Starting phenix.real_space_refine on Wed Mar 20 02:28:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8b_4754/03_2024/6r8b_4754_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8b_4754/03_2024/6r8b_4754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8b_4754/03_2024/6r8b_4754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8b_4754/03_2024/6r8b_4754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8b_4754/03_2024/6r8b_4754_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8b_4754/03_2024/6r8b_4754_trim_updated.pdb" } resolution = 3.1 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= 0.156 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 84 5.16 5 C 8328 2.51 5 N 2340 2.21 5 O 2504 1.98 5 H 12788 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ASP 126": "OD1" <-> "OD2" 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 GLU 185": "OE1" <-> "OE2" 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 ASP 219": "OD1" <-> "OD2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D ASP 243": "OD1" <-> "OD2" Residue "D TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ASP 126": "OD1" <-> "OD2" 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 GLU 185": "OE1" <-> "OE2" 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 ASP 219": "OD1" <-> "OD2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B ASP 243": "OD1" <-> "OD2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 219": "OD1" <-> "OD2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 300": "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 GLU 398": "OE1" <-> "OE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C ASP 243": "OD1" <-> "OD2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 300": "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 GLU 398": "OE1" <-> "OE2" Residue "C TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26052 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 6493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6493 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 400} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 6493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6493 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 400} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 6493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6493 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 400} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 6493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6493 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 400} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 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: "B" 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: "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: 11.37, per 1000 atoms: 0.44 Number of scatterers: 26052 At special positions: 0 Unit cell: (105.747, 103.653, 101.559, 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 84 16.00 P 8 15.00 O 2504 8.00 N 2340 7.00 C 8328 6.00 H 12788 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: 19.54 Conformation dependent library (CDL) restraints added in 2.6 seconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 24 sheets defined 25.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.13 Creating SS restraints... Processing helix chain 'D' and resid 13 through 19 Proline residue: D 17 - end of helix No H-bonds generated for 'chain 'D' and resid 13 through 19' 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 53 through 63 removed outlier: 3.809A pdb=" N ALA D 57 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 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 117 through 122 removed outlier: 3.561A pdb=" N THR D 122 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 131 removed outlier: 3.711A pdb=" N TYR D 131 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 159 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 220 through 232 removed outlier: 3.947A pdb=" N GLU D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 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 400 through 406 Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'B' and resid 13 through 19 Proline residue: B 17 - end of helix No H-bonds generated for 'chain 'B' and resid 13 through 19' 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 53 through 63 removed outlier: 3.809A pdb=" N ALA B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) 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 87 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 117 through 122 removed outlier: 3.561A pdb=" N THR B 122 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 131 removed outlier: 3.711A pdb=" N TYR B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 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 220 through 232 removed outlier: 3.947A pdb=" N GLU B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 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 400 through 406 Processing helix chain 'B' and resid 419 through 424 Processing helix chain 'A' and resid 13 through 19 Proline residue: A 17 - end of helix No H-bonds generated for 'chain 'A' and resid 13 through 19' 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: 3.809A pdb=" N ALA