (tt0) cc_final: 0.6650 (tm-30) REVERT: B 93 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7077 (mp0) REVERT: B 134 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6520 (mt-10) REVERT: B 298 ASP cc_start: 0.7744 (t0) cc_final: 0.7368 (t0) REVERT: B 421 MET cc_start: 0.7162 (mtt) cc_final: 0.6857 (mtt) REVERT: B 430 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7185 (mm-30) REVERT: C 100 ASP cc_start: 0.6931 (t0) cc_final: 0.6204 (t0) REVERT: C 186 ASN cc_start: 0.7882 (m-40) cc_final: 0.7593 (m-40) outliers start: 37 outliers final: 26 residues processed: 212 average time/residue: 0.7163 time to fit residues: 211.2375 Evaluate side-chains 214 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 2.369 ------------------------------------------------------------------------------- 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 235 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 235 ASN 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 20 SER 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN D 147 GLN D 303 ASN D 357 ASN D 429 GLN ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 357 ASN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13374 Z= 0.350 Angle : 0.545 4.929 18150 Z= 0.286 Chirality : 0.047 0.139 2012 Planarity : 0.005 0.063 2364 Dihedral : 7.813 59.818 2012 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.29 % Allowed : 15.88 % Favored : 80.83 % 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: -2.81 (0.19), residues: 1652 helix: -1.96 (0.24), residues: 410 sheet: -2.58 (0.31), residues: 240 loop : -1.63 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 284 HIS 0.004 0.001 HIS A 78 PHE 0.010 0.001 PHE A 318 TYR 0.024 0.002 TYR C 75 ARG 0.008 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 5 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 227 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 185 time to evaluate : 2.075 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: D 134 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6618 (mt-10) REVERT: D 250 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8007 (mm-30) REVERT: D 421 MET cc_start: 0.7136 (mtt) cc_final: 0.6837 (mtt) REVERT: D 430 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: A 108 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7506 (mtm) REVERT: A 134 GLU cc_start: 0.6823 (tp30) cc_final: 0.6516 (mm-30) REVERT: A 151 ARG cc_start: 0.5571 (OUTLIER) cc_final: 0.5200 (tpp80) REVERT: A 174 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8596 (pt0) REVERT: A 213 MET cc_start: 0.8299 (mtp) cc_final: 0.8028 (mtp) REVERT: A 328 MET cc_start: 0.5911 (mtt) cc_final: 0.5554 (mtt) REVERT: A 355 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6129 (ttt90) REVERT: A 424 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7430 (mptm) REVERT: A 430 GLU cc_start: 0.6933 (tt0) cc_final: 0.6717 (tm-30) REVERT: B 134 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6608 (mt-10) REVERT: B 253 LEU cc_start: 0.7800 (mt) cc_final: 0.7587 (mp) REVERT: B 298 ASP cc_start: 0.7738 (t0) cc_final: 0.7380 (t0) REVERT: B 430 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7187 (mm-30) REVERT: C 424 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7418 (mptm) outliers start: 42 outliers final: 28 residues processed: 216 average time/residue: 0.6994 time to fit residues: 205.0679 Evaluate side-chains 212 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU 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 424 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN A 235 ASN ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5639 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13374 Z= 0.268 Angle : 0.515 4.636 18150 Z= 0.269 Chirality : 0.045 0.136 2012 Planarity : 0.004 0.057 2364 Dihedral : 7.664 59.695 2012 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.22 % Allowed : 16.17 % Favored : 80.62 % 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: -2.68 (0.19), residues: 1652 helix: -1.83 (0.24), residues: 410 sheet: -2.47 (0.31), residues: 240 loop : -1.57 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 284 HIS 0.003 0.001 HIS A 78 PHE 0.007 0.001 PHE A 91 TYR 0.021 0.001 TYR C 75 ARG 0.008 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 6 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 225 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 1.983 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: D 134 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6596 (mt-10) REVERT: D 250 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7990 (mm-30) REVERT: D 421 MET cc_start: 0.7135 (mtt) cc_final: 0.6834 (mtt) REVERT: D 430 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7100 (mm-30) REVERT: A 108 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7550 (mtm) REVERT: A 134 GLU cc_start: 0.6845 (tp30) cc_final: 0.6539 (mm-30) REVERT: A 151 ARG cc_start: 0.5551 (OUTLIER) cc_final: 0.5209 (tpp80) REVERT: A 174 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8514 (pt0) REVERT: A 213 MET cc_start: 0.8352 (mtp) cc_final: 0.8091 (mtp) REVERT: A 328 MET cc_start: 0.5912 (mtt) cc_final: 0.5538 (mtt) REVERT: A 355 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.5800 (ttt90) REVERT: A 424 