Starting phenix.real_space_refine on Mon Mar 25 05:27:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqw_27662/03_2024/8dqw_27662_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqw_27662/03_2024/8dqw_27662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqw_27662/03_2024/8dqw_27662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqw_27662/03_2024/8dqw_27662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqw_27662/03_2024/8dqw_27662_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqw_27662/03_2024/8dqw_27662_trim.pdb" } resolution = 2.1 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= 0.050 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: 7 Type Number sf(0) Gaussians P 49 5.49 5 Mg 4 5.21 5 S 122 5.16 5 C 14540 2.51 5 N 3969 2.21 5 O 4945 1.98 5 H 22936 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 65": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 427": "OE1" <-> "OE2" Residue "H PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46565 Number of models: 1 Model: "" Number of chains: 25 Chain: "B" Number of atoms: 5027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5027 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5196 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 5318 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5698 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 339} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4624 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 4, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 5440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5440 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 5057 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 8507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 8507 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 19, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 804 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "I" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 309 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 20.02, per 1000 atoms: 0.43 Number of scatterers: 46565 At special positions: 0 Unit cell: (129.682, 135.464, 147.854, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 122 16.00 P 49 15.00 Mg 4 11.99 O 4945 8.00 N 3969 7.00 C 14540 6.00 H 22936 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: 35.36 Conformation dependent library (CDL) restraints added in 3.9 seconds 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5360 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 18 sheets defined 55.2% alpha, 16.4% beta 7 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 21.11 Creating SS restraints... Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.233A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 135 removed outlier: 3.645A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.551A pdb=" N GLU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.743A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.595A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.512A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 260 Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.750A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.503A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 5.115A pdb=" N SER C 76 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.993A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.572A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.530A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.539A pdb=" N CYS C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.763A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.537A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.057A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.016A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 4.226A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'D' and resid 21 through 25 removed outlier: 4.308A pdb=" N GLN D 25 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.479A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.997A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 152 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.551A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.591A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.493A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 97 through 103 removed outlier: 6.950A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.644A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.721A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.670A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.431A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 86 through 97 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.592A pdb=" N LEU F 145 " --> pdb=" O THR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 173 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.817A pdb=" N ILE F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 329 Processing helix chain 'G' and resid 9 through 27 Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 98 through 106 Processing helix chain 'G' and resid 161 through 175 Processing helix chain 'G' and resid 188 through 205 Processing helix chain 'G' and resid 222 through 226 Processing helix chain 'G' and resid 234 through 243 removed outlier: 4.214A pdb=" N ASN G 243 " --> pdb=" O ASN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 333 Processing helix chain 'G' and resid 334 through 339 Proline residue: G 337 - end of helix No H-bonds generated for 'chain 'G' and resid 334 through 339' Processing helix chain 'H' and resid 12 through 30 removed outlier: 3.627A pdb=" N TYR H 16 " --> pdb=" O ALA H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 56 Processing helix chain 'H' and resid 57 through 63 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 