Starting phenix.real_space_refine on Fri Mar 15 19:55:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/03_2024/7xyc_33519.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/03_2024/7xyc_33519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/03_2024/7xyc_33519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/03_2024/7xyc_33519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/03_2024/7xyc_33519.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/03_2024/7xyc_33519.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7944 2.51 5 N 2148 2.21 5 O 2475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 464": "OE1" <-> "OE2" Residue "C TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12621 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4207 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 16, 'TRANS': 545} Chain: "B" Number of atoms: 4207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4207 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 16, 'TRANS': 545} Chain: "C" Number of atoms: 4207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4207 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 16, 'TRANS': 545} Time building chain proxies: 6.83, per 1000 atoms: 0.54 Number of scatterers: 12621 At special positions: 0 Unit cell: (91.26, 90.09, 136.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2475 8.00 N 2148 7.00 C 7944 6.00 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: 4.75 Conformation dependent library (CDL) restraints added in 2.3 seconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 27 sheets defined 6.2% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 101 through 114 removed outlier: 3.857A pdb=" N SER A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.574A pdb=" N ASP A 390 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'B' and resid 21 through 28 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.857A pdb=" N SER B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.574A pdb=" N ASP B 390 " --> pdb=" O GLN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'C' and resid 21 through 28 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 101 through 114 removed outlier: 3.857A pdb=" N SER C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.574A pdb=" N ASP C 390 " --> pdb=" O GLN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 removed outlier: 6.352A pdb=" N TRP A 17 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU A 53 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.755A pdb=" N ILE A 86 " --> pdb=" O PHE A 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 136 removed outlier: 7.116A pdb=" N GLY A 198 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ARG A 231 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 199 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 230 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 151 Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 184 removed outlier: 6.133A pdb=" N LEU A 183 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR A 216 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR A 242 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 218 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE A 239 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N TYR A 272 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE A 241 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE A 291 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N THR A 316 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET A 293 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A 318 " --> pdb=" O MET A 293 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A 295 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 313 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASN A 345 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 315 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL A 347 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA A 317 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE A 344 " --> pdb=" O ASN A 373 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N SER A 375 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A 346 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE A 372 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER A 406 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 374 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.866A pdb=" N PHE A 223 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 246 " --> pdb=" O GLN A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 284 through 286 removed outlier: 5.994A pdb=" N ILE A 284 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE A 305 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 334 " --> pdb=" O HIS A 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 442 through 445 removed outlier: 3.754A pdb=" N VAL A 476 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 559 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY A 522 " --> pdb=" O TYR A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 456 removed outlier: 3.727A pdb=" N LEU A 456 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 567 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE A 570 " --> pdb=" O SER A 494 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER