Starting phenix.real_space_refine on Sat Dec 9 04:53:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ral_4779/12_2023/6ral_4779_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ral_4779/12_2023/6ral_4779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ral_4779/12_2023/6ral_4779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ral_4779/12_2023/6ral_4779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ral_4779/12_2023/6ral_4779_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ral_4779/12_2023/6ral_4779_updated.pdb" } resolution = 3.5 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= 0.003 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 6532 2.51 5 N 1783 2.21 5 O 1780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A ASP 563": "OD1" <-> "OD2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B GLU 575": "OE1" <-> "OE2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10127 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4662 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 24, 'TRANS': 558} Chain: "B" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4508 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 18, 'TRANS': 552} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.77, per 1000 atoms: 0.57 Number of scatterers: 10127 At special positions: 0 Unit cell: (102.315, 82.929, 155.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 5 15.00 Mg 2 11.99 O 1780 8.00 N 1783 7.00 C 6532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.06 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: 4.06 Conformation dependent library (CDL) restraints added in 1.9 seconds 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 9 sheets defined 48.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 14 through 43 removed outlier: 3.622A pdb=" N ILE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Proline residue: A 24 - end of helix removed outlier: 6.301A pdb=" N LEU A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.688A pdb=" N ALA A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 117 removed outlier: 3.746A pdb=" N THR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 127 No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.964A pdb=" N ILE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 removed outlier: 3.929A pdb=" N VAL A 163 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 172 removed outlier: 3.554A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 172' Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.744A pdb=" N LEU A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.891A pdb=" N THR A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 221 removed outlier: 3.970A pdb=" N LEU A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.618A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 254 through 275 removed outlier: 3.626A pdb=" N ALA A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.546A pdb=" N ASP A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.977A pdb=" N VAL A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 284 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 285 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 314 through 321 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.859A pdb=" N ARG A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 434' Processing helix chain 'A' and resid 450 through 453 No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.729A pdb=" N GLU A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.549A pdb=" N ALA A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.503A pdb=" N LYS A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 Processing helix chain 'A' and resid 587 through 592 removed outlier: 3.913A pdb=" N ALA A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 11 No H-bonds generated for 'chain 'B' and resid 8 through 11' Processing helix chain 'B' and resid 14 through 38 removed outlier: 4.073A pdb=" N ARG B 19 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TYR B 20 " --> pdb=" O TYR B 16 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TRP B 26 " --> pdb=" O TRP B 22 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 30 " --> pdb=" O TRP B 26 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.654A pdb=" N ALA B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.605A pdb=" N ALA B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 80 No H-bonds generated for 'chain 'B' and resid 77 through 80' Processing helix chain 'B' and resid 82 through 100 removed outlier: 3.677A pdb=" N ALA B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.837A pdb=" N ASN B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.536A pdb=" N MET B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 156 removed outlier: 3.725A pdb=" N GLY B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 162 No H-bonds generated for 'chain 'B' and resid 159 through 162' Processing helix chain 'B' and resid 169 through 189 removed outlier: 3.980A pdb=" N ALA B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 removed outlier: 3.728A pdb=" N THR B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 228 through 235 removed outlier: 3.523A pdb=" N VAL B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 removed outlier: 4.180A pdb=" N GLY B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 removed outlier: 3.500A pdb=" N PHE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 307 removed outlier: 3.784A pdb=" N VAL B 298 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N MET B 299 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 300 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 306 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR B 307 