97 through 114 Processing helix chain 'H' and resid 213 through 219 removed outlier: 3.571A pdb=" N ARG H 219 " --> pdb=" O ALA H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 252 Processing helix chain 'H' and resid 253 through 256 Processing helix chain 'H' and resid 412 through 425 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.659A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 175 through 176 No H-bonds generated for 'chain 'A' and resid 175 through 176' Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.755A pdb=" N LYS A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 385 through 390 removed outlier: 5.154A pdb=" N ASN A 388 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 408 removed outlier: 3.557A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.590A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 472 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 483 through 509 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 565 through 591 removed outlier: 4.022A pdb=" N ARG A 586 " --> pdb=" O ASP A 582 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 Processing sheet with id=AA1, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.342A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 79 through 82 Processing sheet with id=AA3, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.965A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.392A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 69 through 76 removed outlier: 6.496A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 122 through 124 Processing sheet with id=AA7, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.530A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 69 through 72 removed outlier: 3.516A pdb=" N HIS H 291 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU H 281 " --> pdb=" O TRP H 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 79 through 85 removed outlier: 6.862A pdb=" N ASP F 36 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU F 51 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL F 305 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL F 264 " --> pdb=" O ASP F 260 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL F 255 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE F 157 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE F 257 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU F 155 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET F 259 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS F 216 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LYS F 159 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU F 214 " --> pdb=" O LYS F 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 232 through 238 removed outlier: 4.691A pdb=" N PHE F 192 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER G 115 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU G 63 " --> pdb=" O THR G 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 78 through 82 removed outlier: 4.371A pdb=" N SER G 93 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 78 through 82 removed outlier: 7.100A pdb=" N ASP G 29 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N MET G 44 " --> pdb=" O ASP G 29 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN G 365 " --> pdb=" O ASN G 348 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN G 348 " --> pdb=" O GLN G 365 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 282 through 289 Processing sheet with id=AB5, first strand: chain 'G' and resid 270 through 271 removed outlier: 6.208A pdb=" N VAL G 270 " --> pdb=" O LEU G 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 80 through 82 removed outlier: 5.863A pdb=" N LEU H 3 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU H 123 " --> pdb=" O LEU H 3 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 80 through 82 removed outlier: 5.863A pdb=" N LEU H 3 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU H 123 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN H 96 " --> pdb=" O PRO H 208 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN H 463 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU H 427 " --> pdb=" O SER H 443 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.378A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 105 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 223 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 107 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 226 through 227 1289 hydrogen bonds defined for protein. 3630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 20.67 Time building geometry restraints manager: 36.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 22881 1.05 - 1.27: 3889 1.27 - 1.49: 9298 1.49 - 1.70: 10345 1.70 - 1.92: 185 Bond restraints: 46598 Sorted by residual: bond pdb=" C2' AGS D 402 " pdb=" C3' AGS D 402 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.01e+02 bond pdb=" C2' AGS B 402 " pdb=" C3' AGS B 402 " ideal model delta sigma weight residual 1.530 1.241 0.289 1.30e-02 5.92e+03 4.94e+02 bond pdb=" C2' AGS C 402 " pdb=" C3' AGS C 402 " ideal model delta sigma weight residual 1.530 1.242 0.288 1.30e-02 5.92e+03 4.89e+02 bond pdb=" C2' AGS A 901 " pdb=" C3' AGS A 901 " ideal model delta sigma weight residual 1.530 1.243 0.287 1.30e-02 5.92e+03 4.89e+02 bond pdb=" C6 AGS C 402 " pdb=" N6 AGS C 402 " ideal model delta sigma weight residual 1.335 1.469 -0.134 1.00e-02 1.00e+04 1.80e+02 ... (remaining 46593 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.61: 724 106.61 - 113.46: 56051 113.46 - 120.32: 14648 120.32 - 127.17: 12714 127.17 - 134.03: 252 Bond angle restraints: 84389 Sorted by residual: angle pdb=" N1 AGS A 901 " pdb=" C2 AGS A 901 " pdb=" N3 AGS A 901 " ideal model delta sigma weight residual 128.80 120.04 8.76 8.41e-01 1.41e+00 