Starting phenix.real_space_refine on Tue Mar 19 18:55:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/03_2024/7mdo_23776_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/03_2024/7mdo_23776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/03_2024/7mdo_23776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/03_2024/7mdo_23776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/03_2024/7mdo_23776_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/03_2024/7mdo_23776_updated.pdb" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 132 5.16 5 C 15786 2.51 5 N 4380 2.21 5 O 4788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 205": "OD1" <-> "OD2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 671": "OD1" <-> "OD2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 751": "OD1" <-> "OD2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 671": "OD1" <-> "OD2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 751": "OD1" <-> "OD2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 534": "OE1" <-> "OE2" Residue "C ASP 671": "OD1" <-> "OD2" Residue "C PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 751": "OD1" <-> "OD2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D ASP 393": "OD1" <-> "OD2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D ASP 671": "OD1" <-> "OD2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 751": "OD1" <-> "OD2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E ASP 393": "OD1" <-> "OD2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 534": "OE1" <-> "OE2" Residue "E ASP 671": "OD1" <-> "OD2" Residue "E PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 751": "OD1" <-> "OD2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "F PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 304": "OD1" <-> "OD2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ASP 393": "OD1" <-> "OD2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 534": "OE1" <-> "OE2" Residue "F ASP 671": "OD1" <-> "OD2" Residue "F PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 751": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25098 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "B" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "C" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "D" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "E" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "F" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.78, per 1000 atoms: 0.51 Number of scatterers: 25098 At special positions: 0 Unit cell: (145.08, 141.96, 95.16, 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 132 16.00 P 12 15.00 O 4788 8.00 N 4380 7.00 C 15786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.54 Conformation dependent library (CDL) restraints added in 4.1 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5988 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 18 sheets defined 45.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 removed outlier: 5.353A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.611A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 322 through 333 removed outlier: 4.860A pdb=" N GLN A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.948A pdb=" N THR A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 483 through 492 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 650 through 662 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 762 removed outlier: 3.909A pdb=" N ILE A 752 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A 753 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET A 757 " --> pdb=" O LYS A 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 5.297A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 229 through 232 No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 251 through 262 removed outlier: 3.567A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 322 through 333 removed outlier: 4.829A pdb=" N GLN B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 383 Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 483 through 492 Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 527 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'B' and resid 650 through 662 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 684 through 702 Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 749 through 762 removed outlier: 3.940A pdb=" N ILE B 752 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG B 753 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET B 757 " --> pdb=" O LYS B 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 5.407A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 229 through 232 No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 251 through 262 removed outlier: 3.610A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 322 through 333 removed outlier: 4.884A pdb=" N GLN C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 Processing helix chain 'C' and resid 397 through 403 removed outlier: 3.543A pdb=" N THR C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 424 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 483 through 492 removed outlier: 3.552A pdb=" N GLU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 498 Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 527 through 534 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 650 through 662 Processing helix chain 'C' and resid 672 through 676 Processing helix chain 'C' and resid 684 through 702 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 749 through 762 removed outlier: 3.990A pdb=" N ILE C 752 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG C 753 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET C 757 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 225 removed outlier: 5.291A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 229 through 232 No H-bonds generated for 'chain 'D' and resid 229 through 232' Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.629A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 275 No H-bonds generated for 'chain 'D' and resid 273 through 275' Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 322 through 333 removed outlier: 4.850A pdb=" N GLN D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 385 removed outlier: 4.009A pdb=" N THR D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 408 through 424 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 483 through 492 Processing helix chain 'D' and resid 494 through 498 Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 599 through 607 Processing helix chain 'D' and resid 650 through 662 Processing helix chain 'D' and resid 672 through 676 Processing helix chain 'D' and resid 684 through 702 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 751 through 762 removed outlier: 4.146A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 5.377A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 229 through 232 No H-bonds generated for 'chain 'E' and resid 229 through 232' Processing helix chain 'E' and resid 251 through 262 removed outlier: 3.586A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 275 No H-bonds generated for 'chain 'E' and resid 273 through 275' Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 322 through 325 No H-bonds generated for 'chain 'E' and resid 322 through 325' Processing helix chain 'E' and resid 328 through 333 removed outlier: 3.700A pdb=" N ASP E 333 " --> pdb=" O LEU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 383 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 408 through 424 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 483 through 492 Processing helix chain 'E' and resid 494 through 498 Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 527 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 Processing helix chain 'E' and resid 579 through 581 No H-bonds generated for 'chain 'E' and resid 579 through 581' Processing helix chain 'E' and resid 599 through 607 Processing helix chain 'E' and resid 650 through 662 Processing helix chain 'E' and resid 672 through 675 No H-bonds generated for 'chain 'E' and resid 672 through 675' Processing helix chain 'E' and resid 684 through 702 Processing helix chain 'E' and resid 732 through 740 Processing helix chain 'E' and resid 749 through 762 removed outlier: 4.027A pdb=" N ILE E 752 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG E 753 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET E 757 " --> pdb=" O LYS E 754 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 225 removed outlier: 5.355A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 229 through 232 No H-bonds generated for 'chain 'F' and resid 229 through 232' Processing helix chain 'F' and resid 251 through 262 removed outlier: 3.615A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 275 No H-bonds generated for 'chain 'F' and resid 273 through 275' Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 322 through 333 removed outlier: 4.854A pdb=" N GLN F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 385 removed outlier: 3.956A pdb=" N THR F 385 " --> pdb=" O LEU F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 403 Processing helix chain 'F' and resid 408 through 425 removed outlier: 3.571A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 483 through 492 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 527 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 Processing helix chain 'F' and resid 579 through 581 No H-bonds generated for 'chain 'F' and resid 579 through 581' Processing helix chain 'F' and resid 599 through 607 Processing helix chain 'F' and resid 650 through 662 Processing helix chain 'F' and resid 672 through 676 Processing helix chain 'F' and resid 684 through 702 Processing helix chain 'F' and resid 733 through 740 Processing helix chain 'F' and resid 749 through 762 removed outlier: 3.911A pdb=" N ILE F 752 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG F 753 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N MET F 757 " --> pdb=" O LYS F 754 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 366 through 368 removed outlier: 5.740A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 515 through 517 removed outlier: 6.655A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 538 through 540 Processing sheet with id= D, first strand: chain 'B' and resid 366 through 