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 377 through 380 No H-bonds generated for 'chain 'B' and resid 377 through 380' Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 407 through 413 removed outlier: 3.579A pdb=" N ARG B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 4.400A pdb=" N PHE B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 448 Processing helix chain 'B' and resid 454 through 458 removed outlier: 3.972A pdb=" N LEU B 458 " --> pdb=" O HIS B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 458' Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.598A pdb=" N ALA B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 519 removed outlier: 5.153A pdb=" N THR B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 removed outlier: 4.086A pdb=" N HIS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 571 removed outlier: 3.710A pdb=" N GLU B 568 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.663A pdb=" N GLU A 354 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 416 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 572 through 577 removed outlier: 3.589A pdb=" N ARG A 569 " --> pdb=" O ARG A 572 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 574 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL A 567 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU A 576 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE A 565 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 358 through 360 removed outlier: 7.902A pdb=" N LEU A 360 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LYS A 377 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 394 through 397 removed outlier: 3.503A pdb=" N ARG B 394 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 550 through 554 removed outlier: 6.951A pdb=" N VAL B 544 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU B 553 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B 542 " --> pdb=" O GLU B 553 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 346 through 348 removed outlier: 3.616A pdb=" N LEU B 354 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG B 348 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N TRP B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.660A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.530A pdb=" N ALA C 92 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 101 through 103 removed outlier: 3.930A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1603 1.31 - 1.43: 2783 1.43 - 1.56: 5894 1.56 - 1.69: 14 1.69 - 1.81: 45 Bond restraints: 10339 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.50e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.42e+01 bond pdb=" CA LEU B 122 " pdb=" C LEU B 122 " ideal model delta sigma weight residual 1.524 1.594 -0.070 1.24e-02 6.50e+03 3.22e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.31e+01 bond pdb=" C8 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.310 1.354 -0.044 1.00e-02 1.00e+04 1.91e+01 ... (remaining 10334 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.90: 321 106.90 - 114.13: 5777 114.13 - 121.36: 5427 121.36 - 128.59: 2418 128.59 - 135.82: 86 Bond angle restraints: 14029 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.06 19.81 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 123.10 13.73 1.00e+00 1.00e+00 1.89e+02 angle pdb=" N ARG A 233 " pdb=" CA ARG A 233 " pdb=" C ARG A 233 " ideal model delta sigma weight residual 111.07 125.42 -14.35 1.07e+00 8.73e-01 1.80e+02 angle pdb=" N LEU B 122 " pdb=" CA LEU B 122 " pdb=" C LEU B 122 " ideal model delta sigma weight residual 111.03 124.73 -13.70 1.11e+00 8.12e-01 1.52e+02 angle pdb=" N ASN B 123 " pdb=" CA ASN B 123 " pdb=" C ASN B 123 " ideal model delta sigma weight residual 111.07 121.84 -10.77 1.07e+00 8.73e-01 1.01e+02 ... (remaining 14024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 5612 19.94 - 39.89: 458 39.89 - 59.83: 65 59.83 - 79.78: 11 79.78 - 99.72: 5 Dihedral angle restraints: 6151 sinusoidal: 2507 harmonic: 3644 Sorted by residual: dihedral pdb=" C LEU A 72 " pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " ideal model delta harmonic sigma weight residual -122.60 -138.97 16.37 0 2.50e+00 1.60e-01 4.29e+01 dihedral pdb=" N LEU A 72 " pdb=" C LEU A 72 " pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " ideal model delta harmonic sigma weight residual 122.80 138.19 -15.39 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" O1B ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PB ADP A 701 " pdb=" PA ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -159.72 99.72 1 2.00e+01 2.50e-03 2.81e+01 ... (remaining 6148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1510 0.127 - 0.255: 73 0.255 - 0.382: 11 0.382 - 0.510: 5 0.510 - 0.637: 1 Chirality restraints: 1600 Sorted by residual: chirality pdb=" CA LEU A 72 " pdb=" N LEU A 72 " pdb=" C LEU A 72 " pdb=" CB LEU A 72 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA LEU B 122 " pdb=" N LEU B 122 " pdb=" C LEU B 122 " pdb=" CB LEU B 122 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CA ILE C 51 " pdb=" N ILE C 51 " pdb=" C ILE C 51 " pdb=" CB ILE C 51 " both_signs ideal model delta sigma weight residual False 2.43 2.89 -0.46 2.00e-01 2.50e+01 5.27e+00 ... (remaining 1597 not shown) Planarity restraints: 1773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 178 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C PHE B 178 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE B 178 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU B 179 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 69 " 0.017 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ARG A 69 " -0.063 2.00e-02 2.50e+03 pdb=" O ARG A 69 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE A 70 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 71 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" C HIS A 71 " -0.052 2.00e-02 2.50e+03 pdb=" O HIS A 71 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 72 " 0.018 2.00e-02 2.50e+03 ... (remaining 1770 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 113 2.64 - 3.21: 8233 3.21 - 3.77: 14627 3.77 - 4.34: 20964 4.34 - 4.90: 34567 Nonbonded interactions: 78504 Sorted by model distance: nonbonded pdb=" O3B ATP B 601 " pdb="MG MG B 602 " model vdw 2.079 2.170 nonbonded pdb=" O2B ADP A 701 " pdb="MG MG A 702 " model vdw 2.085 2.170 nonbonded pdb=" OG1 THR A 400 " pdb="MG MG A 702 " model vdw 2.092 2.170 nonbonded pdb=" OE1 GLN B 419 " pdb="MG MG B 602 " model vdw 2.120 2.170 nonbonded pdb=" OE1 GLN A 441 " pdb="MG MG A 702 " model vdw 2.206 2.170 ... (remaining 78499 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 group one per residue 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: 1.250 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: 0.010 Extract box with map and model: 4.020 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 31.070 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.006 0.081 10339 Z= 0.434 Angle : 1.186 19.811 14029 Z= 0.772 Chirality : 0.072 0.637 1600 Planarity : 0.007 0.064 1773 Dihedral : 14.571 99.721 3813 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Cbeta Deviations : 0.34 % 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: -5.95 (0.16), residues: 1269 helix: -4.66 (0.09), residues: 695 sheet: -1.26 (0.46), residues: 121 loop : -3.12 (0.21), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 223 HIS 0.007 0.001 HIS A 71 PHE 0.025 0.002 PHE A 229 TYR 0.019 0.002 TYR B 155 ARG 0.003 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.3157 time to fit residues: 87.7391 Evaluate side-chains 163 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 115 optimal weight: 0.0770 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN B 120 ASN B 191 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10339 Z= 0.182 Angle : 0.623 10.991 14029 Z= 0.307 Chirality : 0.041 0.145 1600 Planarity : 0.004 0.044 1773 Dihedral : 6.488 86.968 1473 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.34 % Allowed : 14.77 % Favored : 83.89 % 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: -4.60 (0.18), residues: 1269 helix: -3.53 (0.13), residues: 701 sheet: -1.21 (0.42), residues: 137 loop : -2.38 (0.25), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 446 HIS 0.008 0.001 HIS C 80 PHE 0.014 0.001 PHE A 257 TYR 0.018 0.001 TYR A 588 ARG 0.005 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 1.122 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 179 average time/residue: 0.2822 time to fit residues: 67.6893 Evaluate side-chains 162 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1586 time to fit residues: 3.8748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10339 Z= 0.208 Angle : 0.587 7.736 14029 Z= 0.286 Chirality : 0.041 0.137 1600 Planarity : 0.004 0.046 1773 Dihedral : 6.189 92.499 1473 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.05 % Allowed : 16.49 % Favored : 82.45 % 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: -3.71 (0.20), residues: 1269 helix: -2.74 (0.16), residues: 715 sheet: -1.00 (0.43), residues: 132 loop : -2.01 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 262 HIS 0.006 0.001 HIS C 80 PHE 0.013 0.001 PHE A 257 TYR 0.009 0.001 TYR A 202 ARG 0.006 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 1.153 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 170 average time/residue: 0.2757 time to fit residues: 63.5682 Evaluate side-chains 155 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0990 time to fit residues: 2.6305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 0.0270 chunk 55 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 0.2980 chunk 33 optimal weight: 0.0170 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10339 Z= 0.136 Angle : 0.539 7.565 14029 Z= 0.260 Chirality : 0.039 0.135 1600 Planarity : 0.003 0.044 1773 Dihedral : 5.748 94.745 1473 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.53 % Allowed : 16.59 % Favored : 81.88 % 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: -2.90 (0.22), residues: 1269 helix: -2.07 (0.18), residues: 702 sheet: -0.82 (0.44), residues: 138 loop : -1.67 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 262 HIS 0.006 0.001 HIS C 80 PHE 0.027 0.001 PHE B 163 TYR 0.012 0.001 TYR A 202 ARG 0.006 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 1.198 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 164 average time/residue: 0.2552 time to fit residues: 57.6797 Evaluate side-chains 158 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1029 time to fit residues: 3.2819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10339 Z= 0.357 Angle : 0.640 7.572 14029 Z= 0.311 Chirality : 0.043 0.135 1600 Planarity : 0.004 0.043 1773 Dihedral : 6.186 105.867 1473 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.34 % Allowed : 18.31 % Favored : 80.35 % 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: -2.75 (0.22), residues: 1269 helix: -1.97 (0.18), residues: 707 sheet: -0.74 (0.44), residues: 135 loop : -1.55 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 359 HIS 0.004 0.001 HIS C 80 PHE 0.020 0.002 PHE B 341 TYR 0.014 0.002 TYR B 566 ARG 0.007 0.001 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.073 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 164 average time/residue: 0.2553 time to fit residues: 57.1500 Evaluate side-chains 160 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1027 time to fit residues: 