Starting phenix.real_space_refine on Mon Feb 19 19:20:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgd_33186/02_2024/7xgd_33186_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgd_33186/02_2024/7xgd_33186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgd_33186/02_2024/7xgd_33186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgd_33186/02_2024/7xgd_33186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgd_33186/02_2024/7xgd_33186_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xgd_33186/02_2024/7xgd_33186_trim.pdb" } resolution = 4.0 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 85 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 104 5.16 5 C 8488 2.51 5 N 2320 2.21 5 O 2546 1.98 5 H 12030 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25488 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 12693 Classifications: {'peptide': 836} Modifications used: {'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 47, 'TRANS': 785} Chain breaks: 2 Chain: "B" Number of atoms: 12739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 12739 Classifications: {'peptide': 836} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 47, 'TRANS': 786} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.39, per 1000 atoms: 0.45 Number of scatterers: 25488 At special positions: 0 Unit cell: (145.26, 100.068, 138.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 O 2546 8.00 N 2320 7.00 C 8488 6.00 H 12030 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.02 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 672 " distance=2.04 Simple disulfide: pdb=" SG CYS A 670 " - pdb=" SG CYS B 670 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.02 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.04 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 458 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 849 " distance=2.03 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.03 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 21 " " NAG A1002 " - " ASN A 105 " " NAG B1001 " - " ASN B 21 " " NAG B1002 " - " ASN B 105 " Time building additional restraints: 21.74 Conformation dependent library (CDL) restraints added in 3.0 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3144 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 35 sheets defined 17.5% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.126A pdb=" N LEU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.748A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.642A pdb=" N ASN A 198 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 314 through 321 removed outlier: 4.962A pdb=" N MET A 319 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.631A pdb=" N GLU A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 4.045A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.527A pdb=" N ARG A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 506 through 510 removed outlier: 4.460A pdb=" N GLY A 510 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 624 through 629 removed outlier: 3.993A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 678 through 701 removed outlier: 4.094A pdb=" N SER A 699 " --> pdb=" O PHE A 695 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.550A pdb=" N GLU B 20 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.993A pdb=" N LEU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.655A pdb=" N ILE B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.644A pdb=" N ASN B 198 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 314 through 321 removed outlier: 4.965A pdb=" N MET B 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.640A pdb=" N GLU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.903A pdb=" N PHE B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.747A pdb=" N ARG B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N MET B 432 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.547A pdb=" N ASP B 509 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 624 through 629 removed outlier: 4.006A pdb=" N TYR B 628 " --> pdb=" O ASP B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 701 removed outlier: 3.700A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER B 699 " --> pdb=" O PHE B 695 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.471A pdb=" N ILE A 7 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU A 32 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 58 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 60 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 90 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG A 59 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 25 removed outlier: 3.613A pdb=" N ILE A 51 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.511A pdb=" N THR A 177 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 209 removed outlier: 3.638A pdb=" N ALA A 220 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER A 208 