368 removed outlier: 5.740A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 621 through 623 removed outlier: 3.708A pdb=" N GLY B 518 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE B 643 " --> pdb=" O TYR B 517 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.511A pdb=" N ILE B 542 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 366 through 368 removed outlier: 5.644A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 621 through 623 Processing sheet with id= I, first strand: chain 'C' and resid 538 through 542 Processing sheet with id= J, first strand: chain 'D' and resid 366 through 368 removed outlier: 5.671A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 621 through 623 removed outlier: 3.699A pdb=" N GLY D 518 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 643 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 538 through 540 Processing sheet with id= M, first strand: chain 'E' and resid 366 through 368 removed outlier: 5.671A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 621 through 623 removed outlier: 3.765A pdb=" N GLY E 518 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE E 643 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 538 through 542 removed outlier: 3.529A pdb=" N ILE E 542 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 366 through 368 removed outlier: 5.633A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 621 through 623 removed outlier: 3.727A pdb=" N GLY F 518 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE F 643 " --> pdb=" O TYR F 517 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 538 through 542 796 hydrogen bonds defined for protein. 2268 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: 8.02 Time building geometry restraints manager: 10.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8324 1.34 - 1.46: 3273 1.46 - 1.57: 13681 1.57 - 1.69: 18 1.69 - 1.81: 222 Bond restraints: 25518 Sorted by residual: bond pdb=" C TYR C 495 " pdb=" N PRO C 496 " ideal model delta sigma weight residual 1.336 1.357 -0.022 1.23e-02 6.61e+03 3.14e+00 bond pdb=" C TYR F 495 " pdb=" N PRO F 496 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 3.01e+00 bond pdb=" C TYR E 495 " pdb=" N PRO E 496 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.23e-02 6.61e+03 2.71e+00 bond pdb=" CA VAL B 343 " pdb=" CB VAL B 343 " ideal model delta sigma weight residual 1.533 1.552 -0.019 1.19e-02 7.06e+03 2.58e+00 bond pdb=" C TYR A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.28e+00 ... (remaining 25513 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.78: 707 105.78 - 113.45: 13909 113.45 - 121.13: 13029 121.13 - 128.80: 6697 128.80 - 136.48: 140 Bond angle restraints: 34482 Sorted by residual: angle pdb=" N MET B 275 " pdb=" CA MET B 275 " pdb=" C MET B 275 " ideal model delta sigma weight residual 114.75 106.21 8.54 1.26e+00 6.30e-01 4.59e+01 angle pdb=" N MET E 275 " pdb=" CA MET E 275 " pdb=" C MET E 275 " ideal model delta sigma weight residual 114.75 106.24 8.51 1.26e+00 6.30e-01 4.56e+01 angle pdb=" N MET A 275 " pdb=" CA MET A 275 " pdb=" C MET A 275 " ideal model delta sigma weight residual 114.75 106.28 8.47 1.26e+00 6.30e-01 4.52e+01 angle pdb=" N MET C 275 " pdb=" CA MET C 275 " pdb=" C MET C 275 " ideal model delta sigma weight residual 114.75 106.56 8.19 1.26e+00 6.30e-01 4.22e+01 angle pdb=" N MET F 275 " pdb=" CA MET F 275 " pdb=" C MET F 275 " ideal model delta sigma weight residual 114.75 106.63 8.12 1.26e+00 6.30e-01 4.15e+01 ... (remaining 34477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 14728 25.08 - 50.17: 960 50.17 - 75.25: 103 75.25 - 100.33: 7 100.33 - 125.41: 6 Dihedral angle restraints: 15804 sinusoidal: 6612 harmonic: 9192 Sorted by residual: dihedral pdb=" O1B ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PB ADP E 901 " pdb=" PA ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.41 -125.41 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O1B ADP D 901 " pdb=" O3A ADP D 901 " pdb=" PB ADP D 901 " pdb=" PA ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.16 -125.17 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.11 -125.12 1 2.00e+01 2.50e-03 3.78e+01 ... (remaining 15801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3339 0.083 - 0.166: 465 0.166 - 0.249: 62 0.249 - 0.332: 19 0.332 - 0.415: 9 Chirality restraints: 3894 Sorted by residual: chirality pdb=" CB ILE D 620 " pdb=" CA ILE D 620 " pdb=" CG1 ILE D 620 " pdb=" CG2 ILE D 620 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CB ILE B 620 " pdb=" CA ILE B 620 " pdb=" CG1 ILE B 620 " pdb=" CG2 ILE B 620 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB ILE A 620 " pdb=" CA ILE A 620 " pdb=" CG1 ILE A 620 " pdb=" CG2 ILE A 620 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 3891 not shown) Planarity restraints: 4524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 327 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLN A 327 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN A 327 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU A 328 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 327 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C GLN E 327 " -0.061 2.00e-02 2.50e+03 pdb=" O GLN E 327 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU E 328 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 327 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C GLN D 327 " -0.061 2.00e-02 2.50e+03 pdb=" O GLN D 327 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU D 328 " 0.021 2.00e-02 2.50e+03 ... (remaining 4521 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 6934 2.81 - 3.33: 24164 3.33 - 3.85: 43114 3.85 - 4.38: 49756 4.38 - 4.90: 79062 Nonbonded interactions: 203030 Sorted by model distance: nonbonded pdb=" O PRO F 246 " pdb=" OG1 THR F 249 " model vdw 2.283 2.440 nonbonded pdb=" O PRO C 246 " pdb=" OG1 THR C 249 " model vdw 2.286 2.440 nonbonded pdb=" O PRO B 246 " pdb=" OG1 THR B 249 " model vdw 2.291 2.440 nonbonded pdb=" O PRO E 246 " pdb=" OG1 THR E 249 " model vdw 2.293 2.440 nonbonded pdb=" O GLU F 546 " pdb=" OG1 THR F 549 " model vdw 2.303 2.440 ... (remaining 203025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 5.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.470 Check model and map are aligned: 0.280 Set scattering table: 0.230 Process input model: 63.300 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 0.005 0.045 25518 Z= 0.304 Angle : 1.058 12.067 34482 Z= 0.567 Chirality : 0.064 0.415 3894 Planarity : 0.008 0.084 4524 Dihedral : 15.751 125.415 9816 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.13), residues: 3150 helix: -2.46 (0.10), residues: 1590 sheet: -2.22 (0.27), residues: 336 loop : -0.88 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 476 HIS 0.013 0.002 HIS E 735 PHE 0.015 0.002 PHE C 503 TYR 0.016 0.002 TYR D 244 ARG 0.005 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 954 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.9139 (tp) cc_final: 0.8812 (tp) REVERT: A 241 ILE cc_start: 0.9394 (pt) cc_final: 0.9022 (pt) REVERT: A 278 LEU cc_start: 0.8657 (pp) cc_final: 0.7987 (mt) REVERT: A 312 LYS cc_start: 0.9141 (tptt) cc_final: 0.8896 (tptt) REVERT: A 347 THR cc_start: 0.7931 (t) cc_final: 0.7675 (t) REVERT: A 395 ASP cc_start: 0.8515 (m-30) cc_final: 0.7145 (m-30) REVERT: A 449 MET cc_start: 0.8244 (mmm) cc_final: 0.7895 (tpt) REVERT: A 450 ASP cc_start: 0.8227 (p0) cc_final: 0.8016 (t0) REVERT: A 484 ASP cc_start: 0.8202 (p0) cc_final: 0.7768 (p0) REVERT: A 488 GLU cc_start: 0.8175 (tp30) cc_final: 0.7940 (tp30) REVERT: A 503 PHE cc_start: 0.6505 (t80) cc_final: 0.6251 (t80) REVERT: A 543 LYS cc_start: 0.9304 (mmtp) cc_final: 0.8406 (mmtt) REVERT: A 546 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8679 (mp0) REVERT: A 549 THR cc_start: 0.5819 (p) cc_final: 0.5522 (p) REVERT: A 558 ASN cc_start: 0.7624 (m-40) cc_final: 0.7351 (m110) REVERT: A 565 LYS cc_start: 0.8944 (tptp) cc_final: 0.8688 (tptt) REVERT: A 678 MET cc_start: 0.6726 (ptp) cc_final: 0.6426 (ptm) REVERT: A 689 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 690 ILE cc_start: 0.8940 (mm) cc_final: 0.8342 (mm) REVERT: A 692 GLN cc_start: 0.8447 (tp40) cc_final: 0.7968 (tm-30) REVERT: A 761 THR cc_start: 0.6881 (m) cc_final: 0.6494 (m) REVERT: B 217 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8293 (mmtp) REVERT: B 225 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.8184 (ttt180) REVERT: B 278 LEU cc_start: 0.8599 (pp) cc_final: 0.7592 (mt) REVERT: B 306 LEU cc_start: 0.9293 (tt) cc_final: 0.8844 (tp) REVERT: B 349 ARG cc_start: 0.8279 (mtm180) cc_final: 0.7984 (mtp85) REVERT: B 403 THR cc_start: 0.8492 (p) cc_final: 0.8238 (t) REVERT: B 417 GLU cc_start: 0.8578 (tp30) cc_final: 0.8309 (tp30) REVERT: B 484 ASP cc_start: 0.8487 (p0) cc_final: 0.8004 (p0) REVERT: B 508 MET cc_start: 0.0762 (mtt) cc_final: -0.0872 (mtt) REVERT: B 543 LYS cc_start: 0.9292 (mmtp) cc_final: 0.8338 (mmtm) REVERT: B 558 ASN cc_start: 0.7486 (m-40) cc_final: 0.6975 (m110) REVERT: B 560 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.8079 (mtp-110) REVERT: B 662 ARG cc_start: 0.8333 (ttt90) cc_final: 0.8023 (ttt90) REVERT: B 678 MET cc_start: 0.7559 (ptp) cc_final: 0.7067 (ptp) REVERT: B 689 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7438 (tm-30) REVERT: B 690 ILE cc_start: 0.8677 (mm) cc_final: 0.8224 (mm) REVERT: B 700 ARG cc_start: 0.8785 (ttp-170) cc_final: 0.8494 (ttm170) REVERT: C 203 TYR cc_start: 0.7845 (m-10) cc_final: 0.7602 (m-10) REVERT: C 241 ILE cc_start: 0.9226 (pt) cc_final: 0.8849 (pt) REVERT: C 252 THR cc_start: 0.8639 (p) cc_final: 0.8318 (p) REVERT: C 256 ARG cc_start: 0.8498 (ttm170) cc_final: 0.8086 (ttm110) REVERT: C 262 THR cc_start: 0.8400 (m) cc_final: 0.7843 (t) REVERT: C 278 LEU cc_start: 0.8938 (pp) cc_final: 0.8563 (mt) REVERT: C 283 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7249 (tm-30) REVERT: C 306 LEU cc_start: 0.9135 (tt) cc_final: 0.8751 (tt) REVERT: C 332 MET cc_start: 0.8824 (mmp) cc_final: 0.8594 (mmm) REVERT: C 442 MET cc_start: 0.7643 (tmm) cc_final: 0.7044 (tmm) REVERT: C 482 LEU cc_start: 0.7312 (mp) cc_final: 0.7100 (mt) REVERT: C 486 LYS cc_start: 0.8369 (mttt) cc_final: 0.7793 (mmmt) REVERT: C 508 MET cc_start: 0.2332 (mtt) cc_final: 0.1478 (mtt) REVERT: C 543 LYS cc_start: 0.9127 (mmtp) cc_final: 0.8390 (mmmm) REVERT: C 560 ARG cc_start: 0.8175 (mtp-110) cc_final: 