A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.561A pdb=" N THR A 122 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.711A pdb=" N TYR A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 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 232 removed outlier: 3.947A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 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 280 through 288 Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'C' and resid 13 through 19 Proline residue: C 17 - end of helix No H-bonds generated for 'chain 'C' and resid 13 through 19' 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: 3.809A pdb=" N ALA C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.561A pdb=" N THR C 122 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 131 removed outlier: 3.711A pdb=" N TYR C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 159 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 232 removed outlier: 3.947A pdb=" N GLU C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 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 280 through 288 Processing helix chain 'C' and resid 400 through 406 Processing helix chain 'C' and resid 419 through 424 Processing sheet with id= A, first strand: chain 'D' and resid 98 through 103 removed outlier: 7.339A pdb=" N SER D 20 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLY D 70 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA D 22 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE D 72 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE D 24 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR D 135 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU D 23 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL D 137 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU D 25 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU D 139 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE D 215 " --> pdb=" O ALA D 166 " (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 317 through 319 Processing sheet with id= D, first strand: chain 'D' and resid 361 through 363 Processing sheet with id= E, first strand: chain 'D' and resid 365 through 367 removed outlier: 6.772A pdb=" N CYS D 382 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D 415 " --> pdb=" O VAL D 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 180 through 183 Processing sheet with id= G, first strand: chain 'B' and resid 98 through 103 removed outlier: 7.339A pdb=" N SER B 20 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLY B 70 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA B 22 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE B 72 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE B 24 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR B 135 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU B 23 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 137 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU B 25 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU B 139 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE B 215 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 167 through 171 Processing sheet with id= I, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= J, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= K, first strand: chain 'B' and resid 365 through 367 removed outlier: 6.772A pdb=" N CYS B 382 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 415 " --> pdb=" O VAL B 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 180 through 183 Processing sheet with id= M, first strand: chain 'A' and resid 98 through 103 removed outlier: 7.339A pdb=" N SER A 20 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N GLY A 70 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA A 22 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE A 72 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 24 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 135 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU A 23 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 137 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 25 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU A 139 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE A 215 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 167 through 171 Processing sheet with id= O, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= P, first strand: chain 'A' and resid 361 through 363 Processing sheet with id= Q, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.772A pdb=" N CYS A 382 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 415 " --> pdb=" O VAL A 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'A' and resid 180 through 183 Processing sheet with id= S, first strand: chain 'C' and resid 98 through 103 removed outlier: 7.338A pdb=" N SER C 20 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N GLY C 70 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 22 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE C 72 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE C 24 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR C 135 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU C 23 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL C 137 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU C 25 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU C 139 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE C 215 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 167 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: 6.772A pdb=" N CYS C 382 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.428A 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 183 284 hydrogen bonds defined for protein. 