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS A 218 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 226 removed outlier: 3.564A pdb=" N TYR A 224 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 239 through 241 removed outlier: 4.279A pdb=" N ARG A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA9, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AB1, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.686A pdb=" N LYS A 309 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 331 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ARG A 361 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 332 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 358 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU A 393 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 360 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR A 417 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 391 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 325 through 326 removed outlier: 8.125A pdb=" N PHE A 326 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL A 354 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU A 381 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY A 356 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AB4, first strand: chain 'A' and resid 523 through 524 removed outlier: 3.627A pdb=" N THR A 494 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 552 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 587 through 590 Processing sheet with id=AB6, first strand: chain 'A' and resid 747 through 749 removed outlier: 3.604A pdb=" N ASN A 789 " --> pdb=" O ILE A 773 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 809 through 813 Processing sheet with id=AB8, first strand: chain 'A' and resid 846 through 851 removed outlier: 4.078A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 846 through 851 removed outlier: 4.078A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.446A pdb=" N ILE B 7 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU B 32 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 58 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 90 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG B 112 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE B 90 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 24 through 25 removed outlier: 3.543A pdb=" N ILE B 51 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AC4, first strand: chain 'B' and resid 206 through 209 removed outlier: 6.457A pdb=" N SER B 208 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.578A pdb=" N TYR B 224 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 239 through 241 removed outlier: 4.284A pdb=" N ARG B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AC8, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.684A pdb=" N LYS B 309 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 331 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 358 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU B 393 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE B 360 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TYR B 417 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR B 391 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA B 419 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU B 393 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 326 removed outlier: 8.161A pdb=" N PHE B 326 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL B 354 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLU B 381 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLY B 356 " --> pdb=" O GLU B 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 468 through 469 Processing sheet with id=AD2, first strand: chain 'B' and resid 523 through 524 removed outlier: 3.551A pdb=" N PHE B 493 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 567 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 498 through 499 removed outlier: 3.722A pdb=" N LYS B 498 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 548 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 585 through 593 removed outlier: 5.042A pdb=" N VAL B 587 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LYS B 600 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B 589 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 598 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER B 591 " --> pdb=" O GLN B 596 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN B 596 " --> pdb=" O SER B 591 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 747 through 749 removed outlier: 4.178A pdb=" N TYR B 613 " --> pdb=" O CYS B 776 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N CYS B 776 " --> pdb=" O TYR B 613 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 789 " --> pdb=" O ILE B 773 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 809 through 813 Processing sheet with id=AD7, first strand: chain 'B' and resid 846 through 851 removed outlier: 4.093A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 846 through 851 removed outlier: 4.093A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.49 Time building geometry restraints manager: 22.