Starting phenix.real_space_refine on Tue Feb 20 04:10:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvl_21922/02_2024/6wvl_21922_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvl_21922/02_2024/6wvl_21922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvl_21922/02_2024/6wvl_21922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvl_21922/02_2024/6wvl_21922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvl_21922/02_2024/6wvl_21922_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvl_21922/02_2024/6wvl_21922_trim.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 sd= 0.023 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 10 5.49 5 Mg 2 5.21 5 S 96 5.16 5 C 8622 2.51 5 N 2318 2.21 5 O 2650 1.98 5 H 13046 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ARG 215": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C ARG 215": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 220": "OE1" <-> "OE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D ARG 284": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 327": "OE1" <-> "OE2" Residue "D GLU 330": "OE1" <-> "OE2" Residue "D PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D GLU 431": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26744 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 6659 Classifications: {'peptide': 430} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Chain: "B" Number of atoms: 6590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6590 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "C" Number of atoms: 6659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 6659 Classifications: {'peptide': 430} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Chain: "D" Number of atoms: 6590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6590 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.45, per 1000 atoms: 0.47 Number of scatterers: 26744 At special positions: 0 Unit cell: (122.636, 83.979, 122.636, 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 96 16.00 P 10 15.00 Mg 2 11.99 O 2650 8.00 N 2318 7.00 C 8622 6.00 H 13046 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: 21.67 Conformation dependent library (CDL) restraints added in 2.9 seconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 10 sheets defined 54.0% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.715A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 4.152A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 127 removed outlier: 3.958A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 3.868A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 4.673A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.911A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.910A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.166A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.749A pdb=" N CYS A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 6.338A pdb=" N ALA A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.636A pdb=" N THR A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 400 removed outlier: 3.604A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.353A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.754A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 48 removed outlier: 3.806A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 71 through 80 removed outlier: 4.639A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.835A pdb=" N PHE B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 109 through 129 removed outlier: 3.744A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 removed outlier: 3.752A pdb=" N THR B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.560A pdb=" N HIS B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.548A pdb=" N THR B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.673A pdb=" N THR B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.782A pdb=" N ASN B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.515A pdb=" N ARG B 284 " --> pdb=" O GLN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 3.549A pdb=" N GLN B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.961A pdb=" N GLN B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 400 removed outlier: 3.503A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 414 through 436 removed outlier: 3.859A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 removed outlier: 3.729A pdb=" N GLU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.159A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 79 Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 127 removed outlier: 3.912A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 125 " --> pdb=" O ARG C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 3.868A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 4.673A pdb=" N HIS C 192 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C 198 " --> pdb=" O THR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.801A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.834A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 