816 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: 10.17 Time building geometry restraints manager: 20.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 12752 1.04 - 1.23: 877 1.23 - 1.43: 4859 1.43 - 1.63: 7704 1.63 - 1.83: 132 Bond restraints: 26324 Sorted by residual: bond pdb=" C5 FBP A 501 " pdb=" O5 FBP A 501 " ideal model delta sigma weight residual 1.608 1.430 0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" C5 FBP D 501 " pdb=" O5 FBP D 501 " ideal model delta sigma weight residual 1.608 1.430 0.178 2.00e-02 2.50e+03 7.89e+01 bond pdb=" C5 FBP C 501 " pdb=" O5 FBP C 501 " ideal model delta sigma weight residual 1.608 1.431 0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" C5 FBP B 501 " pdb=" O5 FBP B 501 " ideal model delta sigma weight residual 1.608 1.431 0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C4 FBP C 501 " pdb=" C5 FBP C 501 " ideal model delta sigma weight residual 1.346 1.512 -0.166 2.00e-02 2.50e+03 6.85e+01 ... (remaining 26319 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.57: 380 104.57 - 111.95: 28981 111.95 - 119.33: 7288 119.33 - 126.70: 10588 126.70 - 134.08: 207 Bond angle restraints: 47444 Sorted by residual: angle pdb=" N ARG B 115 " pdb=" CA ARG B 115 " pdb=" C ARG B 115 " ideal model delta sigma weight residual 111.56 101.33 10.23 1.43e+00 4.89e-01 5.12e+01 angle pdb=" N ARG C 115 " pdb=" CA ARG C 115 " pdb=" C ARG C 115 " ideal model delta sigma weight residual 111.56 101.35 10.21 1.43e+00 4.89e-01 5.10e+01 angle pdb=" N ARG D 115 " pdb=" CA ARG D 115 " pdb=" C ARG D 115 " ideal model delta sigma weight residual 111.56 101.35 10.21 1.43e+00 4.89e-01 5.10e+01 angle pdb=" N ARG A 115 " pdb=" CA ARG A 115 " pdb=" C ARG A 115 " ideal model delta sigma weight residual 111.56 101.35 10.21 1.43e+00 4.89e-01 5.09e+01 angle pdb=" N SER B 89 " pdb=" CA SER B 89 " pdb=" C SER B 89 " ideal model delta sigma weight residual 110.65 102.99 7.66 1.26e+00 6.30e-01 3.70e+01 ... (remaining 47439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 11254 17.23 - 34.45: 808 34.45 - 51.68: 324 51.68 - 68.91: 130 68.91 - 86.14: 16 Dihedral angle restraints: 12532 sinusoidal: 6880 harmonic: 5652 Sorted by residual: dihedral pdb=" C PHE A 91 " pdb=" N PHE A 91 " pdb=" CA PHE A 91 " pdb=" CB PHE A 91 " ideal model delta harmonic sigma weight residual -122.60 -112.28 -10.32 0 2.50e+00 1.60e-01 1.70e+01 dihedral pdb=" CA GLY B 342 " pdb=" C GLY B 342 " pdb=" N SER B 343 " pdb=" CA SER B 343 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLY A 342 " pdb=" C GLY A 342 " pdb=" N SER A 343 " pdb=" CA SER A 343 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 12529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1334 0.062 - 0.123: 503 0.123 - 0.185: 143 0.185 - 0.246: 36 0.246 - 0.308: 12 Chirality restraints: 2028 Sorted by residual: chirality pdb=" CA HIS A 238 " pdb=" N HIS A 238 " pdb=" C HIS A 238 " pdb=" CB HIS A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA HIS C 238 " pdb=" N HIS C 238 " pdb=" C HIS C 238 " pdb=" CB HIS C 238 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA HIS B 238 " pdb=" N HIS B 238 " pdb=" C HIS B 238 " pdb=" CB HIS B 238 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2025 not shown) Planarity restraints: 3992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 15 " 0.101 2.00e-02 2.50e+03 1.07e-01 1.73e+02 pdb=" CD GLN B 15 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN B 15 " -0.096 2.00e-02 2.50e+03 pdb=" NE2 GLN B 15 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 15 " -0.156 2.00e-02 2.50e+03 pdb="HE22 GLN B 15 " 0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 15 " -0.101 2.00e-02 2.50e+03 1.07e-01 1.73e+02 pdb=" CD GLN D 15 " 0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN D 15 " 0.096 2.00e-02 2.50e+03 pdb=" NE2 GLN D 15 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN D 15 " 0.156 2.00e-02 2.50e+03 pdb="HE22 GLN D 15 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 15 " -0.101 2.00e-02 2.50e+03 1.07e-01 1.73e+02 pdb=" CD GLN C 15 " 0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN C 15 " 0.096 2.00e-02 2.50e+03 pdb=" NE2 GLN C 15 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C 15 " 0.155 2.00e-02 2.50e+03 pdb="HE22 GLN C 15 " -0.159 2.00e-02 2.50e+03 ... (remaining 3989 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 3121 2.26 - 2.84: 58348 2.84 - 3.43: 68662 3.43 - 4.01: 97906 4.01 - 4.60: 148776 Nonbonded interactions: 376813 Sorted by model distance: nonbonded pdb="HD21 ASN C 92 " pdb=" HB2 MET C 95 " model vdw 1.671 2.270 nonbonded pdb="HD21 ASN D 92 " pdb=" HB2 MET D 95 " model vdw 1.671 2.270 nonbonded pdb="HD21 ASN B 92 " pdb=" HB2 MET B 95 " model vdw 1.672 2.270 nonbonded pdb="HD21 ASN A 92 " pdb=" HB2 MET A 95 " model vdw 1.672 2.270 nonbonded pdb=" HZ1 LYS A 146 " pdb=" O ASP A 298 " model