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12030 1.03 - 1.23: 372 1.23 - 1.43: 5497 1.43 - 1.63: 7779 1.63 - 1.83: 132 Bond restraints: 25810 Sorted by residual: bond pdb=" C PRO A 581 " pdb=" N SER A 582 " ideal model delta sigma weight residual 1.328 1.348 -0.020 1.04e-02 9.25e+03 3.75e+00 bond pdb=" C ILE A 583 " pdb=" N PRO A 584 " ideal model delta sigma weight residual 1.334 1.372 -0.039 2.34e-02 1.83e+03 2.71e+00 bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 NAG A1002 " pdb=" O5 NAG A1002 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 25805 not shown) Histogram of bond angle deviations from ideal: 68.94 - 81.99: 12 81.99 - 95.04: 0 95.04 - 108.09: 4776 108.09 - 121.14: 35287 121.14 - 134.19: 5963 Bond angle restraints: 46038 Sorted by residual: angle pdb=" C PRO B 293 " pdb=" CA PRO B 293 " pdb=" HA PRO B 293 " ideal model delta sigma weight residual 109.00 68.94 40.06 3.00e+00 1.11e-01 1.78e+02 angle pdb=" C PRO A 299 " pdb=" CA PRO A 299 " pdb=" HA PRO A 299 " ideal model delta sigma weight residual 109.00 69.62 39.38 3.00e+00 1.11e-01 1.72e+02 angle pdb=" N PRO A 299 " pdb=" CA PRO A 299 " pdb=" HA PRO A 299 " ideal model delta sigma weight residual 110.00 74.04 35.96 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C ASN A 577 " pdb=" CA ASN A 577 " pdb=" HA ASN A 577 " ideal model delta sigma weight residual 109.00 73.09 35.91 3.00e+00 1.11e-01 1.43e+02 angle pdb=" N PRO B 293 " pdb=" CA PRO B 293 " pdb=" HA PRO B 293 " ideal model delta sigma weight residual 110.00 74.81 35.19 3.00e+00 1.11e-01 1.38e+02 ... (remaining 46033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11294 17.99 - 35.98: 936 35.98 - 53.97: 249 53.97 - 71.97: 53 71.97 - 89.96: 14 Dihedral angle restraints: 12546 sinusoidal: 6790 harmonic: 5756 Sorted by residual: dihedral pdb=" CB CYS A 234 " pdb=" SG CYS A 234 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual -86.00 -167.68 81.68 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS B 234 " pdb=" SG CYS B 234 " pdb=" SG CYS B 246 " pdb=" CB CYS B 246 " ideal model delta sinusoidal sigma weight residual -86.00 -167.59 81.59 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS A 294 " pdb=" SG CYS A 294 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual 93.00 166.56 -73.56 1 1.00e+01 1.00e-02 6.88e+01 ... (remaining 12543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1838 0.095 - 0.190: 168 0.190 - 0.285: 0 0.285 - 0.381: 1 0.381 - 0.476: 3 Chirality restraints: 2010 Sorted by residual: chirality pdb=" CA PRO A 299 " pdb=" N PRO A 299 " pdb=" C PRO A 299 " pdb=" CB PRO A 299 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA ASN B 577 " pdb=" N ASN B 577 " pdb=" C ASN B 577 " pdb=" CB ASN B 577 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA ASN A 577 " pdb=" N ASN A 577 " pdb=" C ASN A 577 " pdb=" CB ASN A 577 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 2007 not shown) Planarity restraints: 3884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 583 " 0.044 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO A 584 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 584 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 584 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 544 " 0.022 2.00e-02 2.50e+03 1.19e-02 5.70e+00 pdb=" CG TRP A 544 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 544 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 544 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 544 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 544 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 544 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 544 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 544 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 544 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP A 544 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 544 " 0.010 2.00e-02 2.50e+03 pdb=" HE3 TRP A 544 " 0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 544 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 544 " -0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP A 544 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 298 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO B 299 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 299 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 299 " -0.028 5.00e-02 4.00e+02 ... (remaining 3881 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 780 2.09 - 2.72: 43676 2.72 - 3.35: 73662 3.35 - 3.97: 92950 3.97 - 4.60: 143267 Nonbonded interactions: 354335 Sorted by model distance: nonbonded pdb=" O THR A 324 " pdb=" H GLU A 352 " model vdw 1.467 1.850 nonbonded pdb=" O THR B 324 " pdb=" H GLU B 352 " model vdw 1.474 1.850 nonbonded