1.09e+02 angle pdb=" N1 AGS B 402 " pdb=" C2 AGS B 402 " pdb=" N3 AGS B 402 " ideal model delta sigma weight residual 128.80 120.09 8.71 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS C 402 " pdb=" C2 AGS C 402 " pdb=" N3 AGS C 402 " ideal model delta sigma weight residual 128.80 120.13 8.67 8.41e-01 1.41e+00 1.06e+02 angle pdb=" N1 AGS D 402 " pdb=" C2 AGS D 402 " pdb=" N3 AGS D 402 " ideal model delta sigma weight residual 128.80 120.18 8.62 8.41e-01 1.41e+00 1.05e+02 angle pdb=" C5 AGS D 402 " pdb=" N7 AGS D 402 " pdb=" C8 AGS D 402 " ideal model delta sigma weight residual 103.67 107.91 -4.24 4.26e-01 5.51e+00 9.90e+01 ... (remaining 84384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.29: 20607 32.29 - 64.58: 931 64.58 - 96.87: 57 96.87 - 129.16: 2 129.16 - 161.45: 4 Dihedral angle restraints: 21601 sinusoidal: 12156 harmonic: 9445 Sorted by residual: dihedral pdb=" O2B GDP E 401 " pdb=" O3A GDP E 401 " pdb=" PB GDP E 401 " pdb=" PA GDP E 401 " ideal model delta sinusoidal sigma weight residual 180.00 52.56 127.44 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" C5' GDP E 401 " pdb=" O5' GDP E 401 " pdb=" PA GDP E 401 " pdb=" O3A GDP E 401 " ideal model delta sinusoidal sigma weight residual 179.98 73.90 106.08 1 2.00e+01 2.50e-03 3.06e+01 dihedral pdb=" O1A AGS A 901 " pdb=" O3A AGS A 901 " pdb=" PA AGS A 901 " pdb=" PB AGS A 901 " ideal model delta sinusoidal sigma weight residual -67.73 93.72 -161.45 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 21598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3262 0.062 - 0.124: 401 0.124 - 0.185: 31 0.185 - 0.247: 4 0.247 - 0.309: 4 Chirality restraints: 3702 Sorted by residual: chirality pdb=" C2' AGS C 402 " pdb=" C1' AGS C 402 " pdb=" C3' AGS C 402 " pdb=" O2' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.37 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C2' AGS B 402 " pdb=" C1' AGS B 402 " pdb=" C3' AGS B 402 " pdb=" O2' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' AGS A 901 " pdb=" C1' AGS A 901 " pdb=" C3' AGS A 901 " pdb=" O2' AGS A 901 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 3699 not shown) Planarity restraints: 6664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 221 " -0.147 9.50e-02 1.11e+02 4.94e-02 2.98e+00 pdb=" NE ARG E 221 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG E 221 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 221 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 221 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG E 221 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG E 221 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG E 221 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 221 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 283 " 0.137 9.50e-02 1.11e+02 4.60e-02 2.55e+00 pdb=" NE ARG E 283 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG E 283 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 283 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 283 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG E 283 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG E 283 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG E 283 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 283 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 67 " -0.011 2.00e-02 2.50e+03 8.83e-03 2.34e+00 pdb=" CG TYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 67 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 67 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 67 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 67 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 67 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR A 67 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 67 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 67 " -0.002 2.00e-02 2.50e+03 ... (remaining 6661 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1892 2.17 - 2.78: 90353 2.78 - 3.38: 133746 3.38 - 3.99: 176776 3.99 - 4.60: 272908 Nonbonded interactions: 675675 Sorted by model distance: nonbonded pdb=" OE1 GLN G 79 " pdb=" H TYR G 157 " model vdw 1.560 1.850 nonbonded pdb=" OD1 ASP G 378 " pdb=" H ASN G 380 " model vdw 1.563 1.850 nonbonded pdb=" O SER H 50 " pdb=" HG SER H 54 " model vdw 1.580 1.850 nonbonded pdb=" O MET B 131 " pdb=" HG SER B 135 " model vdw 1.586 1.850 nonbonded pdb=" OD1 ASN D 338 " pdb=" HZ2 LYS E 301 " model vdw 1.597 1.850 ... (remaining 675670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 12.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.270 Check model and map are aligned: 0.610 Set scattering table: 0.360 Process input model: 155.760 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 0.007 0.291 23662 Z= 0.488 Angle : 0.546 8.929 32137 Z= 0.375 Chirality : 0.041 0.309 3702 Planarity : 0.003 0.064 3955 Dihedral : 18.054 161.455 9024 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.44 % Allowed : 16.69 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.17), residues: 2764 helix: 2.61 (0.15), residues: 1286 sheet: 0.65 (0.21), residues: 585 loop : 0.75 (0.23), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 324 HIS 0.007 0.001 HIS F 79 PHE 0.011 0.001 PHE E 305 TYR 0.027 0.001 TYR A 67 ARG 0.009 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Evaluate side-chains 416 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 405 time to evaluate : 3.