0.7827 (mtp-110) REVERT: C 562 ILE cc_start: 0.9248 (pt) cc_final: 0.9021 (tp) REVERT: C 611 MET cc_start: 0.7808 (mmp) cc_final: 0.7521 (mmp) REVERT: C 678 MET cc_start: 0.7732 (ptp) cc_final: 0.7214 (ptt) REVERT: C 689 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7833 (tm-30) REVERT: C 690 ILE cc_start: 0.8724 (mm) cc_final: 0.8146 (mm) REVERT: C 732 ARG cc_start: 0.3286 (mtm-85) cc_final: 0.2886 (mtp85) REVERT: D 203 TYR cc_start: 0.8156 (m-10) cc_final: 0.7778 (m-10) REVERT: D 221 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7501 (tm-30) REVERT: D 241 ILE cc_start: 0.9392 (pt) cc_final: 0.9191 (pt) REVERT: D 283 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7204 (tm-30) REVERT: D 305 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7454 (mm-30) REVERT: D 306 LEU cc_start: 0.9138 (tt) cc_final: 0.8816 (tp) REVERT: D 327 GLN cc_start: 0.7580 (tp40) cc_final: 0.7110 (mm-40) REVERT: D 352 SER cc_start: 0.9224 (m) cc_final: 0.8481 (p) REVERT: D 395 ASP cc_start: 0.8399 (m-30) cc_final: 0.7869 (p0) REVERT: D 484 ASP cc_start: 0.8757 (p0) cc_final: 0.7949 (p0) REVERT: D 543 LYS cc_start: 0.9224 (mmtp) cc_final: 0.8267 (mmmm) REVERT: D 546 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8753 (mp0) REVERT: D 611 MET cc_start: 0.7824 (mmp) cc_final: 0.7220 (mmm) REVERT: D 634 LEU cc_start: 0.7785 (tp) cc_final: 0.7550 (tt) REVERT: D 678 MET cc_start: 0.7275 (ptp) cc_final: 0.7012 (ptm) REVERT: D 689 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7390 (tm-30) REVERT: D 690 ILE cc_start: 0.8783 (mm) cc_final: 0.8099 (mm) REVERT: E 241 ILE cc_start: 0.9368 (pt) cc_final: 0.9162 (pt) REVERT: E 260 ASN cc_start: 0.8729 (m-40) cc_final: 0.7472 (m-40) REVERT: E 306 LEU cc_start: 0.9245 (tt) cc_final: 0.8794 (tp) REVERT: E 312 LYS cc_start: 0.9287 (tptt) cc_final: 0.9052 (tptt) REVERT: E 344 MET cc_start: 0.7997 (mtt) cc_final: 0.7793 (mtt) REVERT: E 476 TRP cc_start: 0.8087 (m100) cc_final: 0.7291 (m100) REVERT: E 478 ASP cc_start: 0.7003 (m-30) cc_final: 0.6325 (t0) REVERT: E 486 LYS cc_start: 0.8481 (mttt) cc_final: 0.8187 (mmtt) REVERT: E 508 MET cc_start: 0.0455 (mtt) cc_final: -0.1327 (mtt) REVERT: E 526 LEU cc_start: 0.8307 (mt) cc_final: 0.8086 (mp) REVERT: E 542 ILE cc_start: 0.8856 (tp) cc_final: 0.8622 (tp) REVERT: E 546 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8712 (mp0) REVERT: E 558 ASN cc_start: 0.7504 (m-40) cc_final: 0.7127 (m-40) REVERT: E 560 ARG cc_start: 0.8225 (mtp-110) cc_final: 0.7998 (mtp-110) REVERT: E 608 MET cc_start: 0.8685 (ppp) cc_final: 0.8422 (ppp) REVERT: E 611 MET cc_start: 0.7712 (mmp) cc_final: 0.7387 (mmm) REVERT: E 643 ILE cc_start: 0.8330 (tp) cc_final: 0.7602 (mm) REVERT: E 651 LYS cc_start: 0.9157 (ptpt) cc_final: 0.8139 (pttp) REVERT: E 662 ARG cc_start: 0.8440 (ttt90) cc_final: 0.7946 (tmm160) REVERT: E 678 MET cc_start: 0.7383 (ptp) cc_final: 0.6913 (ptm) REVERT: F 203 TYR cc_start: 0.8046 (m-10) cc_final: 0.7606 (m-10) REVERT: F 221 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7571 (tm-30) REVERT: F 222 LEU cc_start: 0.9017 (tp) cc_final: 0.8770 (tp) REVERT: F 241 ILE cc_start: 0.9262 (pt) cc_final: 0.8869 (pt) REVERT: F 278 LEU cc_start: 0.8826 (pp) cc_final: 0.7883 (mt) REVERT: F 312 LYS cc_start: 0.8920 (tptt) cc_final: 0.8681 (ptpp) REVERT: F 327 GLN cc_start: 0.7255 (tp40) cc_final: 0.6675 (mm-40) REVERT: F 395 ASP cc_start: 0.7824 (m-30) cc_final: 0.6986 (m-30) REVERT: F 484 ASP cc_start: 0.8679 (p0) cc_final: 0.8277 (p0) REVERT: F 486 LYS cc_start: 0.8467 (mttt) cc_final: 0.7966 (mmtp) REVERT: F 503 PHE cc_start: 0.6829 (t80) cc_final: 0.6510 (t80) REVERT: F 543 LYS cc_start: 0.9076 (mmtp) cc_final: 0.8379 (mmmt) REVERT: F 546 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8479 (mp0) REVERT: F 700 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7995 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 954 average time/residue: 0.4266 time to fit residues: 598.0792 Evaluate side-chains 665 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.0770 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 151 optimal weight: 0.0270 chunk 185 optimal weight: 2.9990 chunk 288 optimal weight: 10.0000 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN B 260 ASN B 421 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN C 421 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 337 GLN D 602 ASN E 285 ASN E 401 ASN E 533 ASN E 602 ASN F 285 ASN F 499 HIS ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25518 Z= 0.217 Angle : 0.662 7.437 34482 Z= 0.337 Chirality : 0.044 0.166 3894 Planarity : 0.006 0.059 4524 Dihedral : 9.303 114.756 3480 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.15), residues: 3150 helix: -1.04 (0.12), residues: 1578 sheet: -2.10 (0.28), residues: 306 loop : -0.48 (0.19), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS E 735 PHE 0.015 0.001 PHE C 503 TYR 0.017 0.002 TYR B 244 ARG 0.008 0.001 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 745 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.8059 (m-10) cc_final: 0.7314 (m-10) REVERT: A 222 LEU cc_start: 0.8980 (tp) cc_final: 0.8658 (tp) REVERT: A 239 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.6972 (mtm180) REVERT: A 349 ARG cc_start: 0.8560 (tpp80) cc_final: 0.7895 (mtm180) REVERT: A 395 ASP cc_start: 0.8088 (m-30) cc_final: 0.7845 (m-30) REVERT: A 449 MET cc_start: 0.8357 (mmm) cc_final: 0.7848 (mmm) REVERT: A 450 ASP cc_start: 0.8386 (p0) cc_final: 0.8093 (t0) REVERT: A 484 ASP cc_start: 0.8095 (p0) cc_final: 0.7365 (p0) REVERT: A 486 LYS cc_start: 0.8523 (mtpt) cc_final: 0.8117 (mmtt) REVERT: A 499 HIS cc_start: 0.7388 (m170) cc_final: 0.7117 (m170) REVERT: A 503 PHE cc_start: 0.6591 (t80) cc_final: 0.6356 (t80) REVERT: A 524 LYS cc_start: 0.8635 (ptpt) cc_final: 0.8397 (pttt) REVERT: A 526 LEU cc_start: 0.8056 (mt) cc_final: 0.7778 (mp) REVERT: A 543 LYS cc_start: 0.9253 (mmtp) cc_final: 0.9041 (mmtt) REVERT: A 634 LEU cc_start: 0.7466 (tp) cc_final: 0.7132 (tp) REVERT: A 678 MET cc_start: 0.6682 (ptp) cc_final: 0.6156 (ptt) REVERT: A 689 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7464 (tm-30) REVERT: A 690 ILE cc_start: 0.8978 (mm) cc_final: 0.8407 (mm) REVERT: A 692 GLN cc_start: 0.8367 (tp40) cc_final: 0.8066 (tm-30) REVERT: B 199 ASN cc_start: 0.8617 (m110) cc_final: 0.8377 (p0) REVERT: B 225 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8164 (ttt180) REVERT: B 260 ASN cc_start: 0.8829 (m110) cc_final: 0.8100 (m110) REVERT: B 291 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 312 LYS cc_start: 0.9327 (ptpt) cc_final: 0.8957 (ptpp) REVERT: B 410 ASP cc_start: 0.8442 (p0) cc_final: 0.8142 (p0) REVERT: B 484 ASP cc_start: 0.8496 (p0) cc_final: 0.7257 (p0) REVERT: B 508 MET cc_start: 0.0676 (mtt) cc_final: -0.0084 (mtt) REVERT: B 543 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8484 (mmtp) REVERT: B 546 GLU cc_start: 0.8805 (mp0) cc_final: 0.8437 (mp0) REVERT: B 561 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8670 (tp30) REVERT: B 562 ILE cc_start: 0.9439 (tp) cc_final: 0.9213 (tp) REVERT: B 565 LYS cc_start: 0.9198 (mptt) cc_final: 0.8758 (mmtp) REVERT: B 651 LYS cc_start: 0.9157 (ptpt) cc_final: 0.8794 (ptpt) REVERT: B 662 ARG cc_start: 0.8406 (ttt90) cc_final: 0.8097 (ttt90) REVERT: B 668 LYS cc_start: 0.7363 (mttt) cc_final: 0.7141 (mttt) REVERT: B 678 MET cc_start: 0.7617 (ptp) cc_final: 0.7152 (ptp) REVERT: B 682 PHE cc_start: 0.5228 (m-80) cc_final: 0.5023 (m-80) REVERT: B 689 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7593 (tm-30) REVERT: B 690 ILE cc_start: 0.8619 (mm) cc_final: 0.8138 (mm) REVERT: B 700 ARG cc_start: 0.8944 (ttp-170) cc_final: 0.8594 (ttm170) REVERT: C 219 MET cc_start: 0.8247 (tpp) cc_final: 0.7877 (tpp) REVERT: C 222 LEU cc_start: 0.9011 (mm) cc_final: 0.8705 (tp) REVERT: C 252 THR cc_start: 0.8793 (p) cc_final: 0.8478 (p) REVERT: C 312 LYS cc_start: 0.9182 (ptpt) cc_final: 0.8800 (ptpt) REVERT: C 442 MET cc_start: 0.7727 (tmm) cc_final: 0.7498 (tmm) REVERT: C 449 MET cc_start: 0.8611 (mmm) cc_final: 0.8235 (mmm) REVERT: C 450 ASP cc_start: 0.8517 (p0) cc_final: 0.8287 (t0) REVERT: C 486 LYS cc_start: 0.8428 (mttt) cc_final: 0.7877 (mmmt) REVERT: C 508 MET cc_start: 0.2365 (mtt) cc_final: 0.1630 (mtt) REVERT: C 560 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7661 (mtp-110) REVERT: C 611 MET cc_start: 0.7859 (mmp) cc_final: 0.7614 (mmp) REVERT: C 633 ILE cc_start: 0.8815 (pt) cc_final: 0.8595 (tp) REVERT: C 678 MET cc_start: 0.7694 (ptp) cc_final: 0.7130 (ptt) REVERT: C 683 SER cc_start: 0.7782 (m) cc_final: 0.7499 (p) REVERT: C 689 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7739 (tm-30) REVERT: C 690 ILE cc_start: 0.8874 (mm) cc_final: 0.8295 (mm) REVERT: D 203 TYR cc_start: 0.8173 (m-10) cc_final: 0.7729 (m-10) REVERT: D 219 MET cc_start: 0.8382 (tpp) cc_final: 0.8113 (tpp) REVERT: D 221 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7638 (tm-30) REVERT: D 283 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7675 (tm-30) REVERT: D 306 LEU cc_start: 0.9251 (tt) cc_final: 0.9025 (tp) REVERT: D 312 LYS cc_start: 0.8964 (ptpp) cc_final: 0.8610 (ptpp) REVERT: D 315 LYS cc_start: 0.8688 (tttm) cc_final: 0.7858 (tmtt) REVERT: D 392 ASP cc_start: 0.7443 (p0) cc_final: 0.7178 (p0) REVERT: D 395 ASP cc_start: 0.8444 (m-30) cc_final: 0.8033 (p0) REVERT: D 404 HIS cc_start: 0.8346 (p90) cc_final: 0.8083 (p90) REVERT: D 449 MET cc_start: 0.8464 (mmm) cc_final: 0.8192 (mmm) REVERT: D 484 ASP cc_start: 0.8825 (p0) cc_final: 0.7414 (p0) REVERT: D 486 LYS cc_start: 0.8104 (mttt) cc_final: 0.7338 (mmmt) REVERT: D 508 MET cc_start: 0.0930 (mtt) cc_final: 0.0406 (mtt) REVERT: D 543 LYS cc_start: 0.9263 (mmtp) cc_final: 0.8361 (mmmm) REVERT: D 546 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8729 (mp0) REVERT: D 558 ASN cc_start: 0.7474 (m-40) cc_final: 0.7255 (m110) REVERT: D 611 MET cc_start: 0.7672 (mmp) cc_final: 0.7438 (mmm) REVERT: D 678 MET cc_start: 0.7324 (ptp) cc_final: 0.6909 (ptm) REVERT: D 689 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7533 (tm-30) REVERT: D 690 ILE cc_start: 0.8892 (mm) cc_final: 0.8227 (mm) REVERT: D 700 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7694 (ttm110) REVERT: E 204 ASP cc_start: 0.7163 (p0) cc_final: 0.6864 (t0) REVERT: E 219 MET cc_start: 0.8587 (tpp) cc_final: 0.7900 (tpp) REVERT: E 222 LEU cc_start: 0.9156 (tp) cc_final: 0.8929 (tp) REVERT: E 244 TYR