vdw 1.723 1.850 ... (remaining 376808 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.380 Extract box with map and model: 3.200 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 79.660 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 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 : 0.012 0.178 13536 Z= 0.822 Angle : 1.343 12.252 18364 Z= 0.848 Chirality : 0.073 0.308 2028 Planarity : 0.009 0.061 2400 Dihedral : 15.727 86.136 5140 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.05 % Favored : 95.71 % Rotamer: Outliers : 3.12 % Allowed : 5.95 % Favored : 90.93 % Cbeta Deviations : 0.25 % 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: -3.32 (0.16), residues: 1680 helix: -2.50 (0.19), residues: 468 sheet: -2.55 (0.31), residues: 164 loop : -2.05 (0.15), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.007 TRP D 284 HIS 0.012 0.004 HIS A 78 PHE 0.026 0.004 PHE A 240 TYR 0.023 0.004 TYR B 131 ARG 0.017 0.002 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 322 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 278 time to evaluate : 2.168 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7731 (tppp) REVERT: D 93 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7083 (mp0) REVERT: D 94 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6337 (pm20) REVERT: D 117 THR cc_start: 0.8099 (m) cc_final: 0.7805 (p) REVERT: D 134 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7077 (mt-10) REVERT: D 148 ASP cc_start: 0.6526 (t0) cc_final: 0.6225 (t0) REVERT: D 198 ASN cc_start: 0.7922 (t0) cc_final: 0.7532 (p0) REVERT: D 229 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7350 (mp0) REVERT: D 289 ASP cc_start: 0.6719 (t70) cc_final: 0.6140 (t0) REVERT: D 385 ASP cc_start: 0.7947 (t0) cc_final: 0.7724 (t0) REVERT: D 399 ASN cc_start: 0.6323 (t0) cc_final: 0.5760 (t0) REVERT: D 423 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6061 (mtt90) REVERT: B 93 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7064 (mp0) REVERT: B 94 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6233 (pm20) REVERT: B 117 THR cc_start: 0.8247 (m) cc_final: 0.7961 (p) REVERT: B 134 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7138 (tt0) REVERT: B 145 TYR cc_start: 0.7541 (p90) cc_final: 0.7270 (p90) REVERT: B 148 ASP cc_start: 0.6488 (t0) cc_final: 0.6157 (t0) REVERT: B 178 PHE cc_start: 0.5073 (m-80) cc_final: 0.4813 (m-80) REVERT: B 198 ASN cc_start: 0.7944 (t0) cc_final: 0.7314 (p0) REVERT: B 229 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7368 (mp0) REVERT: B 289 ASP cc_start: 0.6954 (t70) cc_final: 0.6331 (t0) REVERT: B 303 ASN cc_start: 0.8003 (m-40) cc_final: 0.7773 (m-40) REVERT: B 423 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6165 (mtt90) REVERT: A 39 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7731 (tppp) REVERT: A 93 GLU cc_start: 0.7483 (tm-30) cc_final: 0.6944 (mp0) REVERT: A 94 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: A 117 THR cc_start: 0.8151 (m) cc_final: 0.7837 (p) REVERT: A 134 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7188 (mt-10) REVERT: A 148 ASP cc_start: 0.6472 (t0) cc_final: 0.6145 (t0) REVERT: A 198 ASN cc_start: 0.7929 (t0) cc_final: 0.7486 (p0) REVERT: A 229 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7445 (mp0) REVERT: A 289 ASP cc_start: 0.6866 (t70) cc_final: 0.6245 (t0) REVERT: A 385 ASP cc_start: 0.7973 (t0) cc_final: 0.7737 (t0) REVERT: A 399 ASN cc_start: 0.6315 (t0) cc_final: 0.5763 (t0) REVERT: A 423 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6075 (mtt90) REVERT: C 117 THR cc_start: 0.8133 (m) cc_final: 0.7831 (p) REVERT: C 134 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7041 (mt-10) REVERT: C 148 ASP cc_start: 0.6492 (t0) cc_final: 0.6194 (t0) REVERT: C 178 PHE cc_start: 0.5060 (m-80) cc_final: 0.4824 (m-80) REVERT: C 221 ASP cc_start: 0.7783 (m-30) cc_final: 0.7240 (p0) REVERT: C 229 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7283 (mp0) REVERT: C 289 ASP cc_start: 0.6958 (t70) cc_final: 0.6361 (t0) REVERT: C 303 ASN cc_start: 0.8006 (m-40) cc_final: 0.7800 (m-40) REVERT: C 423 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.6035 (mtt90) outliers start: 44 outliers final: 20 residues processed: 306 average time/residue: 0.7777 time to fit residues: 316.7696 Evaluate side-chains 248 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 423 ARG Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 423 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 ASN B 82 GLN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS A 82 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 326 HIS C 82 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 13536 Z= 0.138 Angle : 0.510 4.272 18364 Z= 0.263 Chirality : 0.044 0.143 2028 Planarity : 0.005 0.035 2400 Dihedral : 8.275 46.719 2085 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.77 % Allowed : 8.71 % Favored : 89.52 % 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: -1.75 (0.18), residues: 1680 helix: -0.44 (0.24), residues: 428 sheet: -2.14 (0.31), residues: 160 loop : -1.34 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 284 HIS 0.003 0.001 HIS D 78 PHE 0.010 0.001 PHE A 91 TYR 0.009 0.001 TYR D 145 ARG 0.002 0.000 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 227 time