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 MET cc_start: 0.8174 (mtp) cc_final: 0.7909 (mtp) REVERT: E 158 MET cc_start: 0.7118 (mtp) cc_final: 0.6761 (mtp) REVERT: E 352 CYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6667 (p) outliers start: 11 outliers final: 8 residues processed: 415 average time/residue: 3.5981 time to fit residues: 1681.0886 Evaluate side-chains 219 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 210 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 112 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 219 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 163 optimal weight: 0.1980 chunk 254 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 60 HIS B 155 GLN B 250 GLN B 317 HIS C 140 ASN C 171 GLN D 236 GLN D 317 ASN E 104 ASN E 212 GLN F 97 ASN G 132 ASN H 57 ASN H 221 GLN H 297 ASN H 400 GLN A 77 GLN A 298 GLN A 411 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23662 Z= 0.164 Angle : 0.493 5.491 32137 Z= 0.264 Chirality : 0.039 0.142 3702 Planarity : 0.004 0.056 3955 Dihedral : 12.844 175.425 3472 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.35 % Allowed : 18.91 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.17), residues: 2764 helix: 2.57 (0.15), residues: 1322 sheet: 0.65 (0.21), residues: 592 loop : 0.86 (0.24), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 129 HIS 0.005 0.001 HIS F 79 PHE 0.013 0.001 PHE E 305 TYR 0.013 0.001 TYR G 296 ARG 0.010 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 3.959 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: D 145 MET cc_start: 0.8213 (mtp) cc_final: 0.7951 (mtp) REVERT: E 158 MET cc_start: 0.7034 (mtp) cc_final: 0.6705 (mtp) REVERT: E 352 CYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6700 (p) outliers start: 34 outliers final: 9 residues processed: 231 average time/residue: 3.1969 time to fit residues: 842.6776 Evaluate side-chains 200 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 523 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 254 optimal weight: 0.0470 chunk 275 optimal weight: 20.0000 chunk 226 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN D 255 GLN F 52 ASN F 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 23662 Z= 0.270 Angle : 0.526 7.028 32137 Z= 0.283 Chirality : 0.041 0.190 3702 Planarity : 0.004 0.067 3955 Dihedral : 12.654 166.897 3457 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.35 % Allowed : 17.88 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.17), residues: 2764 helix: 2.31 (0.15), residues: 1341 sheet: 0.74 (0.21), residues: 580 loop : 0.73 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 69 HIS 0.009 0.001 HIS B 232 PHE 0.017 0.001 PHE E 305 TYR 0.017 0.001 TYR G 296 ARG 0.011 0.001 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 3.706 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: E 352 CYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6715 (p) outliers start: 34 outliers final: 12 residues processed: 218 average time/residue: 3.1616 time to fit residues: 789.2122 Evaluate side-chains 190 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 177 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain A residue 64 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 0.2980 chunk 171 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 270 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN F 52 ASN F 218 GLN A 411 ASN A 430 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23662 Z= 0.178 Angle : 0.485 6.160 32137 Z= 0.261 Chirality : 0.039 0.177 3702 Planarity : 0.003 0.060 3955 Dihedral : 12.559 167.251 3457 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.07 % Allowed : 18.03 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.17), residues: 2764 helix: 2.34 (0.15), residues: 1347 sheet: 0.75 (0.21), residues: 584 loop : 0.72 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 324 HIS 0.005 0.001 HIS B 232 PHE 0.013 0.001 PHE E 305 TYR 0.018 0.001 TYR G 296 ARG 0.009 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 3.771 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: E 352 CYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6666 (p) REVERT: A 423 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6400 (tm-30) outliers start: 27 outliers final: 12 residues processed: 204 average time/residue: 3.2166 time to fit residues: 756.7575 Evaluate side-chains 190 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 423 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 242 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN E 212 GLN F 52 ASN F 218 GLN A 77 GLN A 411 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23662 Z= 0.262 Angle : 0.513 6.807 32137 Z= 0.277 Chirality : 0.040 0.188 3702 Planarity : 0.004 0.068 3955 Dihedral : 12.632 169.410 3457 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.23 % Allowed : 16.96 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.17), residues: 2764 helix: 2.27 (0.14), residues: 1346 sheet: 0.78 (0.21), residues: 581 loop : 0.70 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 324 HIS 0.008 0.001 HIS B 232 PHE 0.015 0.001 PHE E 305 TYR 0.022 0.001 TYR G 296 ARG 0.009 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 3.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 352 CYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6707 (p) outliers start: 31 outliers final: 18 residues processed: 212 average time/residue: 3.2099 time to fit residues: 778.0802 Evaluate side-chains 194 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 292 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 2.9990 chunk 243 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN F 52 ASN G 132 ASN A 77 GLN A 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23662 Z= 0.319 Angle : 0.543 7.582 32137 Z= 0.293 Chirality : 0.042 0.183 3702 Planarity : 0.004 0.073 3955 Dihedral : 12.744 171.376 3457 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.59 % Allowed : 16.92 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.16), residues: 2764 helix: 2.14 (0.14), residues: 1339 sheet: 0.75 (0.21), residues: 580 loop : 0.59 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 129 HIS 0.009 0.001 HIS B 232 PHE 0.018 0.001 PHE E 305 TYR 0.021 0.001 TYR G 296 ARG 0.010 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 4.