pdb=" OE1 GLU A 826 " pdb=" H GLU A 826 " model vdw 1.536 1.850 nonbonded pdb=" OE1 GLU B 826 " pdb=" H GLU B 826 " model vdw 1.537 1.850 nonbonded pdb=" OE1 GLU A 507 " pdb=" HZ3 LYS A 568 " model vdw 1.541 1.850 ... (remaining 354330 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' and (resid 1 through 455 or (resid 456 and (name N or name CA or name \ C or name O or name CB )) or (resid 457 and (name N or name CA or name C or nam \ e O or name CB or name OG )) or (resid 458 and (name N or name CA or name C or n \ ame O or name CB or name SG )) or resid 459 through 579 or (resid 580 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid \ 581 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or (resid 582 and (name N or name CA or name C or name O or name CB or name O \ G )) or (resid 583 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1)) or resid 584 through 897 or resid 1001 through 10 \ 02)) } 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.410 Extract box with map and model: 11.090 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 83.160 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 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 : 0.003 0.049 13780 Z= 0.214 Angle : 0.713 12.502 18688 Z= 0.395 Chirality : 0.049 0.476 2010 Planarity : 0.005 0.068 2436 Dihedral : 13.044 89.957 5234 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.47 % Favored : 87.11 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.19), residues: 1660 helix: -2.15 (0.36), residues: 159 sheet: -1.56 (0.30), residues: 268 loop : -1.98 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 544 HIS 0.004 0.001 HIS A 269 PHE 0.027 0.002 PHE A 90 TYR 0.023 0.002 TYR B 496 ARG 0.007 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 VAL cc_start: 0.7996 (t) cc_final: 0.7779 (t) REVERT: B 354 VAL cc_start: 0.7883 (t) cc_final: 0.7650 (t) REVERT: B 496 TYR cc_start: 0.7976 (m-80) cc_final: 0.7249 (m-80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.5040 time to fit residues: 88.8571 Evaluate side-chains 84 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 chunk 50 optimal weight: 0.2980 chunk 79 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13780 Z= 0.204 Angle : 0.634 13.219 18688 Z= 0.337 Chirality : 0.049 0.483 2010 Planarity : 0.005 0.065 2436 Dihedral : 6.541 43.834 1936 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.45 % Favored : 88.13 % Rotamer: Outliers : 0.40 % Allowed : 4.83 % Favored : 94.77 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.76 (0.19), residues: 1660 helix: -2.05 (0.37), residues: 139 sheet: -1.60 (0.30), residues: 271 loop : -2.01 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 544 HIS 0.005 0.001 HIS B 563 PHE 0.019 0.002 PHE A 90 TYR 0.012 0.001 TYR A 550 ARG 0.009 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2880 (ptt) cc_final: 0.2677 (ptt) REVERT: A 354 VAL cc_start: 0.8033 (t) cc_final: 0.7786 (t) REVERT: B 354 VAL cc_start: 0.7881 (t) cc_final: 0.7631 (t) REVERT: B 496 TYR cc_start: 0.7976 (m-80) cc_final: 0.7250 (m-80) outliers start: 6 outliers final: 6 residues processed: 94 average time/residue: 0.4941 time to fit residues: 72.1045 Evaluate side-chains 87 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13780 Z= 0.301 Angle : 0.696 11.889 18688 Z= 0.368 Chirality : 0.049 0.482 2010 Planarity : 0.005 0.060 2436 Dihedral : 6.557 38.949 1936 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 31.85 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.92 % Favored : 85.66 % Rotamer: Outliers : 1.01 % Allowed : 8.58 % Favored : 90.42 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.19), residues: 1660 helix: -1.98 (0.37), residues: 144 sheet: -2.00 (0.28), residues: 294 loop : -2.15 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 544 HIS 0.006 0.002 HIS B 539 PHE 0.022 0.002 PHE B 692 TYR 0.038 0.002 TYR A 83 ARG 0.009 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.3105 (ptt) cc_final: 0.2733 (ptt) REVERT: A 354 VAL cc_start: 0.8167 (t) cc_final: 0.7887 (t) REVERT: B 345 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6395 (mp0) REVERT: B 354 VAL cc_start: 0.8143 (t) cc_final: 0.7889 (t) outliers start: 15 outliers final: 14 residues processed: 102 average time/residue: 0.4704 time to fit residues: 75.0164 Evaluate side-chains 98 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 101 optimal weight: 0.1980 chunk 151 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13780 Z= 0.259 Angle : 0.653 11.523 18688 Z= 0.348 Chirality : 0.049 0.480 2010 Planarity : 0.005 0.060 2436 Dihedral : 6.450 38.343 1936 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 29.