to evaluate : 2.034 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: 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 14 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6017 (ttt90) REVERT: D 39 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7826 (tppp) REVERT: D 134 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7121 (mt-10) REVERT: D 162 ARG cc_start: 0.6330 (mmm160) cc_final: 0.6094 (mmm160) REVERT: D 198 ASN cc_start: 0.7908 (t0) cc_final: 0.7517 (p0) REVERT: D 289 ASP cc_start: 0.6930 (t70) cc_final: 0.6320 (t0) REVERT: D 399 ASN cc_start: 0.6228 (t0) cc_final: 0.5834 (t0) REVERT: B 39 LYS cc_start: 0.8029 (tppt) cc_final: 0.7588 (mmtp) REVERT: B 93 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6959 (mp0) REVERT: B 134 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7242 (tt0) REVERT: B 289 ASP cc_start: 0.6926 (t70) cc_final: 0.6306 (t0) REVERT: B 399 ASN cc_start: 0.6085 (t0) cc_final: 0.5674 (t0) REVERT: A 39 LYS cc_start: 0.8104 (mmtp) cc_final: 0.7826 (tppp) REVERT: A 134 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7219 (tt0) REVERT: A 162 ARG cc_start: 0.6348 (mmm160) cc_final: 0.6140 (mmm160) REVERT: A 198 ASN cc_start: 0.7881 (t0) cc_final: 0.7468 (p0) REVERT: A 289 ASP cc_start: 0.6911 (t70) cc_final: 0.6293 (t0) REVERT: A 399 ASN cc_start: 0.6219 (t0) cc_final: 0.5850 (t0) REVERT: C 39 LYS cc_start: 0.8027 (tppt) cc_final: 0.7595 (mmtp) REVERT: C 93 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6788 (mp0) REVERT: C 134 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7173 (mt-10) REVERT: C 162 ARG cc_start: 0.6370 (mmm160) cc_final: 0.6155 (mmm160) REVERT: C 178 PHE cc_start: 0.5140 (m-80) cc_final: 0.4907 (m-80) REVERT: C 289 ASP cc_start: 0.6952 (t70) cc_final: 0.6339 (t0) REVERT: C 353 ARG cc_start: 0.7327 (mtt-85) cc_final: 0.7017 (mtp85) outliers start: 25 outliers final: 21 residues processed: 249 average time/residue: 0.6801 time to fit residues: 231.2877 Evaluate side-chains 225 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 326 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- 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** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5490 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13536 Z= 0.208 Angle : 0.495 4.868 18364 Z= 0.254 Chirality : 0.044 0.144 2028 Planarity : 0.004 0.033 2400 Dihedral : 6.765 48.034 2024 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.34 % Allowed : 8.00 % Favored : 89.66 % 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: -1.18 (0.18), residues: 1680 helix: 0.20 (0.26), residues: 432 sheet: -1.88 (0.33), residues: 160 loop : -1.03 (0.16), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 284 HIS 0.005 0.001 HIS A 326 PHE 0.006 0.001 PHE B 218 TYR 0.009 0.001 TYR B 145 ARG 0.003 0.000 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 210 time to evaluate : 2.214 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 134 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7111 (mt-10) REVERT: D 198 ASN cc_start: 0.7920 (t0) cc_final: 0.7517 (p0) REVERT: D 289 ASP cc_start: 0.6962 (t70) cc_final: 0.6364 (t0) REVERT: B 39 LYS cc_start: 0.8045 (tppt) cc_final: 0.7631 (mmtp) REVERT: B 92 ASN cc_start: 0.7592 (p0) cc_final: 0.7039 (p0) REVERT: B 93 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6969 (mp0) REVERT: B 134 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7253 (tt0) REVERT: B 289 ASP cc_start: 0.6975 (t70) cc_final: 0.6375 (t0) REVERT: A 39 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7730 (tppp) REVERT: A 134 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7243 (tt0) REVERT: A 198 ASN cc_start: 0.7898 (t0) cc_final: 0.7472 (p0) REVERT: A 289 ASP cc_start: 0.6944 (t70) cc_final: 0.6345 (t0) REVERT: C 14 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6508 (ttp80) REVERT: C 39 LYS cc_start: 0.7999 (tppt) cc_final: 0.7593 (mmtp) REVERT: C 92 ASN cc_start: 0.7418 (p0) cc_final: 0.7125 (p0) REVERT: C 134 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7120 (mt-10) REVERT: C 289 ASP cc_start: 0.6940 (t70) cc_final: 0.6337 (t0) REVERT: C 353 ARG cc_start: 0.7285 (mtt-85) cc_final: 0.7057 (mtt-85) outliers start: 33 outliers final: 26 residues processed: 226 average time/residue: 0.7028 time to fit residues: 217.3055 Evaluate side-chains 221 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 310 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 0.0000 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.0020 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 145 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS C 326 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5459 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 13536 Z= 0.106 Angle : 0.457 4.294 18364 Z= 0.231 Chirality : 0.043 0.138 2028 Planarity : 0.004 0.033 2400 Dihedral : 5.826 46.012 2012 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.20 % Allowed : 8.71 % Favored : 89.09 % 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: -0.71 (0.19), residues: 1680 helix: 0.70 (0.26), residues: 432 sheet: -1.81 (0.33), residues: 172 loop : -0.72 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 284 HIS 0.003 0.000 HIS D 257 PHE 0.006 0.001 PHE C 218 TYR 0.008 0.001 TYR A 222 ARG 0.002 