removed outlier: 3.614A pdb=" N CYS C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 6.389A pdb=" N ALA C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.622A pdb=" N THR C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 400 removed outlier: 3.603A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 415 through 435 removed outlier: 4.352A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.754A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 48 removed outlier: 3.819A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 71 through 80 removed outlier: 4.639A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.886A pdb=" N PHE D 87 " --> pdb=" O GLY D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.745A pdb=" N LEU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 removed outlier: 3.751A pdb=" N THR D 151 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.689A pdb=" N HIS D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.756A pdb=" N THR D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 removed outlier: 3.782A pdb=" N ASN D 258 " --> pdb=" O LYS D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.873A pdb=" N ARG D 284 " --> pdb=" O GLN D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 339 removed outlier: 3.982A pdb=" N GLN D 336 " --> pdb=" O MET D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 384 through 400 removed outlier: 3.535A pdb=" N PHE D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 397 " --> pdb=" O GLU D 393 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET D 398 " --> pdb=" O GLN D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 414 through 436 removed outlier: 3.858A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN D 436 " --> pdb=" O TYR D 432 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.040A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.626A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 248 removed outlier: 8.234A pdb=" N LYS A 352 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASN A 356 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.975A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASP B 205 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N PHE B 272 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.157A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.832A pdb=" N LYS C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 246 through 248 removed outlier: 8.233A pdb=" N LYS C 352 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N CYS C 315 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY C 354 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU C 317 " --> pdb=" O GLY C 354 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN C 356 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR C 319 " --> pdb=" O ASN C 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.980A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU D 137 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE D 7 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N HIS D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP D 205 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 12.173A pdb=" N PHE D 272 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR D 314 " --> pdb=" O ASN D 380 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 55 621 hydrogen bonds defined for protein. 1788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.19 Time building geometry restraints manager: 22.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.10: 13008 1.10 - 1.28: 2305 1.28 - 1.46: 4390 1.46 - 1.64: 7209 1.64 - 1.82: 154 Bond restraints: 27066 Sorted by residual: bond pdb=" N SER B 97 " pdb=" H SER B 97 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" CZ PHE B 272 " pdb=" HZ PHE B 272 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N CYS B 213 " pdb=" H CYS B 213 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N GLU B 159 " pdb=" H GLU B 159 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N LEU D 153 " pdb=" H LEU D 153 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 ... (remaining 27061 not shown) Histogram of bond angle deviations from ideal: 84.82 - 94.91: 9 94.91 - 105.00: 551 105.00 - 115.08: 31212 115.08 - 125.17: 16090 125.17 - 135.26: 816 Bond angle restraints: 48678 Sorted by residual: angle pdb=" CA ASP C 392 " pdb=" CB ASP C 392 " pdb=" CG ASP C 392 " ideal model delta sigma weight residual 112.60 118.90 -6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" CA ASP A 392 " pdb=" CB ASP A 392 " pdb=" CG ASP A 392 " ideal model delta sigma weight residual 112.60 118.85 -6.25 1.00e+00 1.00e+00 3.91e+01 angle pdb=" CA ASP A 98 " pdb=" CB ASP A 98 " pdb=" CG ASP A 98 " ideal model delta sigma weight residual 112.60 118.79 -6.19 1.00e+00 1.00e+00 3.83e+01 angle pdb=" CA ASP C 98 " pdb=" CB ASP C 98 " pdb=" CG ASP C 98 " ideal model delta sigma weight residual 112.60 118.75 -6.15 1.00e+00 1.00e+00 3.78e+01 angle pdb=" CA ASN D 167 " pdb=" CB ASN D 167 " pdb=" CG ASN D 167 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 ... (remaining 48673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.73: 12145 27.73 - 55.46: 564 55.46 - 83.20: 226 83.20 - 110.93: 34 110.93 - 138.66: 29 Dihedral angle restraints: 12998 sinusoidal: 7126 harmonic: 5872 Sorted by residual: dihedral pdb=" O3B GTP C 501 " pdb=" O3A GTP C 501 " pdb=" PB GTP C 501 " pdb=" PA GTP C 501 " ideal model delta sinusoidal sigma weight residual -68.92 69.74 -138.66 1 2.00e+01 2.50e-03 4.20e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -32.63 137.22 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -31.62 136.22 1 2.00e+01 2.50e-03 4.13e+01 ... (remaining 12995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1131 0.070 - 0.140: 627 0.140 - 0.210: 232 0.210 - 0.280: 65 0.280 - 0.350: 23 Chirality restraints: 2078 Sorted by residual: chirality pdb=" CA ASP C 47 " pdb=" N ASP C 47 " pdb=" C ASP C 47 " pdb=" CB ASP C 47 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA LEU D 242 " pdb=" N LEU D 242 " pdb=" C LEU D 242 " pdb=" CB LEU D 242 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA ASP A 47 " pdb=" N ASP A 47 " pdb=" C ASP A 47 " pdb=" CB ASP A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 2075 not shown) Planarity restraints: 4098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 21 " -0.301 2.00e-02 2.50e+03 9.87e-02 3.89e+02 pdb=" CG TRP C 21 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP C 21 " 0.087 2.00e-02 2.50e+03 pdb=" CD2 TRP C 21 " 0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP C 21 " 0.090 2.00e-02 2.50e+03 pdb=" CE2 TRP C 21 " 0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP C 21 " 0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 21 " -0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 21 " 0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP C 21 " -0.039 2.00e-02 2.50e+03 pdb=" HD1 TRP C 21 " 0.043 2.00e-02 2.50e+03 pdb=" HE1 TRP C 21 " 0.040 2.00e-02 2.50e+03 pdb=" HE3 TRP C 21 " 0.094 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 21 " -0.116 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 21 " 0.061 2.00e-02 2.50e+03 pdb=" HH2 TRP C 21 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 21 " -0.300 2.00e-02 2.50e+03 9.85e-02 3.88e+02 pdb=" CG TRP A 21 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 21 " 0.086 2.00e-02 2.50e+03 pdb=" CD2 TRP A 21 " 0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP A 21 " 0.090 2.00e-02 2.50e+03 pdb=" CE2 TRP A 21 " 0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP A 21 " 0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 21 " -0.065 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 21 " 0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP A 21 " -0.039 2.00e-02 2.50e+03 pdb=" HD1 TRP A 21 " 0.043 2.00e-02 2.50e+03 pdb=" HE1 TRP A 21 " 0.040 2.00e-02 2.50e+03 pdb=" HE3 TRP A 21 " 0.094 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 21 " -0.116 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 21 " 0.061 2.00e-02 2.50e+03 pdb=" HH2 TRP A 21 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 320 " -0.199 9.50e-02 1.11e+02 1.15e-01 2.03e+02 pdb=" NE ARG A 320 " 0.068 2.00e-02 2.50e+03 pdb=" CZ ARG A 320 " 0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG A 320 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 320 " 0.088 2.00e-02 2.50e+03 pdb="HH11 ARG A 320 " -0.153 2.00e-02 2.50e+03 pdb="HH12 ARG A 320 " 0.154 2.00e-02 2.50e+03 pdb="HH21 ARG A 320 " -0.052 2.00e-02 2.50e+03 pdb="HH22 ARG A 320 " -0.125 2.00e-02 2.50e+03 ... (remaining 4095 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1943 2.18 - 2.79: 47533 2.79 - 3.39: 78699 3.39 - 4.00: 106386 4.00 - 4.60: 156410 Nonbonded interactions: 390971 Sorted by model distance: nonbonded pdb=" OE1 GLU A 71 " pdb=" HG1 THR A 73 " model vdw 1.579 1.850 nonbonded pdb=" OE1 GLU C 71 " pdb=" HG1 THR C 73 " model vdw 1.580 1.850 nonbonded pdb=" HG1 THR C 145 " pdb=" O2G GTP C 501 " model vdw 1.598 1.850 nonbonded pdb=" HG SER C 178 " pdb=" OE1 GLU C 183 " model vdw 1.607 1.850 nonbonded pdb=" HG SER A 178 " pdb=" OE1 GLU A 183 " model vdw 1.608 1.850 ... (remaining 390966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.420 Extract box with map and model: 1.800 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 84.420 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.140 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4678 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 : 0.013 0.114 14020 Z= 0.826 Angle : 1.976 12.097 19062 Z= 1.296 Chirality : 0.100 0.350 2078 Planarity : 0.016 0.142 2472 Dihedral : 19.253 138.661 5306 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.41 % Allowed : 3.76 % Favored : 95.83 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 5.00 % 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: -1.96 (0.18), residues: 1700 helix: -2.04 (0.15), residues: 722 sheet: -0.16 (0.32), residues: 244 loop : -0.67 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.198 0.030 TRP C 21 HIS 0.026 0.005 HIS B 6 PHE 0.090 0.017 PHE A 169 TYR 0.147 0.024 TYR B 283 ARG 0.017 0.002 