cc_start: 0.8038 (p90) cc_final: 0.7303 (p90) REVERT: E 281 GLU cc_start: 0.8474 (mp0) cc_final: 0.8088 (mp0) REVERT: E 287 ARG cc_start: 0.8608 (mmm160) cc_final: 0.8098 (mmm-85) REVERT: E 306 LEU cc_start: 0.9235 (tt) cc_final: 0.8938 (tp) REVERT: E 364 ASP cc_start: 0.8380 (m-30) cc_final: 0.8176 (p0) REVERT: E 449 MET cc_start: 0.8479 (mmm) cc_final: 0.8135 (mmm) REVERT: E 450 ASP cc_start: 0.7944 (p0) cc_final: 0.7710 (p0) REVERT: E 451 ASP cc_start: 0.7821 (m-30) cc_final: 0.7501 (m-30) REVERT: E 478 ASP cc_start: 0.7065 (m-30) cc_final: 0.6267 (t0) REVERT: E 508 MET cc_start: -0.0005 (mtt) cc_final: -0.0359 (mtt) REVERT: E 526 LEU cc_start: 0.8343 (mt) cc_final: 0.8118 (mp) REVERT: E 542 ILE cc_start: 0.8998 (tp) cc_final: 0.8731 (tp) REVERT: E 546 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8687 (mp0) REVERT: E 560 ARG cc_start: 0.8452 (mtp-110) cc_final: 0.8228 (mtp180) REVERT: E 601 ILE cc_start: 0.8796 (mt) cc_final: 0.8586 (mt) REVERT: E 643 ILE cc_start: 0.8406 (tp) cc_final: 0.7937 (pt) REVERT: E 662 ARG cc_start: 0.8501 (ttt90) cc_final: 0.8067 (tmm160) REVERT: F 287 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7469 (mmm-85) REVERT: F 288 LYS cc_start: 0.9185 (mppt) cc_final: 0.8269 (mmmt) REVERT: F 395 ASP cc_start: 0.7771 (m-30) cc_final: 0.7256 (p0) REVERT: F 449 MET cc_start: 0.8270 (mmm) cc_final: 0.8057 (mmm) REVERT: F 484 ASP cc_start: 0.8618 (p0) cc_final: 0.8203 (p0) REVERT: F 494 GLN cc_start: 0.7827 (tp-100) cc_final: 0.7545 (tp40) REVERT: F 499 HIS cc_start: 0.7775 (m90) cc_final: 0.7294 (m-70) REVERT: F 543 LYS cc_start: 0.8999 (mmtp) cc_final: 0.8155 (mmtm) REVERT: F 546 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8514 (mp0) REVERT: F 550 MET cc_start: 0.6013 (mmp) cc_final: 0.5559 (mmp) REVERT: F 560 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8184 (mtp-110) REVERT: F 700 ARG cc_start: 0.8172 (ttp-170) cc_final: 0.7970 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 746 average time/residue: 0.4446 time to fit residues: 494.0940 Evaluate side-chains 596 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 596 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 chunk 312 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 286 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 232 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN B 327 GLN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 602 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 558 ASN E 602 ASN F 533 ASN F 602 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 25518 Z= 0.264 Angle : 0.694 8.253 34482 Z= 0.355 Chirality : 0.044 0.160 3894 Planarity : 0.005 0.053 4524 Dihedral : 9.161 112.384 3480 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.04 % Allowed : 6.40 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3150 helix: -0.63 (0.13), residues: 1572 sheet: -2.06 (0.28), residues: 306 loop : -0.20 (0.20), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 476 HIS 0.008 0.002 HIS A 735 PHE 0.021 0.002 PHE A 618 TYR 0.018 0.002 TYR C 203 ARG 0.014 0.001 ARG C 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 687 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.8016 (m-10) cc_final: 0.7296 (m-10) REVERT: A 219 MET cc_start: 0.7789 (tpt) cc_final: 0.7551 (tpp) REVERT: A 239 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7019 (mtm180) REVERT: A 244 TYR cc_start: 0.8106 (p90) cc_final: 0.7567 (p90) REVERT: A 305 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8189 (mm-30) REVERT: A 332 MET cc_start: 0.9179 (mmm) cc_final: 0.8840 (mmt) REVERT: A 349 ARG cc_start: 0.8705 (ttm170) cc_final: 0.8107 (ttm-80) REVERT: A 449 MET cc_start: 0.8385 (mmm) cc_final: 0.7853 (mmm) REVERT: A 484 ASP cc_start: 0.8079 (p0) cc_final: 0.7283 (p0) REVERT: A 486 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7830 (mmtt) REVERT: A 526 LEU cc_start: 0.8223 (mt) cc_final: 0.7936 (mp) REVERT: A 543 LYS cc_start: 0.9346 (mmtp) cc_final: 0.9038 (mmtt) REVERT: A 560 ARG cc_start: 0.8316 (mtp180) cc_final: 0.7788 (mtp-110) REVERT: A 577 ASP cc_start: 0.7888 (p0) cc_final: 0.7638 (p0) REVERT: A 678 MET cc_start: 0.6719 (ptp) cc_final: 0.6186 (ptt) REVERT: A 689 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 690 ILE cc_start: 0.9036 (mm) cc_final: 0.8433 (mm) REVERT: A 692 GLN cc_start: 0.8251 (tp40) cc_final: 0.7930 (tm-30) REVERT: A 757 MET cc_start: 0.7461 (tmm) cc_final: 0.7170 (tmm) REVERT: B 205 ASP cc_start: 0.8397 (t70) cc_final: 0.8045 (t0) REVERT: B 225 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.8215 (ttt180) REVERT: B 312 LYS cc_start: 0.9355 (ptpt) cc_final: 0.9025 (ptpp) REVERT: B 449 MET cc_start: 0.8761 (mmm) cc_final: 0.8426 (mmm) REVERT: B 508 MET cc_start: 0.1182 (mtt) cc_final: -0.0192 (mtm) REVERT: B 543 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8387 (mmtp) REVERT: B 546 GLU cc_start: 0.8855 (mp0) cc_final: 0.8543 (mp0) REVERT: B 561 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8686 (mm-30) REVERT: B 634 LEU cc_start: 0.7903 (tt) cc_final: 0.7562 (tt) REVERT: B 651 LYS cc_start: 0.9242 (ptpt) cc_final: 0.8893 (ptpt) REVERT: B 678 MET cc_start: 0.7721 (ptp) cc_final: 0.7027 (ptm) REVERT: B 682 PHE cc_start: 0.6065 (m-80) cc_final: 0.5772 (m-80) REVERT: B 689 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7648 (tm-30) REVERT: B 690 ILE cc_start: 0.8460 (mm) cc_final: 0.8123 (mm) REVERT: B 700 ARG cc_start: 0.8931 (ttp-170) cc_final: 0.8651 (ttm170) REVERT: C 221 GLU cc_start: 0.8507 (pt0) cc_final: 0.8230 (pt0) REVERT: C 267 PHE cc_start: 0.8287 (t80) cc_final: 0.8025 (t80) REVERT: C 288 LYS cc_start: 0.9316 (mptt) cc_final: 0.9101 (mmmt) REVERT: C 312 LYS cc_start: 0.9122 (ptpt) cc_final: 0.8878 (ptpt) REVERT: C 442 MET cc_start: 0.7710 (tmm) cc_final: 0.7416 (tmm) REVERT: C 484 ASP cc_start: 0.8776 (p0) cc_final: 0.8389 (p0) REVERT: C 550 MET cc_start: 0.4744 (mmp) cc_final: 0.4485 (mmp) REVERT: C 560 ARG cc_start: 0.8318 (mtp-110) cc_final: 0.7992 (mtp-110) REVERT: C 562 ILE cc_start: 0.9516 (tp) cc_final: 0.9024 (tp) REVERT: C 611 MET cc_start: 0.8049 (mmp) cc_final: 0.7737 (mmp) REVERT: C 678 MET cc_start: 0.8265 (ptp) cc_final: 0.7697 (ptt) REVERT: C 683 SER cc_start: 0.7796 (m) cc_final: 0.7474 (p) REVERT: C 740 MET cc_start: 0.3540 (ttm) cc_final: 0.2881 (ttp) REVERT: D 219 MET cc_start: 0.8430 (tpp) cc_final: 0.8086 (tpp) REVERT: D 306 LEU cc_start: 0.9296 (tt) cc_final: 0.9041 (tp) REVERT: D 312 LYS cc_start: 0.9259 (ptpp) cc_final: 0.8844 (ptpp) REVERT: D 392 ASP cc_start: 0.7534 (p0) cc_final: 0.7255 (p0) REVERT: D 395 ASP cc_start: 0.8608 (m-30) cc_final: 0.8140 (p0) REVERT: D 508 MET cc_start: 0.1007 (mtt) cc_final: 0.0385 (mtt) REVERT: D 543 LYS cc_start: 0.9223 (mmtp) cc_final: 0.8442 (mmmm) REVERT: D 546 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8726 (mp0) REVERT: D 578 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7932 (mm-30) REVERT: D 611 MET cc_start: 0.7665 (mmp) cc_final: 0.7408 (mmm) REVERT: D 678 MET cc_start: 0.7405 (ptp) cc_final: 0.6793 (ptt) REVERT: D 689 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7561 (tm-30) REVERT: D 690 ILE cc_start: 0.9012 (mm) cc_final: 0.8407 (mm) REVERT: D 700 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7820 (ttm170) REVERT: E 244 TYR cc_start: 0.8218 (p90) cc_final: 0.7697 (p90) REVERT: E 278 LEU cc_start: 0.8240 (pp) cc_final: 0.7849 (pp) REVERT: E 281 GLU cc_start: 0.8397 (mp0) cc_final: 0.8157 (mp0) REVERT: E 287 ARG cc_start: 0.8659 (mmm160) cc_final: 0.8143 (mmm-85) REVERT: E 306 LEU cc_start: 0.9323 (tt) cc_final: 0.9029 (tp) REVERT: E 332 MET cc_start: 0.9010 (mmm) cc_final: 0.8465 (mmm) REVERT: E 411 LEU cc_start: 0.9127 (mp) cc_final: 0.8793 (mm) REVERT: E 449 MET cc_start: 0.8515 (mmm) cc_final: 0.8230 (mmm) REVERT: E 543 LYS cc_start: 0.9304 (mmtp) cc_final: 0.8587 (mmmt) REVERT: E 546 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8713 (mp0) REVERT: E 560 ARG cc_start: 0.8437 (mtp-110) cc_final: 0.8101 (mtp180) REVERT: E 565 LYS cc_start: 0.9176 (mtpp) cc_final: 0.8962 (mtpp) REVERT: E 577 ASP cc_start: 0.8088 (p0) cc_final: 0.6967 (p0) REVERT: E 601 ILE cc_start: 0.8745 (mt) cc_final: 0.8496 (mt) REVERT: E 651 LYS cc_start: 0.9145 (ptpt) cc_final: 0.8306 (pttp) REVERT: E 662 ARG cc_start: 0.8538 (ttt90) cc_final: 0.8328 (tmm160) REVERT: F 225 ARG cc_start: 0.9193 (mmm-85) cc_final: 0.8811 (tpp80) REVERT: F 267 PHE cc_start: 0.8108 (t80) cc_final: 0.7834 (t80) REVERT: F 288 LYS cc_start: 0.9209 (mppt) cc_final: 0.8515 (mmmt) REVERT: F 312 LYS cc_start: 0.9291 (ptpt) cc_final: 0.9019 (ptpp) REVERT: F 494 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7688 (tp40) REVERT: F 499 HIS cc_start: 0.7820 (m90) cc_final: 0.7559 (m-70) REVERT: F 543 LYS cc_start: 0.9056 (mmtp) cc_final: 0.8183 (mmtm) REVERT: F 546 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8501 (mp0) REVERT: F 550 MET cc_start: 0.5944 (mmp) cc_final: 0.5356 (mtt) REVERT: F 560 ARG cc_start: 0.8628 (mtp-110) cc_final: 0.8188 (mtp-110) REVERT: F 689 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8114 (tm-30) REVERT: F 696 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8111 (mmmt) REVERT: F 697 LEU cc_start: 0.8396 (mm) cc_final: 0.8057 (mm) outliers start: 1 outliers final: 0 residues processed: 688 average time/residue: 0.4104 time to fit residues: 419.4622 Evaluate side-chains 558 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 558 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 0.0170 chunk 194 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 307 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN B 602 ASN C 499 HIS C 602 ASN D 285 ASN D 558 ASN D 602 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 602 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25518 Z= 0.191 Angle : 0.648 7.195 34482 Z= 0.324 Chirality : 0.044 0.162 3894 Planarity : 0.005 0.064 4524 Dihedral : 8.831 109.785 3480 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 3150 helix: -0.35 (0.13), residues: 1560 sheet: -2.03 (0.27), residues: 306 loop : -0.08 (0.20), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 476 HIS 0.008 0.001 HIS B 499 PHE 0.024 0.001 PHE C 742 TYR 0.014 0.002 TYR F 495 ARG 0.010 0.001 ARG F 700 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 700 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.7853 (tpt) cc_final: 0.7589 (tpp) REVERT: A 239 ARG cc_start: 0.7630 (mtp-110) cc_final: 0.6958 (mtm180) REVERT: A 244 TYR cc_start: 0.7955 (p90) cc_final: 0.7510 (p90) REVERT: A 278 LEU cc_start: 0.8915 (mt) cc_final: 0.8624 (mm) REVERT: A 305 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 306 LEU cc_start: 0.9354 (tt) cc_final: 0.9112 (tt) REVERT: A 332 MET cc_start: 0.9236 (mmm) cc_final: 0.9006 (mmt) REVERT: A 349 ARG cc_start: 0.8485 (ttm170) cc_final: 0.8145 (ttm110) REVERT: A 449 MET cc_start: 0.8136 (mmm) cc_final: 0.7931 (mmm) REVERT: A 484 ASP cc_start: 0.8046 (p0) cc_final: 0.7111 (p0) REVERT: A 494 GLN cc_start: 0.8111 (tp40) cc_final: 0.7888 (mm110) REVERT: A 524 LYS cc_start: 0.8526 (ptpt) cc_final: 0.8080 (pttt) REVERT: A 526 LEU cc_start: 0.8060 (mt) cc_final: 0.7793 (mp) REVERT: A 543 LYS cc_start: 0.9351 (mmtp) cc_final: 0.8985 (mmtt) REVERT: A 549 THR cc_start: 0.6211 (p) cc_final: 0.5956 (p) REVERT: A 564 ASP cc_start: 0.9307 (m-30) cc_final: 0.9084 (m-30) REVERT: A 678 MET cc_start: 0.6645 (ptp) cc_final: 0.6130 (ptt) REVERT: A 689 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7641 (tm-30) REVERT: A 690 ILE cc_start: 0.9002 (mm) cc_final: 0.8775 (mt) REVERT: A 757 MET cc_start: 0.7463 (tmm) cc_final: 0.7186 (tmm) REVERT: B 205 ASP cc_start: 0.8341 (t70) cc_final: 0.8091 (t0) REVERT: B 225 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8194 (ttt180) REVERT: B 261 GLU cc_start: 0.5542 (tm-30) cc_final: 0.5045 (tm-30) REVERT: B 312 LYS cc_start: 0.9583 (ptpt) cc_final: 0.9288 (ptpp) REVERT: B 332 MET cc_start: 0.9117 (mmm) cc_final: 0.8774 (mmm) REVERT: B 403 THR cc_start: 0.8736 (p) cc_final: 0.8364 (t) REVERT: B 460 ASN cc_start: 0.8253 (p0) cc_final: 0.7992 (m-40) REVERT: B 508 MET cc_start: 0.1255 (mtt) cc_final: -0.0024 (mtm) REVERT: B 543 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8419 (mmtp) REVERT: B 546 GLU cc_start: 0.8877 (mp0) cc_final: 0.8483 (mp0) REVERT: B 560 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7741 (mmm160) REVERT: B 561 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8651 (mm-30) REVERT: B 651 LYS cc_start: 0.9206 (ptpt) cc_final: 0.8797 (ptpt) REVERT: B 689 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7595 (tm-30) REVERT: B 690 ILE cc_start: 0.8534 (mm) cc_final: 0.8051 (mm) REVERT: B 700 ARG cc_start: 0.8918 (ttp-170) cc_final: 0.8595 (ttm170) REVERT: C 217 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8028 (mtpt) REVERT: C 221 GLU cc_start: 0.8584 (pt0) cc_final: 0.8342 (pt0) REVERT: C 306 LEU cc_start: 0.9433 (tt) cc_final: 0.9188 (tt) REVERT: C 312 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8764 (ptpt) REVERT: C 442 MET cc_start: 0.7698 (tmm) cc_final: 0.7436 (tmm) REVERT: C 449 MET cc_start: 0.8637 (mmm) cc_final: 0.8299 (mmm) REVERT: C 486 LYS cc_start: 0.8093 (mttt) cc_final: 0.7529 (mmmt) REVERT: C 508 MET cc_start: 0.1844 (mtt) cc_final: 0.1348 (mtt) REVERT: C 543 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8601 (mmtt) REVERT: C 550 MET cc_start: 0.4625 (mmp) cc_final: 0.4366 (mmp) REVERT: C 560 ARG cc_start: 0.8309 (mtp-110) cc_final: 0.7914 (mtp180) REVERT: C 562 ILE cc_start: 0.9093 (tp) cc_final: 0.8843 (tp) REVERT: C 611 MET cc_start: 0.7688 (mmp) cc_final: 0.7393 (mmt) REVERT: C 683 SER cc_start: 0.7862 (m) cc_final: 0.7488 (p) REVERT: D 219 MET cc_start: 0.8334 (tpp) cc_final: 0.8028 (tpp) REVERT: D 244 TYR cc_start: 0.7825 (p90) cc_final: 0.7602 (p90) REVERT: D 288 LYS cc_start: 0.9323 (mptt) cc_final: 0.8765 (mmtp) REVERT: D 306 LEU cc_start: 0.9252 (tt) cc_final: 0.8988 (tp) REVERT: D 312 LYS cc_start: 0.9252 (ptpp) cc_final: 0.8809 (ptpp) REVERT: D 449 MET cc_start: 0.8259 (mmm) cc_final: 0.7932 (mmm) REVERT: D 529 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8264 (tptp) REVERT: D 543 LYS cc_start: 0.9246 (mmtp) cc_final: 0.8407 (mmmm) REVERT: D 546 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8709 (mp0) REVERT: D 611 MET cc_start: 0.7659 (mmp) cc_final: 0.7410 (mmm) REVERT: D 678 MET cc_start: 0.7334 (ptp) cc_final: 0.6591 (ptt) REVERT: D 689 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7594 (tm-30) REVERT: D 690 ILE cc_start: 0.8963 (mm) cc_final: 0.8379 (mm) REVERT: D 700 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7792 (ttm110) REVERT: E 204 ASP cc_start: 0.7354 (p0) cc_final: 0.7151 (t0) REVERT: E 244 TYR cc_start: 0.8206 (p90) cc_final: 0.7703 (p90) REVERT: E 261 GLU cc_start: 0.5217 (tm-30) cc_final: 0.4977 (tm-30) REVERT: E 278 LEU cc_start: 0.8127 (pp) cc_final: 0.7637 (pp) REVERT: E 281 GLU cc_start: 0.8365 (mp0) cc_final: 0.8020 (mp0) REVERT: E 287 ARG cc_start: 0.8616 (mmm160) cc_final: 0.8254 (mmm-85) REVERT: E 306 LEU cc_start: 0.9317 (tt) cc_final: 0.9012 (tp) REVERT: E 312 LYS cc_start: 0.9081 (tptt) cc_final: 0.8852 (ptpp) REVERT: E 332 MET cc_start: 0.9072 (mmm) cc_final: 0.8449 (mmm) REVERT: E 347 THR cc_start: 0.9301 (p) cc_final: 0.9093 (t) REVERT: E 411 LEU cc_start: 0.9080 (mp) cc_final: 0.8749 (mm) REVERT: E 542 ILE cc_start: 0.9022 (tp) cc_final: 0.8776 (tp) REVERT: E 546 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8650 (mp0) REVERT: E 560 ARG cc_start: 0.8366 (mtp-110) cc_final: 0.7998 (mtp180) REVERT: E 601 ILE cc_start: 0.8749 (mt) cc_final: 0.8474 (mt) REVERT: F 225 ARG cc_start: 0.9184 (mmm-85) cc_final: 0.8827 (tpp80) REVERT: F 278 LEU cc_start: 0.8892 (mt) cc_final: 0.8156 (mt) REVERT: F 287 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.7635 (mmm-85) REVERT: F 288 LYS cc_start: 0.9292 (mptt) cc_final: 0.8643 (mmtm) REVERT: F 388 MET cc_start: 0.5384 (mtt) cc_final: 0.4958 (mtm) REVERT: F 449 MET cc_start: 0.8618 (mmm) cc_final: 0.8412 (mmm) REVERT: F 488 GLU cc_start: 0.8861 (mp0) cc_final: 0.8619 (mm-30) REVERT: F 494 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7481 (tm-30) REVERT: F 543 LYS cc_start: 0.9063 (mmtp) cc_final: 0.8401 (mmtm) REVERT: F 546 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8410 (mp0) REVERT: F 550 MET cc_start: 0.5855 (mmp) cc_final: 0.5146 (mtm) REVERT: F 560 ARG cc_start: 0.8599 (mtp-110) cc_final: 0.8331 (mtp-110) REVERT: F 662 ARG cc_start: 0.8289 (ttt90) cc_final: 0.8046 (ttt90) REVERT: F 689 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7991 (tm-30) outliers start: 1 outliers final: 0 residues processed: 701 average time/residue: 0.4024 time to fit residues: 421.7712 Evaluate side-chains 560 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 560 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 228 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 275 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 602 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 25518 Z= 0.365 Angle : 0.763 7.915 34482 Z= 0.394 Chirality : 0.046 0.168 3894 Planarity : 0.006 0.065 4524 Dihedral : 8.834 105.797 3480 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 26.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.16), residues: 3150 helix: -0.69 (0.13), residues: 1608 sheet: -2.17 (0.26), residues: 306 loop : -0.05 (0.21), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 454 HIS 0.010 0.002 HIS A 735 PHE 0.036 0.002 PHE A 452 TYR 0.013 0.002 TYR A 203 ARG 0.027 0.001 ARG E 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8204 (tpt) cc_final: 0.7888 (tpp) REVERT: A 244 TYR cc_start: 0.8093 (p90) cc_final: 0.7235 (p90) REVERT: A 278 LEU cc_start: 0.8808 (mt) cc_final: 0.8527 (mt) REVERT: A 306 LEU cc_start: 0.9404 (tt) cc_final: 0.9167 (tt) REVERT: A 449 MET cc_start: 0.8186 (mmm) cc_final: 0.7985 (mmm) REVERT: A 494 GLN cc_start: 0.8158 (tp40) cc_final: 0.7926 (mm110) REVERT: A 526 LEU cc_start: 0.8128 (mt) cc_final: 0.7889 (mp) REVERT: A 543 LYS cc_start: 0.9345 (mmtp) cc_final: 0.9052 (mmtt) REVERT: A 560 ARG cc_start: 0.8665 (mtp180) cc_final: 0.8320 (mtp-110) REVERT: A 678 MET cc_start: 0.7081 (ptp) cc_final: 0.6556 (ptt) REVERT: A 690 ILE cc_start: 0.9030 (mm) cc_final: 0.8779 (mt) REVERT: A 757 MET cc_start: 0.7581 (tmm) cc_final: 0.7255 (tmm) REVERT: A 761 THR cc_start: 0.6946 (m) cc_final: 0.6465 (m) REVERT: B 205 ASP cc_start: 0.8444 (t70) cc_final: 0.8187 (t0) REVERT: B 218 GLU cc_start: 0.9144 (pp20) cc_final: 0.8563 (tm-30) REVERT: B 225 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.8263 (ttt180) REVERT: B 267 PHE cc_start: 0.8552 (t80) cc_final: 0.8350 (t80) REVERT: B 312 LYS cc_start: 0.9513 (ptpt) cc_final: 0.9225 (ptpp) REVERT: B 410 ASP cc_start: 0.8484 (p0) cc_final: 0.8277 (p0) REVERT: B 460 ASN cc_start: 0.8405 (p0) cc_final: 0.8126 (m-40) REVERT: B 494 GLN cc_start: 0.7871 (tp40) cc_final: 0.7556 (tp40) REVERT: B 508 MET cc_start: 0.1633 (mtt) cc_final: 0.0923 (mtm) REVERT: B 543 LYS cc_start: 0.8912 (mmtp) cc_final: 0.8288 (mmtm) REVERT: B 546 GLU cc_start: 0.8922 (mp0) cc_final: 0.8550 (mp0) REVERT: B 563 PHE cc_start: 0.8353 (t80) cc_final: 0.7883 (t80) REVERT: B 565 LYS cc_start: 0.9436 (mmtp) cc_final: 0.9233 (mmtp) REVERT: B 651 LYS cc_start: 0.9399 (ptpt) cc_final: 0.9166 (ptpt) REVERT: B 668 LYS cc_start: 0.7712 (mtmt) cc_final: 0.7109 (mttp) REVERT: B 689 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 690 ILE cc_start: 0.8713 (mm) cc_final: 0.8330 (mm) REVERT: B 700 ARG cc_start: 0.8964 (ttp-170) cc_final: 0.8646 (ttm170) REVERT: C 217 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8256 (mtpt) REVERT: C 221 GLU cc_start: 0.8679 (pt0) cc_final: 0.8360 (pt0) REVERT: C 267 PHE cc_start: 0.8457 (t80) cc_final: 0.8117 (t80) REVERT: C 287 ARG cc_start: 0.8449 (mtm110) cc_final: 0.8036 (mtm110) REVERT: C 306 LEU cc_start: 0.9602 (tt) cc_final: 0.9307 (tt) REVERT: C 312 LYS cc_start: 0.9396 (ptpt) cc_final: 0.9138 (ptpp) REVERT: C 442 MET cc_start: 0.7728 (tmm) cc_final: 0.7408 (tmm) REVERT: C 449 MET cc_start: 0.8510 (mmm) cc_final: 0.8300 (mmm) REVERT: C 543 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8501 (mmtt) REVERT: C 560 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.8077 (mtp180) REVERT: C 611 MET cc_start: 0.7682 (mmp) cc_final: 0.7312 (mmt) REVERT: C 683 SER cc_start: 0.8025 (m) cc_final: 0.7602 (p) REVERT: D 244 TYR cc_start: 0.8086 (p90) cc_final: 0.7687 (p90) REVERT: D 288 LYS cc_start: 0.9480 (mptt) cc_final: 0.9210 (mmtm) REVERT: D 312 LYS cc_start: 0.9351 (ptpp) cc_final: 0.9021 (ptpp) REVERT: D 486 LYS cc_start: 0.8230 (tttt) cc_final: 0.7909 (mtpt) REVERT: D 508 MET cc_start: 0.0783 (mtt) cc_final: 0.0530 (mtt) REVERT: D 543 LYS cc_start: 0.9228 (mmtp) cc_final: 0.8489 (mmmm) REVERT: D 546 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8756 (mp0) REVERT: D 578 