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.89 % Favored : 86.69 % Rotamer: Outliers : 1.61 % Allowed : 9.58 % Favored : 88.81 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.99 (0.19), residues: 1660 helix: -1.81 (0.39), residues: 136 sheet: -2.06 (0.28), residues: 286 loop : -2.14 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 544 HIS 0.004 0.001 HIS A 539 PHE 0.015 0.002 PHE B 82 TYR 0.018 0.002 TYR A 626 ARG 0.005 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2902 (ptt) cc_final: 0.2526 (ptt) REVERT: A 184 MET cc_start: 0.4348 (mpp) cc_final: 0.4124 (mpp) REVERT: A 345 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: A 354 VAL cc_start: 0.8086 (t) cc_final: 0.7777 (t) REVERT: B 354 VAL cc_start: 0.7998 (t) cc_final: 0.7691 (t) REVERT: B 496 TYR cc_start: 0.8088 (m-80) cc_final: 0.7884 (m-80) outliers start: 24 outliers final: 21 residues processed: 101 average time/residue: 0.4516 time to fit residues: 73.9651 Evaluate side-chains 104 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13780 Z= 0.169 Angle : 0.594 11.748 18688 Z= 0.313 Chirality : 0.048 0.483 2010 Planarity : 0.005 0.059 2436 Dihedral : 6.061 36.652 1936 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.69 % Favored : 87.89 % Rotamer: Outliers : 1.27 % Allowed : 10.32 % Favored : 88.40 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.80 (0.20), residues: 1660 helix: -1.88 (0.38), residues: 148 sheet: -1.83 (0.28), residues: 278 loop : -2.00 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 544 HIS 0.004 0.001 HIS A 630 PHE 0.013 0.001 PHE A 82 TYR 0.015 0.001 TYR A 626 ARG 0.003 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2471 (ptt) cc_final: 0.2119 (ptt) REVERT: A 345 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6418 (mp0) REVERT: A 354 VAL cc_start: 0.8103 (t) cc_final: 0.7790 (t) REVERT: B 345 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6308 (mp0) REVERT: B 354 VAL cc_start: 0.7967 (t) cc_final: 0.7654 (t) REVERT: B 688 TYR cc_start: 0.7715 (t80) cc_final: 0.7383 (m-80) outliers start: 19 outliers final: 16 residues processed: 103 average time/residue: 0.4466 time to fit residues: 72.9711 Evaluate side-chains 100 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 586 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13780 Z= 0.294 Angle : 0.669 10.816 18688 Z= 0.354 Chirality : 0.048 0.481 2010 Planarity : 0.005 0.065 2436 Dihedral : 6.302 38.235 1936 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 32.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.04 % Favored : 85.54 % Rotamer: Outliers : 1.54 % Allowed : 10.46 % Favored : 88.00 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.98 (0.19), residues: 1660 helix: -1.79 (0.39), residues: 142 sheet: -2.09 (0.28), residues: 286 loop : -2.12 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 544 HIS 0.007 0.002 HIS B 539 PHE 0.019 0.002 PHE B 82 TYR 0.035 0.002 TYR B 496 ARG 0.005 0.001 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2349 (ptt) cc_final: 0.1896 (ptt) REVERT: A 499 GLU cc_start: 0.8891 (pm20) cc_final: 0.8664 (mp0) REVERT: B 345 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: B 496 TYR cc_start: 0.8136 (m-80) cc_final: 0.7576 (m-80) outliers start: 23 outliers final: 21 residues processed: 101 average time/residue: 0.4307 time to fit residues: 69.8895 Evaluate side-chains 105 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 520 ASN Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 90 optimal weight: 0.0570 chunk 135 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13780 Z= 0.160 Angle : 0.586 11.567 18688 Z= 0.308 Chirality : 0.049 0.478 2010 Planarity : 0.005 0.062 2436 Dihedral : 5.923 37.249 1936 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.66 % Favored : 88.92 % Rotamer: Outliers : 1.41 % Allowed : 10.99 % Favored : 87.60 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.79 (0.20), residues: 1660 helix: -1.81 (0.38), residues: 148 sheet: -1.91 (0.28), residues: 278 loop : -1.98 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 544 HIS 0.004 0.001 HIS A 362 PHE 0.012 0.001 PHE A 82 TYR 0.015 0.001 TYR B 496 ARG 0.004 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8034 (t80) cc_final: 0.7046 (t80) REVERT: A 156 MET cc_start: 0.2300 (ptt) cc_final: 0.1950 (ptt) REVERT: A 345 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: A 354 VAL cc_start: 0.8088 (t) cc_final: 0.7766 (t) REVERT: A 458 CYS cc_start: 0.5408 (OUTLIER) cc_final: 0.4980 (p) REVERT: B 345 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: B 354 VAL cc_start: 0.7925 (t) cc_final: 0.7607 (t) REVERT: B 688 TYR cc_start: 0.7709 (t80) cc_final: 0.7378 (m-80) outliers start: 21 outliers final: 16 residues processed: 105 average time/residue: 0.4989 time to fit residues: 83.9005 Evaluate side-chains 102 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 125 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13780 Z= 0.156 Angle : 0.577 11.114 18688 Z= 0.302 Chirality : 0.048 0.477 2010 Planarity : 0.005 0.064 2436 Dihedral : 5.785 36.321 1936 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.51 % Favored : 88.07 % Rotamer: Outliers : 1.21 % Allowed : 11.53 % Favored : 87.27 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.72 (0.20), residues: 