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7417 (mptm) REVERT: B 134 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6571 (mt-10) REVERT: B 298 ASP cc_start: 0.7733 (t0) cc_final: 0.7382 (t0) REVERT: B 430 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: C 424 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7415 (mptm) outliers start: 41 outliers final: 30 residues processed: 212 average time/residue: 0.6986 time to fit residues: 201.1619 Evaluate side-chains 215 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5625 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13374 Z= 0.175 Angle : 0.490 4.730 18150 Z= 0.253 Chirality : 0.044 0.134 2012 Planarity : 0.004 0.060 2364 Dihedral : 7.376 59.997 2012 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.15 % Allowed : 16.74 % Favored : 80.11 % 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: -2.46 (0.19), residues: 1652 helix: -1.55 (0.25), residues: 412 sheet: -2.22 (0.33), residues: 226 loop : -1.53 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 284 HIS 0.002 0.001 HIS A 46 PHE 0.008 0.001 PHE A 56 TYR 0.024 0.001 TYR C 75 ARG 0.009 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 7 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 229 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 189 time to evaluate : 2.256 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: D 134 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6612 (mt-10) REVERT: D 190 ILE cc_start: 0.8602 (tp) cc_final: 0.8400 (tp) REVERT: D 250 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7974 (mm-30) REVERT: D 421 MET cc_start: 0.7183 (mtt) cc_final: 0.6880 (mtt) REVERT: A 108 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7308 (mtm) REVERT: A 134 GLU cc_start: 0.6809 (tp30) cc_final: 0.6485 (mm-30) REVERT: A 151 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.5197 (tpp80) REVERT: A 174 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8476 (pt0) REVERT: A 213 MET cc_start: 0.8421 (mtp) cc_final: 0.7904 (mtp) REVERT: A 328 MET cc_start: 0.5896 (mtt) cc_final: 0.5443 (mtt) REVERT: A 355 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.5761 (ttt90) REVERT: A 424 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7423 (mptm) REVERT: B 134 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6545 (mt-10) REVERT: B 298 ASP cc_start: 0.7722 (t0) cc_final: 0.7370 (t0) REVERT: B 421 MET cc_start: 0.7214 (mtt) cc_final: 0.6906 (mtt) REVERT: C 424 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7373 (mptm) outliers start: 40 outliers final: 28 residues processed: 219 average time/residue: 0.7286 time to fit residues: 221.5386 Evaluate side-chains 211 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13374 Z= 0.157 Angle : 0.478 4.452 18150 Z= 0.247 Chirality : 0.044 0.133 2012 Planarity : 0.004 0.059 2364 Dihedral : 7.038 59.814 2006 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.65 % Allowed : 17.38 % Favored : 79.97 % 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: -2.25 (0.20), residues: 1652 helix: -1.21 (0.26), residues: 414 sheet: -2.12 (0.33), residues: 222 loop : -1.47 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 284 HIS 0.002 0.000 HIS C 46 PHE 0.008 0.001 PHE A 192 TYR 0.020 0.001 TYR C 75 ARG 0.010 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 8 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 219 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 2.029 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: D 134 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6598 (mt-10) REVERT: D 250 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7973 (mm-30) REVERT: D 421 MET cc_start: 0.7192 (mtt) cc_final: 0.6890 (mtt) REVERT: A 134 GLU cc_start: 0.6815 (tp30) cc_final: 0.6484 (mm-30) REVERT: A 151 ARG cc_start: 0.5535 (OUTLIER) cc_final: 0.5196 (tpp80) REVERT: A 174 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8469 (pt0) REVERT: A 213 MET cc_start: 0.8411 (mtp) cc_final: 0.7903 (mtp) REVERT: A 328 MET cc_start: 0.5905 (mtt) cc_final: 0.5443 (mtt) REVERT: A 355 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.5767 (ttt90) REVERT: B 134 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6525 (mt-10) REVERT: B 190 ILE cc_start: 0.8253 (mm) cc_final: 0.7930 (mm) REVERT: B 298 ASP cc_start: 0.7738 (t0) cc_final: 0.7391 (t0) REVERT: B 421 MET cc_start: 0.7218 (mtt) cc_final: 0.6905 (mtt) REVERT: C 186 ASN cc_start: 0.8029 (m-40) cc_final: 0.7743 (m-40) REVERT: C 424 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7319 (mptm) outliers start: 33 outliers final: 27 residues processed: 209 average time/residue: 0.7260 time to fit residues: 208.1064 Evaluate side-chains 212 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN C 235 ASN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5628 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13374 Z= 0.210 Angle : 0.488 4.729 18150 Z= 0.252 Chirality : 0.045 0.133 2012 Planarity : 0.004 0.061 2364 Dihedral : 6.922 59.811 2003 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.72 % Allowed : 17.53 % Favored : 79.76 % 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: -2.18 (0.20), residues: 1652 helix: -1.21 (0.26), residues: 412 sheet: -2.00 (0.33), residues: 230 loop : -1.41 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 