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7989 (mm-30) REVERT: D 611 MET cc_start: 0.7787 (mmp) cc_final: 0.7584 (mmm) REVERT: D 658 LYS cc_start: 0.8575 (tptp) cc_final: 0.8364 (tppt) REVERT: D 678 MET cc_start: 0.7385 (ptp) cc_final: 0.6782 (ptt) REVERT: D 690 ILE cc_start: 0.8961 (mm) cc_final: 0.8344 (mm) REVERT: D 700 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7874 (ttm170) REVERT: E 244 TYR cc_start: 0.8307 (p90) cc_final: 0.7525 (p90) REVERT: E 261 GLU cc_start: 0.5871 (tm-30) cc_final: 0.5641 (tm-30) REVERT: E 281 GLU cc_start: 0.8762 (mp0) cc_final: 0.8516 (mp0) REVERT: E 287 ARG cc_start: 0.8689 (mmm160) cc_final: 0.8249 (mmm-85) REVERT: E 288 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8056 (mttt) REVERT: E 306 LEU cc_start: 0.9369 (tt) cc_final: 0.9165 (tp) REVERT: E 312 LYS cc_start: 0.9142 (tptt) cc_final: 0.8923 (tppt) REVERT: E 332 MET cc_start: 0.9055 (mmm) cc_final: 0.8531 (mmm) REVERT: E 411 LEU cc_start: 0.9266 (mp) cc_final: 0.8930 (mm) REVERT: E 543 LYS cc_start: 0.9407 (mmtp) cc_final: 0.8907 (mmmt) REVERT: E 562 ILE cc_start: 0.9545 (tp) cc_final: 0.9297 (tp) REVERT: E 601 ILE cc_start: 0.8869 (mt) cc_final: 0.8568 (mt) REVERT: E 651 LYS cc_start: 0.9186 (ptpt) cc_final: 0.8500 (pttp) REVERT: F 205 ASP cc_start: 0.8573 (m-30) cc_final: 0.8330 (t0) REVERT: F 225 ARG cc_start: 0.9232 (mmm-85) cc_final: 0.8902 (tpp80) REVERT: F 278 LEU cc_start: 0.9089 (mt) cc_final: 0.8206 (mt) REVERT: F 288 LYS cc_start: 0.9423 (mptt) cc_final: 0.8800 (mmtp) REVERT: F 494 GLN cc_start: 0.7781 (tp-100) cc_final: 0.7541 (tm-30) REVERT: F 499 HIS cc_start: 0.7758 (m90) cc_final: 0.7506 (m-70) REVERT: F 543 LYS cc_start: 0.9200 (mmtp) cc_final: 0.8555 (mmtm) REVERT: F 550 MET cc_start: 0.5896 (mmp) cc_final: 0.5501 (mmp) REVERT: F 560 ARG cc_start: 0.8517 (mtp-110) cc_final: 0.8286 (mtp-110) REVERT: F 561 GLU cc_start: 0.8886 (tp30) cc_final: 0.8595 (tp30) REVERT: F 662 ARG cc_start: 0.8341 (ttt90) cc_final: 0.7966 (ttt90) REVERT: F 689 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7964 (tm-30) outliers start: 0 outliers final: 0 residues processed: 625 average time/residue: 0.4067 time to fit residues: 378.9220 Evaluate side-chains 513 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 5.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 602 ASN B 558 ASN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 285 ASN D 602 ASN E 285 ASN E 602 ASN F 602 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25518 Z= 0.190 Angle : 0.669 7.680 34482 Z= 0.333 Chirality : 0.045 0.209 3894 Planarity : 0.005 0.059 4524 Dihedral : 8.544 103.409 3480 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 3150 helix: -0.36 (0.13), residues: 1578 sheet: -1.97 (0.28), residues: 288 loop : -0.02 (0.20), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 476 HIS 0.009 0.001 HIS B 499 PHE 0.026 0.001 PHE B 576 TYR 0.027 0.002 TYR C 203 ARG 0.007 0.000 ARG C 700 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.7913 (tpt) cc_final: 0.7667 (tpp) REVERT: A 244 TYR cc_start: 0.8139 (p90) cc_final: 0.7415 (p90) REVERT: A 278 LEU cc_start: 0.8694 (mt) cc_final: 0.8480 (mt) REVERT: A 288 LYS cc_start: 0.9405 (mptt) cc_final: 0.8460 (mmtm) REVERT: A 306 LEU cc_start: 0.9343 (tt) cc_final: 0.9082 (tt) REVERT: A 494 GLN cc_start: 0.8205 (tp40) cc_final: 0.7888 (mm110) REVERT: A 526 LEU cc_start: 0.8022 (mt) cc_final: 0.7759 (mp) REVERT: A 543 LYS cc_start: 0.9369 (mmtp) cc_final: 0.9017 (mmtt) REVERT: A 678 MET cc_start: 0.6959 (ptp) cc_final: 0.6468 (ptt) REVERT: A 757 MET cc_start: 0.7566 (tmm) cc_final: 0.7189 (tmm) REVERT: A 761 THR cc_start: 0.6882 (m) cc_final: 0.6410 (m) REVERT: B 218 GLU cc_start: 0.9095 (pp20) cc_final: 0.8682 (tm-30) REVERT: B 221 GLU cc_start: 0.8362 (pp20) cc_final: 0.7949 (tm-30) REVERT: B 222 LEU cc_start: 0.9390 (mm) cc_final: 0.9137 (mm) REVERT: B 225 ARG cc_start: 0.8681 (mmm-85) cc_final: 0.8189 (ttt180) REVERT: B 312 LYS cc_start: 0.9532 (ptpt) cc_final: 0.9183 (ptpp) REVERT: B 332 MET cc_start: 0.9131 (mmm) cc_final: 0.8612 (mmm) REVERT: B 403 THR cc_start: 0.8791 (p) cc_final: 0.8456 (t) REVERT: B 448 THR cc_start: 0.8048 (m) cc_final: 0.7685 (m) REVERT: B 508 MET cc_start: 0.0642 (mtt) cc_final: 0.0094 (mtm) REVERT: B 546 GLU cc_start: 0.8680 (mp0) cc_final: 0.8349 (mp0) REVERT: B 558 ASN cc_start: 0.8184 (m-40) cc_final: 0.6957 (t0) REVERT: B 560 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7732 (mmm160) REVERT: B 563 PHE cc_start: 0.8484 (t80) cc_final: 0.7831 (t80) REVERT: B 565 LYS cc_start: 0.9290 (mmtp) cc_final: 0.9077 (mmtp) REVERT: B 651 LYS cc_start: 0.9317 (ptpt) cc_final: 0.8884 (ptpt) REVERT: B 658 LYS cc_start: 0.8071 (tptp) cc_final: 0.7552 (tppt) REVERT: B 668 LYS cc_start: 0.7655 (mtmt) cc_final: 0.7252 (mttp) REVERT: B 689 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7399 (tm-30) REVERT: B 690 ILE cc_start: 0.8520 (mm) cc_final: 0.8005 (mm) REVERT: B 700 ARG cc_start: 0.8926 (ttp-170) cc_final: 0.8601 (ttm170) REVERT: C 221 GLU cc_start: 0.8570 (pt0) cc_final: 0.8213 (tm-30) REVERT: C 222 LEU cc_start: 0.9240 (mm) cc_final: 0.8678 (mm) REVERT: C 244 TYR cc_start: 0.8313 (p90) cc_final: 0.8110 (p90) REVERT: C 267 PHE cc_start: 0.8282 (t80) cc_final: 0.8037 (t80) REVERT: C 306 LEU cc_start: 0.9559 (tt) cc_final: 0.9202 (tt) REVERT: C 312 LYS cc_start: 0.9333 (ptpt) cc_final: 0.9034 (ptpp) REVERT: C 366 GLU cc_start: 0.7989 (mp0) cc_final: 0.7722 (mp0) REVERT: C 442 MET cc_start: 0.7678 (tmm) cc_final: 0.7405 (tmm) REVERT: C 486 LYS cc_start: 0.8372 (mttt) cc_final: 0.7777 (mmmt) REVERT: C 508 MET cc_start: 0.1799 (mtt) cc_final: 0.0706 (mtt) REVERT: C 543 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8522 (mmtt) REVERT: C 560 ARG cc_start: 0.8238 (mtp-110) cc_final: 0.7998 (mtp180) REVERT: C 611 MET cc_start: 0.7592 (mmp) cc_final: 0.7274 (mmt) REVERT: C 683 SER cc_start: 0.7780 (m) cc_final: 0.7381 (p) REVERT: D 219 MET cc_start: 0.8414 (tpp) cc_final: 0.7959 (tpp) REVERT: D 244 TYR cc_start: 0.8092 (p90) cc_final: 0.7594 (p90) REVERT: D 288 LYS cc_start: 0.9438 (mptt) cc_final: 0.8860 (mmtm) REVERT: D 312 LYS cc_start: 0.9263 (ptpp) cc_final: 0.8878 (ptpp) REVERT: D 486 LYS cc_start: 0.8180 (tttt) cc_final: 0.7470 (mtpt) REVERT: D 508 MET cc_start: 0.0245 (mtt) cc_final: -0.0297 (mtt) REVERT: D 543 LYS cc_start: 0.9209 (mmtp) cc_final: 0.8436 (mmmm) REVERT: D 546 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8756 (mp0) REVERT: D 611 MET cc_start: 0.7574 (mmp) cc_final: 0.7353 (mmm) REVERT: D 678 MET cc_start: 0.7293 (ptp) cc_final: 0.6548 (ptt) REVERT: D 690 ILE cc_start: 0.8855 (mm) cc_final: 0.8271 (mm) REVERT: D 700 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7724 (ttm110) REVERT: E 218 GLU cc_start: 0.9051 (pp20) cc_final: 0.8665 (pp20) REVERT: E 281 GLU cc_start: 0.8614 (mp0) cc_final: 0.8357 (mp0) REVERT: E 287 ARG cc_start: 0.8637 (mmm160) cc_final: 0.8191 (mmm-85) REVERT: E 306 LEU cc_start: 0.9277 (tt) cc_final: 0.9015 (tp) REVERT: E 331 LEU cc_start: 0.9196 (mm) cc_final: 0.8913 (mm) REVERT: E 332 MET cc_start: 0.9055 (mmm) cc_final: 0.8514 (mmm) REVERT: E 411 LEU cc_start: 0.9071 (mp) cc_final: 0.8741 (mm) REVERT: E 465 ARG cc_start: 0.7707 (mmm160) cc_final: 0.7483 (mmm160) REVERT: E 486 LYS cc_start: 0.8311 (mttt) cc_final: 0.7892 (mmmt) REVERT: E 529 LYS cc_start: 0.8532 (mmmt) cc_final: 0.7868 (tptt) REVERT: E 561 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8726 (mm-30) REVERT: E 568 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8405 (tm-30) REVERT: E 577 ASP cc_start: 0.8028 (p0) cc_final: 0.7271 (p0) REVERT: E 601 ILE cc_start: 0.8883 (mt) cc_final: 0.8569 (mt) REVERT: E 611 MET cc_start: 0.7745 (mmp) cc_final: 0.7522 (mmm) REVERT: F 205 ASP cc_start: 0.8494 (m-30) cc_final: 0.8037 (t0) REVERT: F 225 ARG cc_start: 0.9201 (mmm-85) cc_final: 0.8803 (tpp80) REVERT: F 267 PHE cc_start: 0.8447 (t80) cc_final: 0.8093 (t80) REVERT: F 278 LEU cc_start: 0.8936 (mt) cc_final: 0.8548 (mt) REVERT: F 288 LYS cc_start: 0.9387 (mptt) cc_final: 0.8686 (mmtm) REVERT: F 499 HIS cc_start: 0.7798 (m90) cc_final: 0.7516 (m-70) REVERT: F 543 LYS cc_start: 0.9137 (mmtp) cc_final: 0.8920 (mmtm) REVERT: F 549 THR cc_start: 0.6198 (p) cc_final: 0.5963 (p) REVERT: F 550 MET cc_start: 0.5722 (mmp) cc_final: 0.5113 (mtt) REVERT: F 560 ARG cc_start: 0.8660 (mtp-110) cc_final: 0.8286 (mtp-110) REVERT: F 662 ARG cc_start: 0.8301 (ttt90) cc_final: 0.7921 (ttt90) REVERT: F 689 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7977 (tm-30) outliers start: 0 outliers final: 0 residues processed: 668 average time/residue: 0.3963 time to fit residues: 397.5952 Evaluate side-chains 537 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 306 optimal weight: 0.9990 chunk 191 optimal weight: 0.6980 chunk 186 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN A 602 ASN B 327 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN E 602 ASN F 602 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25518 Z= 0.275 Angle : 0.710 7.714 34482 Z= 0.360 Chirality : 0.045 0.216 3894 Planarity : 0.005 0.043 4524 Dihedral : 8.579 100.633 3480 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 3150 helix: -0.55 (0.13), residues: 1614 sheet: -2.00 (0.26), residues: 306 loop : 0.03 (0.21), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 476 HIS 0.010 0.002 HIS B 499 PHE 0.020 0.002 PHE B 576 TYR 0.018 0.002 TYR C 203 ARG 0.006 0.001 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 622 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TYR cc_start: 0.8112 (p90) cc_final: 0.7256 (p90) REVERT: A 278 LEU cc_start: 0.8755 (mt) cc_final: 0.8546 (mt) REVERT: A 288 LYS cc_start: 0.9451 (mptt) cc_final: 0.8572 (mmtm) REVERT: A 306 LEU cc_start: 0.9335 (tt) cc_final: 0.9080 (tt) REVERT: A 395 ASP cc_start: 0.8731 (m-30) cc_final: 0.7826 (p0) REVERT: A 449 MET cc_start: 0.8334 (mmm) cc_final: 0.7863 (mmm) REVERT: A 494 GLN cc_start: 0.8079 (tp40) cc_final: 0.7736 (mm110) REVERT: A 543 LYS cc_start: 0.9384 (mmtp) cc_final: 0.9056 (mmtt) REVERT: A 678 MET cc_start: 0.6968 (ptp) cc_final: 0.6472 (ptt) REVERT: A 757 MET cc_start: 0.7617 (tmm) cc_final: 0.7259 (tmm) REVERT: A 761 THR cc_start: 0.7076 (m) cc_final: 0.6571 (m) REVERT: B 205 ASP cc_start: 0.8474 (t70) cc_final: 0.8176 (t0) REVERT: B 218 GLU cc_start: 0.9138 (pp20) cc_final: 0.8698 (tm-30) REVERT: B 221 GLU cc_start: 0.8402 (pp20) cc_final: 0.7857 (tm-30) REVERT: B 225 