A 494 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 19 removed outlier: 6.352A pdb=" N TRP B 17 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU B 53 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 86 through 87 removed outlier: 6.755A pdb=" N ILE B 86 " --> pdb=" O PHE B 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 134 through 136 removed outlier: 7.116A pdb=" N GLY B 198 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ARG B 231 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 199 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 230 " --> pdb=" O TYR B 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 149 through 151 Processing sheet with id=AB5, first strand: chain 'B' and resid 183 through 184 removed outlier: 6.133A pdb=" N LEU B 183 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR B 216 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR B 242 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 218 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE B 239 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N TYR B 272 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 241 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE B 291 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N THR B 316 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET B 293 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU B 318 " --> pdb=" O MET B 293 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 295 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL B 313 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASN B 345 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 315 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL B 347 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA B 317 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE B 344 " --> pdb=" O ASN B 373 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N SER B 375 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 346 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE B 372 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER B 406 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B 374 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 222 through 224 removed outlier: 6.866A pdb=" N PHE B 223 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 246 " --> pdb=" O GLN B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 284 through 286 removed outlier: 5.994A pdb=" N ILE B 284 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE B 305 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 334 " --> pdb=" O HIS B 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 442 through 445 removed outlier: 3.754A pdb=" N VAL B 476 " --> pdb=" O THR B 559 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 559 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 522 " --> pdb=" O TYR B 513 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 455 through 456 removed outlier: 3.728A pdb=" N LEU B 456 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 567 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE B 570 " --> pdb=" O SER B 494 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER B 494 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 17 through 19 removed outlier: 6.352A pdb=" N TRP C 17 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU C 53 " --> pdb=" O VAL C 81 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 86 through 87 removed outlier: 6.755A pdb=" N ILE C 86 " --> pdb=" O PHE C 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 134 through 136 removed outlier: 7.116A pdb=" N GLY C 198 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ARG C 231 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C 199 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 230 " --> pdb=" O TYR C 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 149 through 151 Processing sheet with id=AC5, first strand: chain 'C' and resid 183 through 184 removed outlier: 6.132A pdb=" N LEU C 183 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR C 216 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR C 242 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 218 " --> pdb=" O TYR C 242 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE C 239 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N TYR C 272 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE C 241 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE C 291 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N THR C 316 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET C 293 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N LEU C 318 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 295 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 313 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASN C 345 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 315 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL C 347 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA C 317 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE C 344 " --> pdb=" O ASN C 373 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER C 375 " --> pdb=" O PHE C 344 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 346 