3.4268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.0870 chunk 110 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 0.0980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10339 Z= 0.236 Angle : 0.574 6.871 14029 Z= 0.278 Chirality : 0.041 0.136 1600 Planarity : 0.004 0.041 1773 Dihedral : 5.990 106.804 1473 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.63 % Allowed : 19.37 % Favored : 79.00 % 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: -2.39 (0.23), residues: 1269 helix: -1.65 (0.19), residues: 702 sheet: -0.59 (0.45), residues: 135 loop : -1.46 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 359 HIS 0.004 0.001 HIS C 80 PHE 0.015 0.001 PHE A 257 TYR 0.009 0.001 TYR A 202 ARG 0.005 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 1.069 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 165 average time/residue: 0.2498 time to fit residues: 56.9811 Evaluate side-chains 156 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1005 time to fit residues: 3.6877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 89 optimal weight: 0.0970 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 56 optimal weight: 7.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10339 Z= 0.149 Angle : 0.539 7.472 14029 Z= 0.260 Chirality : 0.039 0.135 1600 Planarity : 0.003 0.037 1773 Dihedral : 5.618 103.180 1473 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.38 % Allowed : 20.52 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.23), residues: 1269 helix: -1.23 (0.20), residues: 698 sheet: -0.45 (0.45), residues: 136 loop : -1.29 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.004 0.000 HIS C 80 PHE 0.014 0.001 PHE A 257 TYR 0.007 0.001 TYR A 202 ARG 0.007 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 1.154 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 159 average time/residue: 0.2518 time to fit residues: 55.6535 Evaluate side-chains 146 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0942 time to fit residues: 1.7508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.0000 chunk 96 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10339 Z= 0.200 Angle : 0.566 8.384 14029 Z= 0.272 Chirality : 0.040 0.159 1600 Planarity : 0.004 0.038 1773 Dihedral : 5.674 104.578 1473 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.67 % Allowed : 21.57 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.24), residues: 1269 helix: -1.01 (0.20), residues: 699 sheet: -0.34 (0.45), residues: 136 loop : -1.20 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 290 HIS 0.004 0.001 HIS C 80 PHE 0.012 0.001 PHE A 257 TYR 0.008 0.001 TYR A 202 ARG 0.007 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.139 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 151 average time/residue: 0.2514 time to fit residues: 52.5243 Evaluate side-chains 151 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1054 time to fit residues: 2.3055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10339 Z= 0.224 Angle : 0.582 8.130 14029 Z= 0.279 Chirality : 0.041 0.133 1600 Planarity : 0.004 0.038 1773 Dihedral : 5.723 105.921 1473 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.19 % Allowed : 21.96 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.24), residues: 1269 helix: -0.97 (0.20), residues: 700 sheet: -0.30 (0.45), residues: 136 loop : -1.16 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.004 0.001 HIS C 80 PHE 0.012 0.001 PHE B 58 TYR 0.008 0.001 TYR A 202 ARG 0.007 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.262 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 150 average time/residue: 0.2851 time to fit residues: 60.7661 Evaluate side-chains 144 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.4980 chunk 120 optimal weight: 0.8980 chunk 73 optimal weight: 0.0570 chunk 57 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10339 Z= 0.180 Angle : 0.572 8.274 14029 Z= 0.272 Chirality : 0.040 0.153 1600 Planarity : 0.004 0.037 1773 Dihedral : 5.585 103.385 1473 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.19 % Allowed : 22.34 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1269 helix: -0.81 (0.20), residues: 700 sheet: -0.17 (0.45), residues: 136 loop : -1.10 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.004 0.001 HIS C 80 PHE 0.013 0.001 PHE B 58 TYR 0.007 0.001 TYR A 202 ARG 0.007 0.000 ARG A 384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.205 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 149 average time/residue: 0.2414 time to fit residues: 50.6289 Evaluate side-chains 140 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1342 time to fit residues: 1.8571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 308 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.139945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118198 restraints weight = 15331.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121776 restraints weight = 7969.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124055 restraints weight = 5231.606| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10339 Z= 0.167 Angle : 0.574 8.357 14029 Z= 0.271 Chirality : 0.040 0.130 1600 Planarity : 0.003 0.037 1773 Dihedral : 5.438 100.549 1473 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.38 % Allowed : 22.53 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.24), residues: 1269 helix: -0.66 (0.21), residues: 707 sheet: 0.34 (0.47), residues: 125 loop : -1.06 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.003 0.001 HIS C 80 PHE 0.015 0.001 PHE B 58 TYR 0.006 0.001 TYR A 541 ARG 0.008 0.000 ARG A 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2190.22 seconds wall clock time: 40 minutes 18.49 seconds (2418.49 seconds total)