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8139 (ttt180) REVERT: B 312 LYS cc_start: 0.9525 (ptpt) cc_final: 0.9205 (ptpp) REVERT: B 448 THR cc_start: 0.8205 (m) cc_final: 0.7549 (p) REVERT: B 508 MET cc_start: 0.1449 (mtt) cc_final: 0.0796 (mtm) REVERT: B 546 GLU cc_start: 0.8655 (mp0) cc_final: 0.8340 (mp0) REVERT: B 608 MET cc_start: 0.9001 (ptp) cc_final: 0.8663 (ptt) REVERT: B 651 LYS cc_start: 0.9414 (ptpt) cc_final: 0.8930 (ptpt) REVERT: B 658 LYS cc_start: 0.8179 (tptp) cc_final: 0.7862 (tptp) REVERT: B 668 LYS cc_start: 0.7690 (mtmt) cc_final: 0.7183 (mttp) REVERT: B 689 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 690 ILE cc_start: 0.8606 (mm) cc_final: 0.8232 (mm) REVERT: B 700 ARG cc_start: 0.8745 (ttp-170) cc_final: 0.8457 (ttm170) REVERT: C 221 GLU cc_start: 0.8612 (pt0) cc_final: 0.8298 (tm-30) REVERT: C 222 LEU cc_start: 0.9266 (mm) cc_final: 0.8697 (mm) REVERT: C 267 PHE cc_start: 0.8384 (t80) cc_final: 0.8075 (t80) REVERT: C 312 LYS cc_start: 0.9328 (ptpt) cc_final: 0.9064 (ptpp) REVERT: C 366 GLU cc_start: 0.8131 (mp0) cc_final: 0.7867 (mp0) REVERT: C 442 MET cc_start: 0.7701 (tmm) cc_final: 0.7425 (tmm) REVERT: C 508 MET cc_start: 0.1965 (mtt) cc_final: 0.1019 (mtt) REVERT: C 611 MET cc_start: 0.7531 (mmp) cc_final: 0.7132 (mmt) REVERT: C 683 SER cc_start: 0.7862 (m) cc_final: 0.7423 (p) REVERT: D 219 MET cc_start: 0.8327 (tpp) cc_final: 0.7957 (tpp) REVERT: D 244 TYR cc_start: 0.8260 (p90) cc_final: 0.7363 (p90) REVERT: D 312 LYS cc_start: 0.9277 (ptpp) cc_final: 0.8894 (ptpp) REVERT: D 465 ARG cc_start: 0.6557 (mmt90) cc_final: 0.5811 (mmm160) REVERT: D 508 MET cc_start: 0.0386 (mtt) cc_final: -0.0145 (mtt) REVERT: D 543 LYS cc_start: 0.9240 (mmtp) cc_final: 0.8534 (mmmm) REVERT: D 546 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8797 (mp0) REVERT: D 560 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7732 (mtp180) REVERT: D 565 LYS cc_start: 0.9312 (ptmm) cc_final: 0.8942 (ptmt) REVERT: D 577 ASP cc_start: 0.7902 (p0) cc_final: 0.6746 (p0) REVERT: D 601 ILE cc_start: 0.9132 (mt) cc_final: 0.8923 (mt) REVERT: D 678 MET cc_start: 0.7313 (ptp) cc_final: 0.6703 (ptt) REVERT: D 690 ILE cc_start: 0.8891 (mm) cc_final: 0.8303 (mm) REVERT: D 700 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7864 (ttm170) REVERT: D 757 MET cc_start: 0.7511 (ppp) cc_final: 0.6946 (ppp) REVERT: E 281 GLU cc_start: 0.8630 (mp0) cc_final: 0.8354 (mp0) REVERT: E 287 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8194 (mmm-85) REVERT: E 288 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8096 (mttt) REVERT: E 306 LEU cc_start: 0.9345 (tt) cc_final: 0.9052 (tp) REVERT: E 332 MET cc_start: 0.8976 (mmm) cc_final: 0.8446 (mmm) REVERT: E 411 LEU cc_start: 0.9206 (mp) cc_final: 0.8854 (mm) REVERT: E 529 LYS cc_start: 0.8577 (mmmt) cc_final: 0.7848 (tptt) REVERT: E 542 ILE cc_start: 0.9167 (mm) cc_final: 0.8575 (tp) REVERT: E 561 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8832 (mm-30) REVERT: E 568 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8490 (tm-30) REVERT: E 601 ILE cc_start: 0.8901 (mt) cc_final: 0.8591 (mt) REVERT: F 205 ASP cc_start: 0.8477 (m-30) cc_final: 0.8270 (m-30) REVERT: F 225 ARG cc_start: 0.9219 (mmm-85) cc_final: 0.8859 (tpp80) REVERT: F 267 PHE cc_start: 0.8396 (t80) cc_final: 0.8105 (t80) REVERT: F 278 LEU cc_start: 0.8976 (mt) cc_final: 0.8549 (mt) REVERT: F 287 ARG cc_start: 0.8565 (mmm-85) cc_final: 0.7706 (mmm-85) REVERT: F 288 LYS cc_start: 0.9448 (mptt) cc_final: 0.8853 (mmtp) REVERT: F 499 HIS cc_start: 0.7686 (m90) cc_final: 0.7399 (m-70) REVERT: F 503 PHE cc_start: 0.6884 (t80) cc_final: 0.6540 (t80) REVERT: F 550 MET cc_start: 0.5756 (mmp) cc_final: 0.5090 (mtm) REVERT: F 560 ARG cc_start: 0.8680 (mtp-110) cc_final: 0.8310 (mtp-110) REVERT: F 662 ARG cc_start: 0.8334 (ttt90) cc_final: 0.7883 (ttt90) REVERT: F 689 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8026 (tm-30) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.4160 time to fit residues: 390.6359 Evaluate side-chains 494 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 240 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN E 215 GLN E 602 ASN E 692 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25518 Z= 0.214 Angle : 0.680 7.839 34482 Z= 0.340 Chirality : 0.045 0.183 3894 Planarity : 0.005 0.180 4524 Dihedral : 8.473 103.748 3480 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 3150 helix: -0.45 (0.13), residues: 1596 sheet: -2.03 (0.28), residues: 294 loop : 0.11 (0.21), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 476 HIS 0.012 0.001 HIS B 499 PHE 0.019 0.001 PHE B 576 TYR 0.016 0.002 TYR C 203 ARG 0.014 0.000 ARG C 638 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 621 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TYR cc_start: 0.8156 (p90) cc_final: 0.7302 (p90) REVERT: A 278 LEU cc_start: 0.8663 (mt) cc_final: 0.8448 (mt) REVERT: A 288 LYS cc_start: 0.9426 (mptt) cc_final: 0.8575 (mmmm) REVERT: A 306 LEU cc_start: 0.9320 (tt) cc_final: 0.9110 (tp) REVERT: A 395 ASP cc_start: 0.8578 (m-30) cc_final: 0.7853 (p0) REVERT: A 543 LYS cc_start: 0.9388 (mmtp) cc_final: 0.9047 (mmtt) REVERT: A 560 ARG cc_start: 0.8760 (mtp180) cc_final: 0.8274 (mtp180) REVERT: A 678 MET cc_start: 0.6914 (ptp) cc_final: 0.6408 (ptt) REVERT: A 757 MET cc_start: 0.7655 (tmm) cc_final: 0.7258 (tmm) REVERT: A 761 THR cc_start: 0.7120 (m) cc_final: 0.6599 (m) REVERT: B 219 MET cc_start: 0.8236 (tpp) cc_final: 0.7983 (tpp) REVERT: B 221 GLU cc_start: 0.8421 (pp20) cc_final: 0.8033 (tm-30) REVERT: B 225 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8056 (ttt180) REVERT: B 312 LYS cc_start: 0.9505 (ptpt) cc_final: 0.9195 (ptpp) REVERT: B 410 ASP cc_start: 0.8358 (p0) cc_final: 0.8139 (p0) REVERT: B 448 THR cc_start: 0.8177 (m) cc_final: 0.7506 (p) REVERT: B 508 MET cc_start: 0.0729 (mtt) cc_final: 0.0224 (mtm) REVERT: B 546 GLU cc_start: 0.8619 (mp0) cc_final: 0.8319 (mp0) REVERT: B 563 PHE cc_start: 0.8458 (t80) cc_final: 0.7945 (t80) REVERT: B 608 MET cc_start: 0.8927 (ptp) cc_final: 0.8625 (ptt) REVERT: B 651 LYS cc_start: 0.9407 (ptpt) cc_final: 0.9094 (ptpt) REVERT: B 658 LYS cc_start: 0.8083 (tptp) cc_final: 0.7816 (tptp) REVERT: B 689 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7418 (tm-30) REVERT: B 690 ILE cc_start: 0.8741 (mm) cc_final: 0.8411 (mm) REVERT: B 700 ARG cc_start: 0.8768 (ttp-170) cc_final: 0.8414 (ttm170) REVERT: B 740 MET cc_start: 0.5084 (ttm) cc_final: 0.4871 (ttp) REVERT: C 221 GLU cc_start: 0.8589 (pt0) cc_final: 0.8219 (pt0) REVERT: C 244 TYR cc_start: 0.8302 (p90) cc_final: 0.8091 (p90) REVERT: C 267 PHE cc_start: 0.8309 (t80) cc_final: 0.8044 (t80) REVERT: C 312 LYS cc_start: 0.9326 (ptpt) cc_final: 0.9051 (ptpp) REVERT: C 366 GLU cc_start: 0.8103 (mp0) cc_final: 0.7804 (mp0) REVERT: C 442 MET cc_start: 0.7682 (tmm) cc_final: 0.7315 (tmm) REVERT: C 486 LYS cc_start: 0.8364 (mttt) cc_final: 0.7865 (mmmt) REVERT: C 508 MET cc_start: 0.1819 (mtt) cc_final: 0.0924 (mtt) REVERT: C 560 ARG cc_start: 0.8261 (mtp-110) cc_final: 0.8052 (mtp-110) REVERT: C 561 GLU cc_start: 0.8956 (pp20) cc_final: 0.8736 (pp20) REVERT: C 611 MET cc_start: 0.7538 (mmp) cc_final: 0.7027 (mmt) REVERT: C 683 SER cc_start: 0.7728 (m) cc_final: 0.7321 (p) REVERT: D 219 MET cc_start: 0.8275 (tpp) cc_final: 0.7959 (tpp) REVERT: D 244 TYR cc_start: 0.8171 (p90) cc_final: 0.7440 (p90) REVERT: D 253 LEU cc_start: 0.9448 (mt) cc_final: 0.9204 (mp) REVERT: D 306 LEU cc_start: 0.9490 (tp) cc_final: 0.9243 (tt) REVERT: D 312 LYS cc_start: 0.9258 (ptpp) cc_final: 0.8886 (ptpp) REVERT: D 465 ARG cc_start: 0.6283 (mmt90) cc_final: 0.5565 (mmm160) REVERT: D 508 MET cc_start: 0.0222 (mtt) cc_final: -0.0230 (mtt) REVERT: D 543 LYS cc_start: 0.9265 (mmtp) cc_final: 0.8432 (mmmm) REVERT: D 546 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8780 (mp0) REVERT: D 560 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7831 (mtp180) REVERT: D 562 ILE cc_start: 0.9567 (tp) cc_final: 0.9292 (tp) REVERT: D 565 LYS cc_start: 0.9317 (ptmm) cc_final: 0.8950 (pttm) REVERT: D 578 GLU cc_start: 0.7386 (mp0) cc_final: 0.6867 (mp0) REVERT: D 678 MET cc_start: 0.7245 (ptp) cc_final: 0.6831 (ptp) REVERT: D 690 ILE cc_start: 0.8961 (mm) cc_final: 0.8385 (mm) REVERT: D 700 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7777 (ttm110) REVERT: E 218 GLU cc_start: 0.9097 (pp20) cc_final: 0.8690 (pp20) REVERT: E 244 TYR cc_start: 0.8237 (p90) cc_final: 0.7645 (p90) REVERT: E 281 GLU cc_start: 0.8577 (mp0) cc_final: 0.8286 (mp0) REVERT: E 287 ARG cc_start: 0.8673 (mmm160) cc_final: 0.8147 (mmm-85) REVERT: E 288 LYS cc_start: 0.8920 (mtmm) cc_final: 0.8052 (mttt) REVERT: E 306 LEU cc_start: 0.9312 (tt) cc_final: 0.9005 (tp) REVERT: E 312 LYS cc_start: 0.9067 (tptt) cc_final: 0.8787 (tppt) REVERT: E 332 MET cc_start: 0.8987 (mmm) cc_final: 0.8446 (mmm) REVERT: E 366 GLU cc_start: 0.8189 (mp0) cc_final: 0.7650 (mp0) REVERT: E 368 ASP cc_start: 0.8807 (t0) cc_final: 0.8594 (t0) REVERT: E 411 LEU cc_start: 0.9133 (mp) cc_final: 0.8770 (mm) REVERT: E 529 LYS cc_start: 0.8549 (mmmt) cc_final: 0.7818 (tptt) REVERT: E 542 ILE cc_start: 0.9320 (mm) cc_final: 0.8847 (tp) REVERT: E 568 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8528 (tm-30) REVERT: E 601 ILE cc_start: 0.8867 (mt) cc_final: 0.8560 (mt) REVERT: F 205 ASP cc_start: 0.8467 (m-30) cc_final: 0.8079 (t0) REVERT: F 219 MET cc_start: 0.8528 (tpp) cc_final: 0.8270 (tpp) REVERT: F 225 ARG cc_start: 0.9182 (mmm-85) cc_final: 0.8809 (tpp80) REVERT: F 267 PHE cc_start: 0.8166 (t80) cc_final: 0.7948 (t80) REVERT: F 278 LEU cc_start: 0.9181 (mt) cc_final: 0.8722 (pp) REVERT: F 287 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.7995 (mmm-85) REVERT: F 288 LYS cc_start: 0.9438 (mptt) cc_final: 0.8904 (mmtp) REVERT: F 499 HIS cc_start: 0.7767 (m90) cc_final: 0.7460 (m-70) REVERT: F 503 PHE cc_start: 0.6806 (t80) cc_final: 0.6460 (t80) REVERT: F 550 MET cc_start: 0.5733 (mmp) cc_final: 0.5312 (mmp) REVERT: F 560 ARG cc_start: 0.8669 (mtp-110) cc_final: 0.8469 (mtp-110) REVERT: F 563 PHE cc_start: 0.9283 (m-80) cc_final: 0.9003 (m-10) REVERT: F 577 ASP cc_start: 0.7935 (p0) cc_final: 0.7581 (p0) REVERT: F 578 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7485 (mm-30) REVERT: F 662 ARG cc_start: 0.8327 (ttt90) cc_final: 0.7862 (ttt90) REVERT: F 689 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7987 (tm-30) outliers start: 0 