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 372 " --> pdb=" O SER C 404 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER C 406 " --> pdb=" O ILE C 372 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 374 " --> pdb=" O SER C 406 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 222 through 224 removed outlier: 6.866A pdb=" N PHE C 223 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER C 246 " --> pdb=" O GLN C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 284 through 286 removed outlier: 5.994A pdb=" N ILE C 284 " --> pdb=" O THR C 306 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE C 305 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 334 " --> pdb=" O HIS C 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 442 through 445 removed outlier: 3.754A pdb=" N VAL C 476 " --> pdb=" O THR C 559 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 559 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY C 522 " --> pdb=" O TYR C 513 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 455 through 456 removed outlier: 3.727A pdb=" N LEU C 456 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 567 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE C 570 " --> pdb=" O SER C 494 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER C 494 " --> pdb=" O ILE C 570 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 513 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: 4.12 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4143 1.35 - 1.46: 3170 1.46 - 1.58: 5500 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 12888 Sorted by residual: bond pdb=" CA TYR B 176 " pdb=" CB TYR B 176 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.62e-02 3.81e+03 2.19e+00 bond pdb=" CA TYR C 176 " pdb=" CB TYR C 176 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.62e-02 3.81e+03 2.18e+00 bond pdb=" CA TYR A 176 " pdb=" CB TYR A 176 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.62e-02 3.81e+03 2.17e+00 bond pdb=" N GLY B 233 " pdb=" CA GLY B 233 " ideal model delta sigma weight residual 1.442 1.450 -0.008 7.70e-03 1.69e+04 1.10e+00 bond pdb=" N GLY A 233 " pdb=" CA GLY A 233 " ideal model delta sigma weight residual 1.442 1.450 -0.008 7.70e-03 1.69e+04 1.08e+00 ... (remaining 12883 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.95: 261 106.95 - 113.70: 7052 113.70 - 120.46: 4456 120.46 - 127.21: 5646 127.21 - 133.97: 114 Bond angle restraints: 17529 Sorted by residual: angle pdb=" CA ILE C 268 " pdb=" CB ILE C 268 " pdb=" CG2 ILE C 268 " ideal model delta sigma weight residual 110.50 115.24 -4.74 1.70e+00 3.46e-01 7.78e+00 angle pdb=" CA ILE A 268 " pdb=" CB ILE A 268 " pdb=" CG2 ILE A 268 " ideal model delta sigma weight residual 110.50 115.24 -4.74 1.70e+00 3.46e-01 7.76e+00 angle pdb=" CA ILE B 268 " pdb=" CB ILE B 268 " pdb=" CG2 ILE B 268 " ideal model delta sigma weight residual 110.50 115.23 -4.73 1.70e+00 3.46e-01 7.74e+00 angle pdb=" C ASP C 263 " pdb=" N ASP C 264 " pdb=" CA ASP C 264 " ideal model delta sigma weight residual 121.54 126.80 -5.26 1.91e+00 2.74e-01 7.59e+00 angle pdb=" C SER C 447 " pdb=" CA SER C 447 " pdb=" CB SER C 447 " ideal model delta sigma weight residual 110.42 115.89 -5.47 1.99e+00 2.53e-01 7.55e+00 ... (remaining 17524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 6752 16.50 - 32.99: 540 32.99 - 49.49: 127 49.49 - 65.99: 9 65.99 - 82.48: 30 Dihedral angle restraints: 7458 sinusoidal: 2685 harmonic: 4773 Sorted by residual: dihedral pdb=" CA LYS B 115 " pdb=" C LYS B 115 " pdb=" N LEU B 116 " pdb=" CA LEU B 116 " ideal model delta harmonic sigma weight residual -180.00 -164.96 -15.04 0 5.00e+00 4.00e-02 9.05e+00 dihedral pdb=" CA LYS A 115 " pdb=" C LYS A 115 " pdb=" N LEU A 116 " pdb=" CA LEU A 116 " ideal model delta harmonic sigma weight residual -180.00 -164.98 -15.02 0 5.00e+00 4.00e-02 9.02e+00 dihedral pdb=" CA LYS C 115 " pdb=" C LYS C 115 " pdb=" N LEU C 116 " pdb=" CA LEU C 116 " ideal model delta harmonic sigma weight residual -180.00 -165.02 -14.98 0 5.00e+00 4.00e-02 8.98e+00 ... (remaining 7455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1584 0.054 - 0.108: 327 0.108 - 0.162: 72 0.162 - 0.216: 0 0.216 - 0.270: 3 Chirality restraints: 1986 Sorted by residual: chirality pdb=" CB ILE C 268 " pdb=" CA ILE C 268 " pdb=" CG1 ILE C 268 " pdb=" CG2 ILE C 268 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB ILE B 268 " pdb=" CA ILE B 268 " pdb=" CG1 ILE B 268 " pdb=" CG2 ILE B 268 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE A 268 " pdb=" CA ILE A 268 " pdb=" CG1 ILE A 268 " pdb=" CG2 ILE A 268 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1983 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 448 " -0.052 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO C 449 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO C 449 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 449 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 448 " -0.052 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO A 449 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 448 " 0.052 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO B 449 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 449 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 449 " 0.043 5.00e-02 4.00e+02 