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 2.034 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 39 LYS cc_start: 0.8097 (tppt) cc_final: 0.7557 (tppp) REVERT: D 134 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7215 (mt-10) REVERT: D 162 ARG cc_start: 0.6248 (mmm160) cc_final: 0.6023 (mmm160) REVERT: D 198 ASN cc_start: 0.7920 (t0) cc_final: 0.7525 (p0) REVERT: D 289 ASP cc_start: 0.6853 (t70) cc_final: 0.6265 (t0) REVERT: B 39 LYS cc_start: 0.8049 (tppt) cc_final: 0.7553 (tppp) REVERT: B 93 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7106 (mp0) REVERT: B 134 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7275 (tt0) REVERT: B 178 PHE cc_start: 0.5315 (m-80) cc_final: 0.5019 (m-80) REVERT: B 289 ASP cc_start: 0.6869 (t70) cc_final: 0.6281 (t0) REVERT: A 69 MET cc_start: 0.7395 (mtm) cc_final: 0.7187 (mtt) REVERT: A 134 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7279 (tt0) REVERT: A 198 ASN cc_start: 0.7895 (t0) cc_final: 0.7487 (p0) REVERT: A 289 ASP cc_start: 0.6818 (t70) cc_final: 0.6230 (t0) REVERT: C 39 LYS cc_start: 0.8017 (tppt) cc_final: 0.7563 (mmtp) REVERT: C 92 ASN cc_start: 0.7407 (p0) cc_final: 0.6994 (p0) REVERT: C 93 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6905 (mp0) REVERT: C 134 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7293 (mt-10) REVERT: C 178 PHE cc_start: 0.5333 (m-80) cc_final: 0.5056 (m-80) REVERT: C 190 ILE cc_start: 0.7756 (mt) cc_final: 0.7483 (mp) REVERT: C 289 ASP cc_start: 0.6817 (t70) cc_final: 0.6243 (t0) REVERT: C 353 ARG cc_start: 0.7284 (mtt-85) cc_final: 0.7069 (mtt-85) outliers start: 31 outliers final: 17 residues processed: 232 average time/residue: 0.7090 time to fit residues: 222.7782 Evaluate side-chains 204 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 326 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 ASN ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN A 326 HIS ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN C 326 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13536 Z= 0.348 Angle : 0.541 7.426 18364 Z= 0.280 Chirality : 0.046 0.145 2028 Planarity : 0.004 0.034 2400 Dihedral : 5.918 44.574 2004 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.76 % Allowed : 9.70 % Favored : 87.54 % 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: -0.86 (0.19), residues: 1680 helix: 0.50 (0.27), residues: 428 sheet: -1.92 (0.31), residues: 192 loop : -0.74 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 284 HIS 0.008 0.001 HIS C 326 PHE 0.010 0.001 PHE B 218 TYR 0.008 0.001 TYR D 149 ARG 0.005 0.000 ARG D 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 2.079 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: 0.7613 (mm-30) cc_final: 0.7180 (mt-10) REVERT: D 198 ASN cc_start: 0.7913 (t0) cc_final: 0.7510 (p0) REVERT: D 289 ASP cc_start: 0.7128 (t70) cc_final: 0.6575 (t0) REVERT: D 421 MET cc_start: 0.7737 (mtt) cc_final: 0.7461 (mtt) REVERT: B 39 LYS cc_start: 0.8093 (tppt) cc_final: 0.7649 (mmtp) REVERT: B 93 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6813 (mp0) REVERT: B 134 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7249 (mt-10) REVERT: B 198 ASN cc_start: 0.7926 (t0) cc_final: 0.7329 (p0) REVERT: B 289 ASP cc_start: 0.7115 (t70) cc_final: 0.6567 (t0) REVERT: A 39 LYS cc_start: 0.7995 (tppt) cc_final: 0.7497 (mmtp) REVERT: A 134 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7261 (mt-10) REVERT: A 198 ASN cc_start: 0.7919 (t0) cc_final: 0.7473 (p0) REVERT: A 289 ASP cc_start: 0.7113 (t70) cc_final: 0.6563 (t0) REVERT: A 421 MET cc_start: 0.7739 (mtt) cc_final: 0.7461 (mtt) REVERT: C 39 LYS cc_start: 0.8073 (tppt) cc_final: 0.7625 (mmtp) REVERT: C 134 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7238 (mt-10) REVERT: C 289 ASP cc_start: 0.7128 (t70) cc_final: 0.6573 (t0) outliers start: 39 outliers final: 27 residues processed: 209 average time/residue: 0.6705 time to fit residues: 194.0220 Evaluate side-chains 196 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain C residue 348 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN A 310 ASN A 326 HIS C 326 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5492 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13536 Z= 0.228 Angle : 0.497 4.597 18364 Z= 0.253 Chirality : 0.044 0.144 2028 Planarity : 0.004 0.052 2400 Dihedral : 5.710 45.901 2004 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.34 % Allowed : 9.99 % Favored : 87.68 % 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: -0.78 (0.19), residues: 1680 helix: 0.65 (0.27), residues: 428 sheet: -1.97 (0.32), residues: 196 loop : -0.69 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 284 HIS 0.008 0.001 HIS C 326 PHE 0.009 0.001 PHE B 218 TYR 0.007 0.001 TYR B 145 ARG 0.009 0.000 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 1.957 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: D 134 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7238 (mt-10) REVERT: D 198 ASN cc_start: 0.7923 (t0) cc_final: 0.7514 (p0) REVERT: D 271 GLU cc_start: 0.7911 (tt0) cc_final: 0.7589 (tp30) REVERT: D 289 ASP cc_start: 0.7117 (t70) cc_final: 0.6574 (t0) REVERT: D 421 MET cc_start: 0.7742 (mtt) cc_final: 0.7448 (mtt) REVERT: B 39 LYS cc_start: 0.8117 (tppt) cc_final: 0.7573 (mmtp) REVERT: B 93 