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 57 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Evaluate side-chains 442 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 436 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 382 THR cc_start: 0.5803 (p) cc_final: 0.5460 (p) REVERT: D 420 GLU cc_start: 0.4205 (mt-10) cc_final: 0.3673 (mp0) outliers start: 6 outliers final: 1 residues processed: 441 average time/residue: 0.6481 time to fit residues: 404.2889 Evaluate side-chains 322 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 321 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 101 ASN A 249 ASN A 342 GLN A 356 ASN B 37 HIS B 43 GLN ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 101 ASN C 176 GLN C 206 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN D 37 HIS D 136 GLN D 167 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14020 Z= 0.394 Angle : 0.848 9.479 19062 Z= 0.437 Chirality : 0.051 0.372 2078 Planarity : 0.007 0.065 2472 Dihedral : 12.398 117.713 2126 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.47 % Favored : 97.35 % Rotamer: Outliers : 2.39 % Allowed : 10.31 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.19), residues: 1700 helix: -0.70 (0.17), residues: 762 sheet: -0.72 (0.30), residues: 246 loop : -0.65 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 21 HIS 0.013 0.002 HIS A 8 PHE 0.026 0.003 PHE A 87 TYR 0.027 0.003 TYR C 224 ARG 0.009 0.001 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 57 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Evaluate side-chains 467 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 432 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASN cc_start: 0.7313 (m-40) cc_final: 0.7038 (m110) REVERT: A 309 HIS cc_start: 0.6430 (OUTLIER) cc_final: 0.5739 (t-90) REVERT: A 367 ASP cc_start: 0.4293 (OUTLIER) cc_final: 0.3799 (m-30) REVERT: B 401 ARG cc_start: 0.5315 (ttm170) cc_final: 0.4542 (ttm170) outliers start: 35 outliers final: 15 residues processed: 453 average time/residue: 0.5734 time to fit residues: 385.8708 Evaluate side-chains 364 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 347 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 286 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 154 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 124 optimal weight: 5.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS B 433 GLN D 136 GLN D 167 ASN D 249 ASN D 406 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.7675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14020 Z= 0.193 Angle : 0.593 6.496 19062 Z= 0.302 Chirality : 0.042 0.237 2078 Planarity : 0.005 0.091 2472 Dihedral : 9.789 117.058 2126 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.25 % Allowed : 14.48 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 1700 helix: 0.31 (0.18), residues: 762 sheet: -0.87 (0.33), residues: 212 loop : -0.45 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 21 HIS 0.011 0.001 HIS C 8 PHE 0.014 0.002 PHE A 49 TYR 0.015 0.001 TYR A 108 ARG 0.007 0.001 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 57 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Evaluate side-chains 412 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 379 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASN cc_start: 0.7400 (m-40) cc_final: 0.7184 (m110) REVERT: B 234 THR cc_start: 0.5510 (p) cc_final: 0.5281 (p) REVERT: B 283 TYR cc_start: 0.7634 (m-80) cc_final: 0.7267 (m-80) REVERT: B 401 ARG cc_start: 0.5693 (ttm170) cc_final: 0.4779 (ttp-170) REVERT: D 90 ASP cc_start: 0.5914 (m-30) cc_final: 0.5659 (m-30) REVERT: D 325 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6492 (mmt) REVERT: D 385 GLN cc_start: 0.6326 (tt0) cc_final: 0.6119 (tt0) outliers start: 33 outliers final: 22 residues processed: 391 average time/residue: 0.5342 time to fit residues: 311.6379 Evaluate side-chains 348 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 325 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 429 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 1.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14020 Z= 0.342 Angle : 0.723 10.328 19062 Z= 0.370 Chirality : 0.047 0.243 2078 Planarity : 0.006 0.057 2472 Dihedral : 9.173 140.253 2124 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.21 % Allowed : 15.44 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1700 helix: 0.31 (0.18), residues: 772 sheet: -0.92 (0.33), residues: 240 loop : -0.87 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 21 HIS 0.014 0.002 HIS A 8 PHE 0.087 0.003 PHE A 67 TYR 0.019 0.002 TYR D 224 ARG 0.005 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 57 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 440 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ASP cc_start: 0.5404 (t70) cc_final: 0.5144 (t0) REVERT: A 425 MET cc_start: 0.6803 (tpt) cc_final: 0.6199 (tpt) REVERT: B 401 ARG cc_start: 0.4986 (ttm170) cc_final: 0.3395 (ttp-170) REVERT: C 176 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6637 (mm110) REVERT: C 326 LYS cc_start: 0.5491 (ptpp) cc_final: 0.5255 (ptpp) outliers start: 47 outliers final: 23 residues processed: 462 average time/residue: 0.5527 time to fit residues: 372.3032 Evaluate side-chains 359 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 336 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 396 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 113 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 overall best weight: 7.