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2059 2.77 - 3.30: 12265 3.30 - 3.83: 20182 3.83 - 4.37: 23268 4.37 - 4.90: 41722 Nonbonded interactions: 99496 Sorted by model distance: nonbonded pdb=" OG1 THR A 205 " pdb=" OD1 ASP A 207 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR B 205 " pdb=" OD1 ASP B 207 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR C 205 " pdb=" OD1 ASP C 207 " model vdw 2.237 2.440 nonbonded pdb=" O ILE C 336 " pdb=" OG SER C 367 " model vdw 2.289 2.440 nonbonded pdb=" O ILE B 336 " pdb=" OG SER B 367 " model vdw 2.289 2.440 ... (remaining 99491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.340 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 34.600 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.002 0.030 12888 Z= 0.153 Angle : 0.631 6.591 17529 Z= 0.341 Chirality : 0.046 0.270 1986 Planarity : 0.004 0.080 2268 Dihedral : 13.853 82.483 4446 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.14 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.18), residues: 1680 helix: 2.87 (0.70), residues: 63 sheet: 0.40 (0.23), residues: 462 loop : -2.30 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 237 HIS 0.004 0.001 HIS B 468 PHE 0.014 0.001 PHE C 300 TYR 0.018 0.001 TYR B 176 ARG 0.002 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.459 Fit side-chains REVERT: A 375 SER cc_start: 0.8872 (m) cc_final: 0.8670 (m) REVERT: A 454 GLU cc_start: 0.7416 (pp20) cc_final: 0.7094 (pt0) REVERT: B 83 ASP cc_start: 0.7603 (t0) cc_final: 0.7385 (t0) REVERT: B 375 SER cc_start: 0.8955 (m) cc_final: 0.8658 (m) REVERT: C 83 ASP cc_start: 0.7412 (t0) cc_final: 0.7054 (t0) REVERT: C 268 ILE cc_start: 0.8651 (tp) cc_final: 0.8450 (tp) REVERT: C 454 GLU cc_start: 0.7465 (pp20) cc_final: 0.7092 (pt0) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1862 time to fit residues: 61.2690 Evaluate side-chains 150 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 0.0470 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12888 Z= 0.190 Angle : 0.567 5.944 17529 Z= 0.295 Chirality : 0.047 0.239 1986 Planarity : 0.003 0.057 2268 Dihedral : 4.265 16.876 1812 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 1.39 % Allowed : 10.53 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.19), residues: 1680 helix: 2.73 (0.69), residues: 63 sheet: -0.16 (0.22), residues: 558 loop : -2.21 (0.16), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 237 HIS 0.005 0.001 HIS C 468 PHE 0.009 0.001 PHE B 277 TYR 0.017 0.001 TYR B 176 ARG 0.003 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.459 Fit side-chains REVERT: A 375 SER cc_start: 0.8874 (m) cc_final: 0.8672 (m) REVERT: A 454 GLU cc_start: 0.7781 (pp20) cc_final: 0.7275 (pp20) REVERT: A 491 MET cc_start: 0.8150 (mmm) cc_final: 0.7949 (tpp) REVERT: B 232 MET cc_start: 0.8475 (mmt) cc_final: 0.8204 (mmt) REVERT: B 370 ASN cc_start: 0.7780 (m110) cc_final: 0.7567 (m110) REVERT: B 375 SER cc_start: 0.9000 (m) cc_final: 0.8752 (m) REVERT: C 83 ASP cc_start: 0.7436 (t0) cc_final: 0.7093 (t0) REVERT: C 454 GLU cc_start: 0.7700 (pp20) cc_final: 0.7110 (pp20) outliers start: 19 outliers final: 13 residues processed: 161 average time/residue: 0.1688 time to fit residues: 44.8809 Evaluate side-chains 143 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 343 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 152 optimal weight: 0.0980 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 151 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12888 Z= 0.215 Angle : 0.552 5.861 17529 Z= 0.291 Chirality : 0.047 0.265 1986 Planarity : 0.003 0.042 2268 Dihedral : 4.357 17.738 1812 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.34 % Allowed : 12.94 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.19), residues: 1680 helix: 1.33 (0.64), residues: 81 sheet: -0.00 (0.22), residues: 576 loop : -2.26 (0.16), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 237 HIS 0.005 0.001 HIS C 468 PHE 0.011 0.001 PHE A 54 TYR 0.016 0.001 TYR B 176 ARG 0.003 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 1.232 Fit side-chains REVERT: A 43 TRP cc_start: 0.9174 (t60) cc_final: 0.8712 (t60) REVERT: A 116 LEU cc_start: 0.8444 (pt) cc_final: 0.8134 (pp) REVERT: A 496 MET cc_start: 0.8999 (mmm) cc_final: 0.8780 (mmm) REVERT: B 283 ASN cc_start: 0.8417 (m-40) cc_final: 0.8191 (m-40) REVERT: B 370 ASN cc_start: 0.7867 (m110) cc_final: 0.7654 (m110) REVERT: B 493 MET cc_start: 0.7983 (tpt) cc_final: 0.7747 (tpt) REVERT: C 83 ASP cc_start: 0.7440 (t0) cc_final: 0.7111 (t0) outliers start: 32 outliers final: 27 residues processed: 164 average time/residue: 0.1788 time to fit residues: 47.2730 Evaluate side-chains 157 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 467 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 0.0010 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12888 Z= 0.205 Angle : 0.543 5.952 17529 Z= 0.286 Chirality : 0.047 0.251 1986 Planarity : 0.003 0.049 2268 Dihedral : 4.363 17.959 1812 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 4.24 % Allowed : 14.04 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.19), residues: 1680 helix: 1.42 (0.64), residues: 81 sheet: -0.03 (0.22), residues: 546 loop : -2.29 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 237 HIS 0.005 0.001 HIS B 422 PHE 0.010 