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6839 (mp0) REVERT: B 134 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7210 (mt-10) REVERT: B 198 ASN cc_start: 0.7908 (t0) cc_final: 0.7352 (p0) REVERT: B 289 ASP cc_start: 0.7031 (t70) cc_final: 0.6502 (t0) REVERT: A 39 LYS cc_start: 0.8053 (tppt) cc_final: 0.7613 (mmtp) REVERT: A 134 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7251 (mt-10) REVERT: A 198 ASN cc_start: 0.7930 (t0) cc_final: 0.7479 (p0) REVERT: A 289 ASP cc_start: 0.7008 (t70) cc_final: 0.6479 (t0) REVERT: A 421 MET cc_start: 0.7828 (mtt) cc_final: 0.7529 (mtt) REVERT: C 39 LYS cc_start: 0.8084 (tppt) cc_final: 0.7559 (mmtp) REVERT: C 93 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6505 (mp0) REVERT: C 134 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7244 (mt-10) REVERT: C 289 ASP cc_start: 0.7141 (t70) cc_final: 0.6618 (t0) outliers start: 33 outliers final: 28 residues processed: 196 average time/residue: 0.6707 time to fit residues: 182.4491 Evaluate side-chains 197 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 348 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.0970 chunk 18 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13536 Z= 0.253 Angle : 0.497 4.850 18364 Z= 0.253 Chirality : 0.045 0.144 2028 Planarity : 0.004 0.056 2400 Dihedral : 5.662 45.632 2004 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.69 % Allowed : 10.27 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.20), residues: 1680 helix: 0.69 (0.28), residues: 428 sheet: -2.00 (0.33), residues: 192 loop : -0.69 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 284 HIS 0.006 0.001 HIS A 326 PHE 0.009 0.001 PHE A 218 TYR 0.008 0.001 TYR A 222 ARG 0.010 0.000 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 170 time to evaluate : 2.034 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: D 39 LYS cc_start: 0.8084 (tppt) cc_final: 0.7652 (mmtp) REVERT: D 134 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7243 (mt-10) REVERT: D 198 ASN cc_start: 0.7935 (t0) cc_final: 0.7515 (p0) REVERT: D 271 GLU cc_start: 0.7896 (tt0) cc_final: 0.7583 (tp30) REVERT: D 289 ASP cc_start: 0.7145 (t70) cc_final: 0.6626 (t0) REVERT: D 303 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7502 (t0) REVERT: B 39 LYS cc_start: 0.8125 (tppt) cc_final: 0.7720 (mmtp) REVERT: B 93 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6836 (mp0) REVERT: B 134 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7258 (mt-10) REVERT: B 289 ASP cc_start: 0.7050 (t70) cc_final: 0.6530 (t0) REVERT: A 39 LYS cc_start: 0.8108 (tppt) cc_final: 0.7660 (mmtp) REVERT: A 134 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7272 (mt-10) REVERT: A 198 ASN cc_start: 0.7935 (t0) cc_final: 0.7492 (p0) REVERT: A 271 GLU cc_start: 0.7844 (tt0) cc_final: 0.7520 (tp30) REVERT: A 289 ASP cc_start: 0.7038 (t70) cc_final: 0.6517 (t0) REVERT: C 39 LYS cc_start: 0.8066 (tppt) cc_final: 0.7679 (mmtp) REVERT: C 134 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7245 (mt-10) REVERT: C 289 ASP cc_start: 0.7125 (t70) cc_final: 0.6607 (t0) outliers start: 38 outliers final: 35 residues processed: 193 average time/residue: 0.6687 time to fit residues: 178.5561 Evaluate side-chains 200 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain C residue 348 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 0.0370 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 ASN ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS A 399 ASN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13536 Z= 0.325 Angle : 0.525 4.944 18364 Z= 0.269 Chirality : 0.046 0.151 2028 Planarity : 0.004 0.063 2400 Dihedral : 5.761 45.481 2004 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.26 % Allowed : 9.77 % Favored : 86.97 % 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: -0.92 (0.20), residues: 1680 helix: 0.57 (0.27), residues: 424 sheet: -1.94 (0.37), residues: 168 loop : -0.87 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.004 0.001 HIS A 156 PHE 0.010 0.001 PHE B 218 TYR 0.007 0.001 TYR C 135 ARG 0.012 0.000 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 2.070 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: symmetry clash revert: symmetry clash REVERT: D 134 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7192 (mt-10) REVERT: D 198 ASN cc_start: 0.7923 (t0) cc_final: 0.7455 (p0) REVERT: D 289 ASP cc_start: 0.7205 (t70) cc_final: 0.6691 (t0) REVERT: B 39 LYS cc_start: 0.8112 (tppt) cc_final: 0.7729 (mmtp) REVERT: B 134 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7249 (mt-10) REVERT: B 289 ASP cc_start: 0.7169 (t70) cc_final: 0.6668 (t0) REVERT: A 134 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7213 (mt-10) REVERT: A 198 ASN cc_start: 0.7902 (t0) cc_final: 0.7393 (p0) REVERT: A 271 GLU cc_start: 0.7835 (tt0) cc_final: 0.7506 (tp30) REVERT: A 289 ASP cc_start: 0.7218 (t70) cc_final: 0.6714 (t0) REVERT: C 134 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7190 (mt-10) REVERT: C 289 ASP cc_start: 0.7216 (t70) cc_final: 0.6724 (t0) REVERT: C 303 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7416 (t0) outliers start: 46 outliers final: 41 residues processed: 196 average time/residue: 0.7063 time to fit residues: 190.3051 Evaluate side-chains 202 