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 350 ASN C 8 HIS C 50 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 1.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14020 Z= 0.259 Angle : 0.598 6.907 19062 Z= 0.302 Chirality : 0.043 0.159 2078 Planarity : 0.005 0.049 2472 Dihedral : 8.456 133.721 2124 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.66 % Allowed : 19.40 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1700 helix: 0.55 (0.19), residues: 780 sheet: -1.05 (0.31), residues: 242 loop : -0.76 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 21 HIS 0.011 0.001 HIS A 8 PHE 0.039 0.002 PHE D 169 TYR 0.016 0.001 TYR B 36 ARG 0.014 0.001 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 57 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Evaluate side-chains 403 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 364 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.6872 (m-30) cc_final: 0.6646 (m-30) REVERT: A 425 MET cc_start: 0.6926 (tpt) cc_final: 0.6311 (tpt) REVERT: B 401 ARG cc_start: 0.5571 (ttm170) cc_final: 0.3502 (mtp180) REVERT: C 6 SER cc_start: 0.7071 (m) cc_final: 0.6858 (m) REVERT: C 176 GLN cc_start: 0.6941 (mm-40) cc_final: 0.6589 (mm110) REVERT: C 326 LYS cc_start: 0.5320 (ptpp) cc_final: 0.4897 (ptpt) outliers start: 39 outliers final: 26 residues processed: 383 average time/residue: 0.5990 time to fit residues: 337.1613 Evaluate side-chains 357 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 331 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 306 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 133 GLN C 50 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 1.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14020 Z= 0.264 Angle : 0.585 6.807 19062 Z= 0.296 Chirality : 0.042 0.142 2078 Planarity : 0.005 0.057 2472 Dihedral : 8.259 134.531 2124 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.87 % Allowed : 20.97 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1700 helix: 0.54 (0.18), residues: 792 sheet: -1.09 (0.32), residues: 242 loop : -0.73 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 21 HIS 0.005 0.001 HIS A 88 PHE 0.024 0.002 PHE D 169 TYR 0.015 0.001 TYR B 36 ARG 0.009 0.001 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 57 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Evaluate side-chains 381 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 339 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6731 (ttmt) cc_final: 0.6422 (ptpt) REVERT: B 401 ARG cc_start: 0.5613 (ttm170) cc_final: 0.3487 (ttm110) REVERT: C 108 TYR cc_start: 0.6595 (m-10) cc_final: 0.6374 (m-80) REVERT: C 326 LYS cc_start: 0.4760 (ptpp) cc_final: 0.4007 (ptpt) outliers start: 42 outliers final: 30 residues processed: 361 average time/residue: 0.5949 time to fit residues: 307.5361 Evaluate side-chains 346 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 316 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 232 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN C 342 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 1.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14020 Z= 0.184 Angle : 0.536 6.968 19062 Z= 0.268 Chirality : 0.041 0.147 2078 Planarity : 0.004 0.049 2472 Dihedral : 7.850 129.714 2124 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.05 % Allowed : 21.93 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1700 helix: 0.76 (0.19), residues: 790 sheet: -1.17 (0.32), residues: 230 loop : -0.57 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 21 HIS 0.003 0.001 HIS B 229 PHE 0.018 0.001 PHE D 169 TYR 0.013 0.001 TYR B 36 ARG 0.006 0.001 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 57 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 342 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 MET cc_start: 0.7061 (tpt) cc_final: 0.6259 (tpt) REVERT: B 401 ARG cc_start: 0.5388 (ttm170) cc_final: 0.3424 (ttm110) REVERT: C 326 LYS cc_start: 0.4865 (ptpp) cc_final: 0.3969 (ptpt) REVERT: D 413 MET cc_start: 0.6807 (mmm) cc_final: 0.6379 (mmm) outliers start: 30 outliers final: 24 residues processed: 355 average time/residue: 0.6109 time to fit residues: 308.0500 Evaluate side-chains 341 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 317 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 172 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 30.0000 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN D 101 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 1.