0.001 PHE A 322 TYR 0.018 0.001 TYR C 176 ARG 0.003 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 141 time to evaluate : 1.395 Fit side-chains REVERT: A 43 TRP cc_start: 0.9231 (t60) cc_final: 0.8738 (t60) REVERT: A 245 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8465 (p0) REVERT: A 496 MET cc_start: 0.9057 (mmm) cc_final: 0.8776 (mmm) REVERT: B 232 MET cc_start: 0.8238 (mmt) cc_final: 0.7963 (mmt) REVERT: B 370 ASN cc_start: 0.7816 (m110) cc_final: 0.7609 (m110) REVERT: C 83 ASP cc_start: 0.7427 (t0) cc_final: 0.7096 (t0) REVERT: C 245 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8555 (p0) outliers start: 58 outliers final: 38 residues processed: 188 average time/residue: 0.1839 time to fit residues: 56.0585 Evaluate side-chains 173 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 468 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 2 optimal weight: 0.0670 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 573 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12888 Z= 0.220 Angle : 0.549 5.859 17529 Z= 0.293 Chirality : 0.047 0.245 1986 Planarity : 0.003 0.041 2268 Dihedral : 4.401 17.288 1812 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 4.97 % Allowed : 14.77 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1680 helix: 1.39 (0.63), residues: 81 sheet: -0.01 (0.22), residues: 576 loop : -2.30 (0.16), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 237 HIS 0.005 0.001 HIS C 468 PHE 0.010 0.001 PHE A 322 TYR 0.018 0.001 TYR B 176 ARG 0.002 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 142 time to evaluate : 1.392 Fit side-chains REVERT: A 43 TRP cc_start: 0.9245 (t60) cc_final: 0.8713 (t60) REVERT: A 245 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8554 (p0) REVERT: A 496 MET cc_start: 0.9050 (mmm) cc_final: 0.8754 (mmm) REVERT: B 43 TRP cc_start: 0.9201 (t60) cc_final: 0.8878 (t60) REVERT: B 232 MET cc_start: 0.8219 (mmt) cc_final: 0.7966 (mmt) REVERT: C 83 ASP cc_start: 0.7333 (t0) cc_final: 0.7025 (t0) REVERT: C 245 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8626 (p0) outliers start: 68 outliers final: 49 residues processed: 193 average time/residue: 0.1777 time to fit residues: 55.5199 Evaluate side-chains 185 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 134 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 575 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 3.9990 chunk 146 optimal weight: 0.0470 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 162 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12888 Z= 0.386 Angle : 0.635 6.221 17529 Z= 0.341 Chirality : 0.050 0.247 1986 Planarity : 0.003 0.035 2268 Dihedral : 4.929 17.547 1812 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 5.12 % Allowed : 16.01 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.19), residues: 1680 helix: 1.00 (0.64), residues: 81 sheet: -0.34 (0.22), residues: 573 loop : -2.37 (0.16), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 237 HIS 0.005 0.001 HIS A 422 PHE 0.014 0.002 PHE A 322 TYR 0.021 0.002 TYR A 176 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 140 time to evaluate : 1.336 Fit side-chains REVERT: A 245 ASN cc_start: 0.9062 (OUTLIER) cc_final: 0.8752 (p0) REVERT: A 283 ASN cc_start: 0.8733 (m-40) cc_final: 0.8510 (m110) REVERT: C 33 TYR cc_start: 0.8628 (t80) cc_final: 0.8325 (t80) REVERT: C 83 ASP cc_start: 0.7419 (t0) cc_final: 0.7096 (t0) outliers start: 70 outliers final: 57 residues processed: 185 average time/residue: 0.1842 time to fit residues: 54.4784 Evaluate side-chains 186 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 128 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 575 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12888 Z= 0.323 Angle : 0.616 6.273 17529 Z= 0.329 Chirality : 0.049 0.246 1986 Planarity : 0.003 0.033 2268 Dihedral : 4.903 18.833 1812 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 5.41 % Allowed : 17.32 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.19), residues: 1680 helix: 0.89 (0.64), residues: 81 sheet: -0.29 (0.22), residues: 597 loop : -2.46 (0.16), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 237 HIS 0.006 0.001 HIS C 422 PHE 0.013 0.002 PHE B 322 TYR 0.017 0.001 TYR A 176 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 132 time to evaluate : 1.390 Fit side-chains REVERT: A 245 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8713 (p0) REVERT: A 283 ASN cc_start: 0.8712 (m-40) cc_final: 0.8467 (m110) REVERT: B 264 ASP cc_start: 0.8453 (p0) cc_final: 0.8246 (p0) REVERT: B 575 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8027 (tp) REVERT: C 25 MET cc_start: 0.8715 (ttm) cc_final: 0.8429 (ttm) REVERT: C 33 TYR cc_start: 0.8641 (t80) cc_final: 0.8324 (t80) REVERT: C 83 ASP cc_start: 0.7329 (t0) cc_final: 0.7022 (t0) outliers start: 74 outliers final: 59 residues processed: 186 average time/residue: 0.1770 time to fit residues: 53.2235 Evaluate side-chains 188 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 127 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 575 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12888 Z= 0.262 Angle : 0.589 6.801 17529 Z= 0.313 Chirality : 0.048 0.239 1986 Planarity : 0.003 0.032 2268 Dihedral : 4.782 18.343 1812 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 