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 160 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 348 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 HIS A 326 HIS C 326 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5486 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13536 Z= 0.195 Angle : 0.486 4.762 18364 Z= 0.246 Chirality : 0.044 0.146 2028 Planarity : 0.004 0.051 2400 Dihedral : 5.490 47.726 2004 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.62 % Allowed : 10.62 % Favored : 86.76 % 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: -0.73 (0.20), residues: 1680 helix: 0.82 (0.28), residues: 424 sheet: -1.92 (0.37), residues: 168 loop : -0.77 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 284 HIS 0.003 0.001 HIS C 326 PHE 0.008 0.001 PHE A 218 TYR 0.007 0.001 TYR B 145 ARG 0.010 0.000 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 172 time to evaluate : 2.195 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: symmetry clash revert: symmetry clash REVERT: D 134 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7232 (mt-10) REVERT: D 198 ASN cc_start: 0.7905 (t0) cc_final: 0.7411 (p0) REVERT: D 271 GLU cc_start: 0.7923 (tt0) cc_final: 0.7593 (tp30) REVERT: D 289 ASP cc_start: 0.7084 (t70) cc_final: 0.6566 (t0) REVERT: D 303 ASN cc_start: 0.8019 (t0) cc_final: 0.7634 (t0) REVERT: B 134 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7284 (mt-10) REVERT: B 289 ASP cc_start: 0.7086 (t70) cc_final: 0.6569 (t0) REVERT: A 134 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7313 (mt-10) REVERT: A 198 ASN cc_start: 0.7965 (t0) cc_final: 0.7444 (p0) REVERT: A 289 ASP cc_start: 0.7136 (t70) cc_final: 0.6598 (t0) REVERT: C 134 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7264 (mt-10) REVERT: C 135 TYR cc_start: 0.6201 (m-80) cc_final: 0.6001 (m-80) REVERT: C 289 ASP cc_start: 0.7078 (t70) cc_final: 0.6569 (t0) REVERT: C 303 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7514 (t0) outliers start: 37 outliers final: 29 residues processed: 193 average time/residue: 0.6640 time to fit residues: 178.6014 Evaluate side-chains 195 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 348 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 167 optimal weight: 0.0970 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS C 326 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5484 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13536 Z= 0.191 Angle : 0.483 4.823 18364 Z= 0.245 Chirality : 0.044 0.145 2028 Planarity : 0.004 0.061 2400 Dihedral : 5.414 48.807 2004 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.34 % Allowed : 11.12 % Favored : 86.54 % 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: -0.63 (0.20), residues: 1680 helix: 0.94 (0.28), residues: 424 sheet: -1.92 (0.37), residues: 168 loop : -0.72 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 284 HIS 0.002 0.001 HIS A 78 PHE 0.008 0.001 PHE B 218 TYR 0.006 0.001 TYR B 145 ARG 0.011 0.000 ARG D 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 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 MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 1.949 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 134 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7225 (mt-10) REVERT: D 198 ASN cc_start: 0.7973 (t0) cc_final: 0.7465 (p0) REVERT: D 271 GLU cc_start: 0.7862 (tt0) cc_final: 0.7583 (tp30) REVERT: D 289 ASP cc_start: 0.7055 (t70) cc_final: 0.6544 (t0) REVERT: D 303 ASN cc_start: 0.7997 (t0) cc_final: 0.7631 (t0) REVERT: B 134 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7281 (mt-10) REVERT: B 289 ASP cc_start: 0.7056 (t70) cc_final: 0.6548 (t0) REVERT: A 134 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7321 (mt-10) REVERT: A 198 ASN cc_start: 0.7972 (t0) cc_final: 0.7454 (p0) REVERT: A 289 ASP cc_start: 0.7109 (t70) cc_final: 0.6583 (t0) REVERT: C 134 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7269 (mt-10) REVERT: C 135 TYR cc_start: 0.6195 (m-80) cc_final: 0.5990 (m-80) REVERT: C 289 ASP cc_start: 0.7056 (t70) cc_final: 0.6550 (t0) REVERT: C 303 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7488 (t0) outliers start: 33 outliers final: 30 residues processed: 194 average time/residue: 0.6678 time to fit residues: 180.1452 Evaluate side-chains 201 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain C residue 348 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116509 restraints weight = 38331.599| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.60 r_work: 0.3281 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13536 Z= 0.208 Angle : 0.739 57.287 18364 Z= 0.470 Chirality : 0.044 0.145 2028 Planarity : 0.005 0.057 2400 Dihedral : 5.415 48.840 2004 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.27 % Allowed : 11.47 % Favored : 86.26 % Cbeta Deviations : 0.06 % 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: -0.63 (0.20), residues: 1680 helix: 0.95 (0.28), residues: 424 sheet: -1.92 (0.37), residues: 168 loop : -0.71 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 284 HIS 0.069 0.002 HIS C 326 PHE 0.008 0.001 PHE B 218 TYR 0.006 0.001 TYR A 222 ARG 0.009 0.000 ARG D 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6313.29 seconds wall clock time: 111 minutes 17.36 seconds (6677.36 seconds total)