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14020 Z= 0.241 Angle : 0.566 6.906 19062 Z= 0.284 Chirality : 0.042 0.150 2078 Planarity : 0.005 0.101 2472 Dihedral : 7.859 134.214 2124 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.39 % Allowed : 21.58 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1700 helix: 0.79 (0.19), residues: 782 sheet: -1.28 (0.32), residues: 230 loop : -0.59 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.010 0.001 HIS D 192 PHE 0.014 0.001 PHE B 319 TYR 0.019 0.001 TYR C 224 ARG 0.008 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 57 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 335 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 ARG cc_start: 0.5385 (ttm170) cc_final: 0.3227 (ttm170) REVERT: C 326 LYS cc_start: 0.4821 (ptpp) cc_final: 0.3767 (ptpt) REVERT: D 157 ILE cc_start: 0.7921 (mt) cc_final: 0.7702 (mt) REVERT: D 413 MET cc_start: 0.6850 (mmm) cc_final: 0.6413 (mmm) outliers start: 35 outliers final: 29 residues processed: 354 average time/residue: 0.6167 time to fit residues: 319.9083 Evaluate side-chains 343 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 314 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 396 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS C 342 GLN D 101 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 1.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14020 Z= 0.250 Angle : 0.563 6.899 19062 Z= 0.283 Chirality : 0.042 0.143 2078 Planarity : 0.004 0.053 2472 Dihedral : 7.827 134.405 2124 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.98 % Allowed : 21.86 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1700 helix: 0.80 (0.19), residues: 782 sheet: -1.34 (0.32), residues: 230 loop : -0.56 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.009 0.001 HIS D 192 PHE 0.013 0.001 PHE B 319 TYR 0.011 0.001 TYR D 224 ARG 0.006 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 57 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 319 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6360 (ptpt) cc_final: 0.5791 (ptpt) REVERT: B 401 ARG cc_start: 0.5243 (ttm170) cc_final: 0.3159 (ttm170) REVERT: C 326 LYS cc_start: 0.4791 (ptpp) cc_final: 0.3712 (ptpt) REVERT: D 157 ILE cc_start: 0.7955 (mt) cc_final: 0.7748 (mt) REVERT: D 413 MET cc_start: 0.6868 (mmm) cc_final: 0.6328 (mmm) outliers start: 29 outliers final: 27 residues processed: 335 average time/residue: 0.5944 time to fit residues: 285.3101 Evaluate side-chains 341 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 314 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 381 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN D 101 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 1.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14020 Z= 0.275 Angle : 0.575 6.822 19062 Z= 0.289 Chirality : 0.042 0.150 2078 Planarity : 0.005 0.052 2472 Dihedral : 7.935 136.971 2124 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.25 % Allowed : 21.65 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1700 helix: 0.82 (0.19), residues: 772 sheet: -1.42 (0.31), residues: 248 loop : -0.58 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 21 HIS 0.009 0.001 HIS D 192 PHE 0.015 0.001 PHE B 319 TYR 0.015 0.001 TYR C 224 ARG 0.007 0.001 ARG A 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 57 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Evaluate side-chains 352 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 319 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6296 (ptpt) cc_final: 0.5933 (ptpt) REVERT: B 401 ARG cc_start: 0.5058 (ttm170) cc_final: 0.3056 (ttm110) REVERT: B 413 MET cc_start: 0.7037 (mmm) cc_final: 0.6721 (mtp) REVERT: C 326 LYS cc_start: 0.4599 (ptpp) cc_final: 0.3505 (ptpt) REVERT: D 323 MET cc_start: 0.6945 (pmm) cc_final: 0.6594 (pmm) outliers start: 33 outliers final: 33 residues processed: 337 average time/residue: 0.5899 time to fit residues: 286.8326 Evaluate side-chains 332 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 299 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 396 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** 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 = 0.3377 r_free = 0.3377 target = 0.111319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.096683 restraints weight = 60485.841| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.12 r_work: 0.3011 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 1.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 14020 Z= 0.309 Angle : 0.795 59.190 19062 Z= 0.472 Chirality : 0.042 0.152 2078 Planarity : 0.005 0.050 2472 Dihedral : 7.936 136.970 2124 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.46 % Allowed : 22.13 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1700 helix: 0.82 (0.19), residues: 772 sheet: -1.43 (0.31), residues: 248 loop : -0.58 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.008 0.001 HIS D 192 PHE 0.012 0.001 PHE B 319 TYR 0.024 0.001 TYR C 224 ARG 0.005 0.000 ARG A 390 =============================================================================== Job complete usr+sys time: 6637.44 seconds wall clock time: 118 minutes 25.72 seconds (7105.72 seconds total)