1660 helix: -1.71 (0.38), residues: 148 sheet: -1.85 (0.28), residues: 276 loop : -1.94 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 544 HIS 0.002 0.001 HIS B 539 PHE 0.012 0.001 PHE B 82 TYR 0.013 0.001 TYR B 688 ARG 0.003 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2447 (ptt) cc_final: 0.2069 (ptt) REVERT: A 345 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: A 354 VAL cc_start: 0.8080 (t) cc_final: 0.7773 (t) REVERT: A 458 CYS cc_start: 0.5316 (OUTLIER) cc_final: 0.4890 (p) REVERT: B 345 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6228 (mp0) REVERT: B 354 VAL cc_start: 0.8004 (t) cc_final: 0.7694 (t) REVERT: B 496 TYR cc_start: 0.7962 (m-80) cc_final: 0.7588 (m-80) outliers start: 18 outliers final: 14 residues processed: 100 average time/residue: 0.4492 time to fit residues: 71.5572 Evaluate side-chains 98 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 586 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 117 optimal weight: 0.0370 chunk 45 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 overall best weight: 1.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13780 Z= 0.219 Angle : 0.610 10.791 18688 Z= 0.321 Chirality : 0.048 0.479 2010 Planarity : 0.005 0.066 2436 Dihedral : 5.876 36.655 1936 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.95 % Favored : 86.63 % Rotamer: Outliers : 1.47 % Allowed : 11.53 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.82 (0.20), residues: 1660 helix: -1.57 (0.40), residues: 142 sheet: -1.97 (0.27), residues: 286 loop : -2.03 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 544 HIS 0.004 0.001 HIS B 630 PHE 0.017 0.002 PHE B 82 TYR 0.015 0.002 TYR B 688 ARG 0.004 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2566 (ptt) cc_final: 0.2239 (ptt) REVERT: A 345 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: A 354 VAL cc_start: 0.8090 (t) cc_final: 0.7787 (t) REVERT: A 458 CYS cc_start: 0.5413 (OUTLIER) cc_final: 0.5001 (p) REVERT: B 83 TYR cc_start: 0.8197 (t80) cc_final: 0.7909 (t80) REVERT: B 345 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: B 354 VAL cc_start: 0.7982 (t) cc_final: 0.7678 (t) REVERT: B 521 MET cc_start: 0.8850 (mmm) cc_final: 0.8623 (mmm) REVERT: B 688 TYR cc_start: 0.7685 (t80) cc_final: 0.7457 (m-80) outliers start: 22 outliers final: 19 residues processed: 100 average time/residue: 0.4162 time to fit residues: 67.0145 Evaluate side-chains 103 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 165 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13780 Z= 0.184 Angle : 0.587 10.861 18688 Z= 0.309 Chirality : 0.048 0.477 2010 Planarity : 0.005 0.066 2436 Dihedral : 5.823 36.768 1936 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.29 % Favored : 87.29 % Rotamer: Outliers : 1.41 % Allowed : 11.86 % Favored : 86.73 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.78 (0.20), residues: 1660 helix: -1.52 (0.40), residues: 142 sheet: -1.96 (0.27), residues: 286 loop : -2.00 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 544 HIS 0.005 0.001 HIS B 630 PHE 0.016 0.001 PHE B 82 TYR 0.013 0.001 TYR A 550 ARG 0.003 0.000 ARG B 620 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2663 (ptt) cc_final: 0.2239 (ptt) REVERT: A 345 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: A 354 VAL cc_start: 0.8033 (t) cc_final: 0.7722 (t) REVERT: A 458 CYS cc_start: 0.5331 (OUTLIER) cc_final: 0.4919 (p) REVERT: B 345 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: B 354 VAL cc_start: 0.7955 (t) cc_final: 0.7648 (t) outliers start: 21 outliers final: 18 residues processed: 100 average time/residue: 0.4631 time to fit residues: 73.1139 Evaluate side-chains 104 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 55 optimal weight: 0.0070 chunk 135 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 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 = 0.4488 r_free = 0.4488 target = 0.102085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.085205 restraints weight = 288270.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.088401 restraints weight = 141119.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.090399 restraints weight = 88302.315| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13780 Z= 0.164 Angle : 0.574 10.822 18688 Z= 0.301 Chirality : 0.048 0.475 2010 Planarity : 0.005 0.065 2436 Dihedral : 5.687 36.578 1936 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.87 % Favored : 87.71 % Rotamer: Outliers : 1.41 % Allowed : 12.20 % Favored : 86.39 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.71 (0.20), residues: 1660 helix: -1.43 (0.41), residues: 142 sheet: -1.90 (0.28), residues: 281 loop : -1.95 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 544 HIS 0.003 0.001 HIS B 630 PHE 0.017 0.001 PHE B 82 TYR 0.014 0.001 TYR B 626 ARG 0.004 0.000 ARG A 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4653.58 seconds wall clock time: 85 minutes 16.12 seconds (5116.12 seconds total)