284 HIS 0.002 0.001 HIS A 78 PHE 0.007 0.001 PHE A 192 TYR 0.022 0.001 TYR C 75 ARG 0.011 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 9 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 216 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 2.162 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: D 134 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6606 (mt-10) REVERT: D 250 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7968 (mm-30) REVERT: D 421 MET cc_start: 0.7186 (mtt) cc_final: 0.6879 (mtt) REVERT: A 134 GLU cc_start: 0.6925 (tp30) cc_final: 0.6573 (mm-30) REVERT: A 151 ARG cc_start: 0.5547 (OUTLIER) cc_final: 0.5196 (tpp80) REVERT: A 174 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8483 (pt0) REVERT: A 213 MET cc_start: 0.8389 (mtp) cc_final: 0.7876 (mtp) REVERT: A 328 MET cc_start: 0.5888 (mtt) cc_final: 0.5453 (mtt) REVERT: A 355 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5795 (ttt90) REVERT: A 424 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7368 (mptm) REVERT: B 134 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6491 (mt-10) REVERT: B 190 ILE cc_start: 0.8255 (mm) cc_final: 0.7923 (mm) REVERT: B 298 ASP cc_start: 0.7699 (t0) cc_final: 0.7326 (t0) REVERT: B 429 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6706 (mp-120) REVERT: C 186 ASN cc_start: 0.8044 (m-40) cc_final: 0.7752 (m-40) REVERT: C 424 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7315 (mptm) outliers start: 34 outliers final: 28 residues processed: 207 average time/residue: 0.7243 time to fit residues: 206.0116 Evaluate side-chains 213 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU 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 100 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 163 optimal weight: 0.0670 chunk 150 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN A 235 ASN ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN C 235 ASN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13374 Z= 0.192 Angle : 0.482 4.496 18150 Z= 0.248 Chirality : 0.044 0.131 2012 Planarity : 0.004 0.060 2364 Dihedral : 6.822 59.844 2003 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.79 % Allowed : 17.31 % Favored : 79.90 % 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: -2.08 (0.20), residues: 1652 helix: -1.04 (0.26), residues: 412 sheet: -1.91 (0.34), residues: 230 loop : -1.39 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 284 HIS 0.003 0.001 HIS A 78 PHE 0.007 0.001 PHE A 192 TYR 0.019 0.001 TYR C 75 ARG 0.010 0.000 ARG B 232 ********************** REFINEMENT MACRO_CYCLE 10 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 219 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 2.158 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: D 134 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6594 (mt-10) REVERT: D 250 GLU cc_start: 0.8215 (mm-30) cc_final: 0.8007 (mm-30) REVERT: D 421 MET cc_start: 0.7187 (mtt) cc_final: 0.6876 (mtt) REVERT: A 134 GLU cc_start: 0.6945 (tp30) cc_final: 0.6591 (mm-30) REVERT: A 151 ARG cc_start: 0.5548 (OUTLIER) cc_final: 0.5198 (tpp80) REVERT: A 174 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8471 (pt0) REVERT: A 213 MET cc_start: 0.8384 (mtp) cc_final: 0.7873 (mtp) REVERT: A 328 MET cc_start: 0.5901 (mtt) cc_final: 0.5472 (mtt) REVERT: A 355 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.5801 (ttt90) REVERT: A 424 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7528 (mptm) REVERT: B 134 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6567 (mt-10) REVERT: B 190 ILE cc_start: 0.8251 (mm) cc_final: 0.7918 (mm) REVERT: B 298 ASP cc_start: 0.7690 (t0) cc_final: 0.7308 (t0) REVERT: B 429 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6692 (mp-120) REVERT: C 186 ASN cc_start: 0.8043 (m-40) cc_final: 0.7798 (m-40) REVERT: C 328 MET cc_start: 0.5864 (mtt) cc_final: 0.5402 (mtt) REVERT: C 424 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7289 (mptm) outliers start: 35 outliers final: 27 residues processed: 210 average time/residue: 0.7250 time to fit residues: 208.7428 Evaluate side-chains 214 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 0.9980 chunk 138 optimal weight: 0.0670 chunk 39 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN A 235 ASN ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN C 235 ASN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.164959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.124109 restraints weight = 57761.719| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.35 r_work: 0.3508 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13374 Z= 0.178 Angle : 0.481 4.931 18150 Z= 0.247 Chirality : 0.044 0.131 2012 Planarity : 0.004 0.081 2364 Dihedral : 6.727 59.820 2003 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.65 % Allowed : 17.60 % Favored : 79.76 % 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: -1.99 (0.20), residues: 1652 helix: -0.91 (0.27), residues: 412 sheet: -1.89 (0.34), residues: 230 loop : -1.36 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 284 HIS 0.002 0.001 HIS C 46 PHE 0.007 0.001 PHE A 192 TYR 0.023 0.001 TYR C 75 ARG 0.015 0.000 ARG D 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6235.27 seconds wall clock time: 110 minutes 29.01 seconds (6629.01 seconds total)