5.19 % Allowed : 17.98 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.19), residues: 1680 helix: 0.97 (0.64), residues: 81 sheet: -0.27 (0.22), residues: 597 loop : -2.43 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 237 HIS 0.006 0.001 HIS C 422 PHE 0.012 0.001 PHE A 322 TYR 0.014 0.001 TYR A 176 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 130 time to evaluate : 1.452 Fit side-chains revert: symmetry clash REVERT: A 245 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8675 (p0) REVERT: B 155 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7159 (mm-30) REVERT: B 575 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7936 (tp) REVERT: C 25 MET cc_start: 0.8743 (ttm) cc_final: 0.8459 (ttm) REVERT: C 33 TYR cc_start: 0.8657 (t80) cc_final: 0.8348 (t80) REVERT: C 83 ASP cc_start: 0.7286 (t0) cc_final: 0.6992 (t0) REVERT: C 253 ASN cc_start: 0.9235 (OUTLIER) cc_final: 0.8780 (m-40) outliers start: 71 outliers final: 62 residues processed: 180 average time/residue: 0.1768 time to fit residues: 51.7855 Evaluate side-chains 192 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 127 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 575 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.2980 chunk 141 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN B 566 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12888 Z= 0.171 Angle : 0.554 6.830 17529 Z= 0.292 Chirality : 0.047 0.243 1986 Planarity : 0.003 0.032 2268 Dihedral : 4.516 17.441 1812 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.51 % Allowed : 19.66 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.20), residues: 1680 helix: 1.17 (0.64), residues: 81 sheet: -0.18 (0.22), residues: 597 loop : -2.34 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 237 HIS 0.006 0.001 HIS C 422 PHE 0.011 0.001 PHE B 322 TYR 0.010 0.001 TYR A 176 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 140 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 245 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8556 (p0) REVERT: A 264 ASP cc_start: 0.8523 (p0) cc_final: 0.8230 (p0) REVERT: B 43 TRP cc_start: 0.9183 (t60) cc_final: 0.8844 (t60) REVERT: B 155 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7131 (mm-30) REVERT: B 575 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7712 (tt) REVERT: C 33 TYR cc_start: 0.8674 (t80) cc_final: 0.8309 (t80) REVERT: C 83 ASP cc_start: 0.7321 (t0) cc_final: 0.7030 (t0) REVERT: C 253 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8785 (m-40) outliers start: 48 outliers final: 42 residues processed: 173 average time/residue: 0.1793 time to fit residues: 50.5710 Evaluate side-chains 180 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 135 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 575 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12888 Z= 0.243 Angle : 0.575 6.996 17529 Z= 0.304 Chirality : 0.047 0.241 1986 Planarity : 0.003 0.031 2268 Dihedral : 4.596 18.147 1812 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.80 % Allowed : 19.52 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.20), residues: 1680 helix: 1.14 (0.63), residues: 81 sheet: -0.19 (0.22), residues: 597 loop : -2.36 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 237 HIS 0.005 0.001 HIS C 422 PHE 0.014 0.001 PHE A 54 TYR 0.017 0.001 TYR B 168 ARG 0.002 0.000 ARG A 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 131 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 245 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8616 (p0) REVERT: A 264 ASP cc_start: 0.8528 (p0) cc_final: 0.8244 (p0) REVERT: B 155 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 575 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7881 (tt) REVERT: C 33 TYR cc_start: 0.8667 (t80) cc_final: 0.8290 (t80) REVERT: C 83 ASP cc_start: 0.7261 (t0) cc_final: 0.6970 (t0) REVERT: C 253 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8789 (m-40) outliers start: 52 outliers final: 49 residues processed: 169 average time/residue: 0.1975 time to fit residues: 53.2910 Evaluate side-chains 179 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 127 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 575 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 chunk 37 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.115308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.096337 restraints weight = 18488.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.098561 restraints weight = 11754.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.100263 restraints weight = 8702.303| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12888 Z= 0.158 Angle : 0.539 7.077 17529 Z= 0.284 Chirality : 0.046 0.300 1986 Planarity : 0.003 0.032 2268 Dihedral : 4.339 16.875 1812 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.80 % Allowed : 19.66 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.20), residues: 1680 helix: 1.27 (0.63), residues: 81 sheet: -0.01 (0.22), residues: 576 loop : -2.31 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 237 HIS 0.004 0.001 HIS A 422 PHE 0.011 0.001 PHE B 322 TYR 0.018 0.001 TYR B 168 ARG 0.002 0.000 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2245.81 seconds wall clock time: 41 minutes 58.56 seconds (2518.56 seconds total)