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 352 CYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6681 (p) outliers start: 40 outliers final: 22 residues processed: 214 average time/residue: 3.2539 time to fit residues: 795.0740 Evaluate side-chains 194 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 292 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 228 optimal weight: 0.5980 chunk 151 optimal weight: 0.1980 chunk 269 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 144 ASN E 212 GLN F 52 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 GLN A 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23662 Z= 0.154 Angle : 0.488 8.619 32137 Z= 0.263 Chirality : 0.039 0.186 3702 Planarity : 0.004 0.074 3955 Dihedral : 12.569 167.123 3457 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.83 % Allowed : 17.72 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.17), residues: 2764 helix: 2.35 (0.15), residues: 1335 sheet: 0.73 (0.21), residues: 582 loop : 0.67 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 324 HIS 0.004 0.001 HIS F 79 PHE 0.010 0.001 PHE E 305 TYR 0.024 0.001 TYR G 296 ARG 0.011 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 352 CYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6629 (p) REVERT: A 423 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6389 (tm-30) outliers start: 21 outliers final: 11 residues processed: 193 average time/residue: 3.3247 time to fit residues: 740.9895 Evaluate side-chains 183 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 423 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN F 52 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 HIS A 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23662 Z= 0.204 Angle : 0.502 9.748 32137 Z= 0.268 Chirality : 0.039 0.174 3702 Planarity : 0.004 0.079 3955 Dihedral : 12.567 168.503 3457 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.07 % Allowed : 17.68 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.17), residues: 2764 helix: 2.39 (0.15), residues: 1328 sheet: 0.73 (0.21), residues: 588 loop : 0.64 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 324 HIS 0.005 0.001 HIS B 232 PHE 0.012 0.001 PHE E 305 TYR 0.024 0.001 TYR G 296 ARG 0.013 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 352 CYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6615 (p) outliers start: 27 outliers final: 17 residues processed: 196 average time/residue: 3.1799 time to fit residues: 712.9005 Evaluate side-chains 188 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain A residue 292 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 52 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 HIS A 77 GLN A 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23662 Z= 0.262 Angle : 0.526 10.482 32137 Z= 0.282 Chirality : 0.040 0.180 3702 Planarity : 0.004 0.082 3955 Dihedral : 12.644 169.707 3457 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.07 % Allowed : 17.52 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.17), residues: 2764 helix: 2.26 (0.14), residues: 1335 sheet: 0.74 (0.21), residues: 583 loop : 0.63 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 129 HIS 0.008 0.001 HIS B 232 PHE 0.016 0.001 PHE E 305 TYR 0.025 0.001 TYR G 296 ARG 0.013 0.000 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 3.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 352 CYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6645 (p) outliers start: 27 outliers final: 19 residues processed: 193 average time/residue: 3.2411 time to fit residues: 716.2727 Evaluate side-chains 188 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain A residue 292 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN F 52 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 HIS A 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23662 Z= 0.287 Angle : 0.540 8.236 32137 Z= 0.289 Chirality : 0.041 0.173 3702 Planarity : 0.004 0.095 3955 Dihedral : 12.691 170.123 3457 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.95 % Allowed : 17.64 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.16), residues: 2764 helix: 2.23 (0.14), residues: 1329 sheet: 0.67 (0.21), residues: 593 loop : 0.57 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 129 HIS 0.008 0.001 HIS B 232 PHE 0.016 0.001 PHE E 305 TYR 0.025 0.001 TYR G 296 ARG 0.017 0.001 ARG A 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 352 CYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6647 (p) outliers start: 24 outliers final: 19 residues processed: 189 average time/residue: 3.2801 time to fit residues: 706.5368 Evaluate side-chains 188 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 414 ASP Chi-restraints excluded: chain A residue 292 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 228 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN F 52 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 HIS A 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.065064 restraints weight = 103261.583| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.30 r_work: 0.2743 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23662 Z= 0.170 Angle : 0.504 11.070 32137 Z= 0.270 Chirality : 0.039 0.174 3702 Planarity : 0.004 0.081 3955 Dihedral : 12.594 167.691 3457 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.99 % Allowed : 17.64 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.17), residues: 2764 helix: 2.39 (0.15), residues: 1328 sheet: 0.68 (0.21), residues: 592 loop : 0.65 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 129 HIS 0.004 0.001 HIS B 317 PHE 0.010 0.001 PHE E 305 TYR 0.026 0.001 TYR G 296 ARG 0.014 0.000 ARG E 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16294.65 seconds wall clock time: 285 minutes 46.79 seconds (17146.79 seconds total)