outliers final: 0 residues processed: 621 average time/residue: 0.3951 time to fit residues: 372.3175 Evaluate side-chains 500 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.9980 chunk 293 optimal weight: 6.9990 chunk 267 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 258 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 602 ASN ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 602 ASN E 602 ASN F 327 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25518 Z= 0.219 Angle : 0.685 7.862 34482 Z= 0.342 Chirality : 0.045 0.163 3894 Planarity : 0.005 0.140 4524 Dihedral : 8.435 106.291 3480 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 3150 helix: -0.40 (0.13), residues: 1602 sheet: -1.97 (0.28), residues: 294 loop : 0.13 (0.21), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 476 HIS 0.009 0.001 HIS F 735 PHE 0.020 0.001 PHE B 516 TYR 0.014 0.002 TYR C 203 ARG 0.011 0.000 ARG C 638 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 616 time to evaluate : 3.063 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: A 244 TYR cc_start: 0.8169 (p90) cc_final: 0.7282 (p90) REVERT: A 278 LEU cc_start: 0.8648 (mt) cc_final: 0.8432 (mt) REVERT: A 287 ARG cc_start: 0.8759 (ttp-110) cc_final: 0.8169 (mtm-85) REVERT: A 288 LYS cc_start: 0.9417 (mptt) cc_final: 0.8593 (mmtm) REVERT: A 306 LEU cc_start: 0.9326 (tt) cc_final: 0.9070 (tt) REVERT: A 366 GLU cc_start: 0.8482 (mp0) cc_final: 0.8054 (mp0) REVERT: A 395 ASP cc_start: 0.8583 (m-30) cc_final: 0.7677 (p0) REVERT: A 543 LYS cc_start: 0.9393 (mmtp) cc_final: 0.9050 (mmtt) REVERT: A 560 ARG cc_start: 0.8725 (mtp180) cc_final: 0.8240 (mtp180) REVERT: A 678 MET cc_start: 0.6905 (ptp) cc_final: 0.6410 (ptt) REVERT: A 757 MET cc_start: 0.7675 (tmm) cc_final: 0.7286 (tmm) REVERT: A 761 THR cc_start: 0.7154 (m) cc_final: 0.6651 (m) REVERT: B 218 GLU cc_start: 0.9134 (pp20) cc_final: 0.8588 (pp20) REVERT: B 221 GLU cc_start: 0.8495 (pp20) cc_final: 0.7948 (tm-30) REVERT: B 225 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8020 (ttt180) REVERT: B 287 ARG cc_start: 0.8660 (mtm110) cc_final: 0.8139 (mtm110) REVERT: B 312 LYS cc_start: 0.9551 (ptpt) cc_final: 0.9278 (ptpp) REVERT: B 326 SER cc_start: 0.8659 (m) cc_final: 0.8006 (p) REVERT: B 410 ASP cc_start: 0.8435 (p0) cc_final: 0.8212 (p0) REVERT: B 448 THR cc_start: 0.8191 (m) cc_final: 0.7531 (p) REVERT: B 508 MET cc_start: 0.0504 (mtt) cc_final: 0.0049 (mtm) REVERT: B 543 LYS cc_start: 0.8829 (mmtp) cc_final: 0.8550 (mmmt) REVERT: B 546 GLU cc_start: 0.8591 (mp0) cc_final: 0.8308 (mp0) REVERT: B 558 ASN cc_start: 0.8955 (t0) cc_final: 0.8373 (t0) REVERT: B 559 VAL cc_start: 0.9034 (t) cc_final: 0.8824 (t) REVERT: B 564 ASP cc_start: 0.9234 (m-30) cc_final: 0.8969 (m-30) REVERT: B 565 LYS cc_start: 0.8986 (mmtp) cc_final: 0.8751 (mmtp) REVERT: B 608 MET cc_start: 0.8923 (ptp) cc_final: 0.8627 (ptt) REVERT: B 651 LYS cc_start: 0.9429 (ptpt) cc_final: 0.9066 (ptpt) REVERT: B 658 LYS cc_start: 0.8062 (tptp) cc_final: 0.7820 (tptp) REVERT: B 689 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7492 (tm-30) REVERT: B 690 ILE cc_start: 0.8742 (mm) cc_final: 0.8394 (mm) REVERT: C 267 PHE cc_start: 0.8275 (t80) cc_final: 0.8073 (t80) REVERT: C 287 ARG cc_start: 0.8576 (ttp-110) cc_final: 0.7841 (mtm110) REVERT: C 312 LYS cc_start: 0.9308 (ptpt) cc_final: 0.9043 (ptpp) REVERT: C 366 GLU cc_start: 0.8076 (mp0) cc_final: 0.7795 (mp0) REVERT: C 442 MET cc_start: 0.7677 (tmm) cc_final: 0.7308 (tmm) REVERT: C 486 LYS cc_start: 0.8724 (mttt) cc_final: 0.8204 (mmmt) REVERT: C 508 MET cc_start: 0.1846 (mtt) cc_final: 0.0932 (mtt) REVERT: C 560 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.8037 (mtp-110) REVERT: C 611 MET cc_start: 0.7479 (mmp) cc_final: 0.6831 (mmm) REVERT: C 683 SER cc_start: 0.7720 (m) cc_final: 0.7360 (p) REVERT: D 219 MET cc_start: 0.8273 (tpp) cc_final: 0.7965 (tpp) REVERT: D 244 TYR cc_start: 0.8282 (p90) cc_final: 0.7418 (p90) REVERT: D 253 LEU cc_start: 0.9448 (mt) cc_final: 0.9234 (mp) REVERT: D 306 LEU cc_start: 0.9457 (tp) cc_final: 0.9206 (tt) REVERT: D 312 LYS cc_start: 0.9303 (ptpp) cc_final: 0.8840 (ptpp) REVERT: D 352 SER cc_start: 0.9337 (m) cc_final: 0.8988 (p) REVERT: D 465 ARG cc_start: 0.6277 (mmt90) cc_final: 0.5546 (mmm160) REVERT: D 508 MET cc_start: 0.0404 (mtt) cc_final: 0.0025 (mtt) REVERT: D 543 LYS cc_start: 0.9234 (mmtp) cc_final: 0.8472 (mmmm) REVERT: D 546 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8807 (mp0) REVERT: D 562 ILE cc_start: 0.9577 (tp) cc_final: 0.9342 (mm) REVERT: D 565 LYS cc_start: 0.9353 (ptmm) cc_final: 0.9134 (ptmt) REVERT: D 678 MET cc_start: 0.7239 (ptp) cc_final: 0.6827 (ptp) REVERT: D 690 ILE cc_start: 0.8964 (mm) cc_final: 0.8383 (mm) REVERT: D 700 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7842 (ttm110) REVERT: E 218 GLU cc_start: 0.9098 (pp20) cc_final: 0.8663 (pp20) REVERT: E 244 TYR cc_start: 0.8223 (p90) cc_final: 0.7593 (p90) REVERT: E 287 ARG cc_start: 0.8661 (mmm160) cc_final: 0.8201 (mmm-85) REVERT: E 288 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8029 (mttt) REVERT: E 332 MET cc_start: 0.8981 (mmm) cc_final: 0.8450 (mmm) REVERT: E 366 GLU cc_start: 0.8173 (mp0) cc_final: 0.7644 (mp0) REVERT: E 368 ASP cc_start: 0.8818 (t0) cc_final: 0.8602 (t0) REVERT: E 411 LEU cc_start: 0.9132 (mp) cc_final: 0.8756 (mm) REVERT: E 529 LYS cc_start: 0.8556 (mmmt) cc_final: 0.7926 (tptp) REVERT: E 542 ILE cc_start: 0.9314 (mm) cc_final: 0.8849 (tp) REVERT: E 561 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8693 (mm-30) REVERT: E 568 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8538 (tm-30) REVERT: E 601 ILE cc_start: 0.8865 (mt) cc_final: 0.8545 (mt) REVERT: F 205 ASP cc_start: 0.8439 (m-30) cc_final: 0.8070 (t0) REVERT: F 225 ARG cc_start: 0.9199 (mmm-85) cc_final: 0.8831 (tpp80) REVERT: F 267 PHE cc_start: 0.8172 (t80) cc_final: 0.7929 (t80) REVERT: F 278 LEU cc_start: 0.9130 (mt) cc_final: 0.8628 (pp) REVERT: F 287 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8046 (mmm-85) REVERT: F 288 LYS cc_start: 0.9434 (mptt) cc_final: 0.8851 (mmtm) REVERT: F 450 ASP cc_start: 0.8460 (m-30) cc_final: 0.7840 (t0) REVERT: F 486 LYS cc_start: 0.7815 (ttmt) cc_final: 0.5627 (ttmt) REVERT: F 499 HIS cc_start: 0.7770 (m90) cc_final: 0.7446 (m-70) REVERT: F 503 PHE cc_start: 0.7064 (t80) cc_final: 0.6848 (t80) REVERT: F 550 MET cc_start: 0.5790 (mmp) cc_final: 0.5376 (mmp) REVERT: F 560 ARG cc_start: 0.8670 (mtp-110) cc_final: 0.8266 (mtp-110) REVERT: F 662 ARG cc_start: 0.8265 (ttt90) cc_final: 0.7791 (ttt90) REVERT: F 689 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7909 (tm-30) outliers start: 0 outliers final: 0 residues processed: 616 average time/residue: 0.3871 time to fit residues: 361.4203 Evaluate side-chains 498 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.9990 chunk 302 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 316 optimal weight: 10.0000 chunk 291 optimal weight: 0.2980 chunk 252 optimal weight: 0.0770 chunk 26 optimal weight: 0.0670 chunk 194 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 602 ASN A 660 ASN B 327 GLN ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 602 ASN D 660 ASN E 602 ASN F 327 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25518 Z= 0.175 Angle : 0.684 9.793 34482 Z= 0.336 Chirality : 0.046 0.178 3894 Planarity : 0.005 0.114 4524 Dihedral : 8.227 109.461 3480 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.04 % Allowed : 0.45 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 3150 helix: -0.31 (0.13), residues: 1602 sheet: -1.85 (0.29), residues: 288 loop : 0.16 (0.20), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 476 HIS 0.008 0.001 HIS F 735 PHE 0.018 0.001 PHE B 576 TYR 0.016 0.001 TYR C 244 ARG 0.010 0.001 ARG C 638 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 644 time to evaluate : 2.874 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: A 244 TYR cc_start: 0.8094 (p90) cc_final: 0.7131 (p90) REVERT: A 278 LEU cc_start: 0.8598 (mt) cc_final: 0.8348 (mt) REVERT: A 287 ARG cc_start: 0.8647 (ttp-110) cc_final: 0.8057 (mtm-85) REVERT: A 288 LYS cc_start: 0.9387 (mptt) cc_final: 0.8558 (mmtm) REVERT: A 306 LEU cc_start: 0.9261 (tt) cc_final: 0.9023 (tp) REVERT: A 366 GLU cc_start: 0.7568 (mp0) cc_final: 0.7356 (mp0) REVERT: A 395 ASP cc_start: 0.8421 (m-30) cc_final: 0.7926 (p0) REVERT: A 397 GLU cc_start: 0.8475 (pm20) cc_final: 0.8175 (pm20) REVERT: A 542 ILE cc_start: 0.9527 (tp) cc_final: 0.9269 (tp) REVERT: A 543 LYS cc_start: 0.9395 (mmtp) cc_final: 0.9137 (mmmt) REVERT: A 558 ASN cc_start: 0.7552 (m-40) cc_final: 0.6772 (t0) REVERT: A 560 ARG cc_start: 0.8680 (mtp180) cc_final: 0.8264 (mtp180) REVERT: A 619 ILE cc_start: 0.9532 (mm) cc_final: 0.9223 (pt) REVERT: A 678 MET cc_start: 0.6856 (ptp) cc_final: 0.6385 (ptt) REVERT: A 757 MET cc_start: 0.7693 (tmm) cc_final: 0.7280 (tmm) REVERT: A 761 THR cc_start: 0.7191 (m) cc_final: 0.6658 (m) REVERT: B 218 GLU cc_start: 0.9050 (pp20) cc_final: 0.8661 (pp20) REVERT: B 225 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8318 (ttt180) REVERT: B 287 ARG cc_start: 0.8460 (mtm110) cc_final: 0.8072 (mtm110) REVERT: B 312 LYS cc_start: 0.9513 (ptpt) cc_final: 0.9265 (ptpp) REVERT: B 326 SER cc_start: 0.8492 (m) cc_final: 0.8040 (p) REVERT: B 401 ASN cc_start: 0.9055 (m110) cc_final: 0.8828 (m110) REVERT: B 410 ASP cc_start: 0.8380 (p0) cc_final: 0.8130 (p0) REVERT: B 448 THR cc_start: 0.8099 (m) cc_final: 0.7684 (m) REVERT: B 508 MET cc_start: 0.0118 (mtt) cc_final: -0.0261 (mtm) REVERT: B 543 LYS cc_start: 0.8954 (mmtp) cc_final: 0.8619 (mmmt) REVERT: B 558 ASN cc_start: 0.8676 (t0) cc_final: 0.8421 (m110) REVERT: B 564 ASP cc_start: 0.9183 (m-30) cc_final: 0.8899 (m-30) REVERT: B 608 MET cc_start: 0.8885 (ptp) cc_final: 0.8551 (ptt) REVERT: B 668 LYS cc_start: 0.7491 (mtmt) cc_final: 0.7249 (mmtp) REVERT: B 689 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7536 (tm-30) REVERT: B 690 ILE cc_start: 0.8466 (mm) cc_final: 0.7950 (mm) REVERT: C 221 GLU cc_start: 0.8381 (pt0) cc_final: 0.8106 (tm-30) REVERT: C 222 LEU cc_start: 0.9174 (mm) cc_final: 0.8655 (mm) REVERT: C 273 GLU cc_start: 0.8793 (tt0) cc_final: 0.8449 (tm-30) REVERT: C 285 ASN cc_start: 0.8169 (m110) cc_final: 0.7889 (m-40) REVERT: C 295 LYS cc_start: 0.9112 (ptpp) cc_final: 0.8725 (ptpp) REVERT: C 305 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8193 (mm-30) REVERT: C 312 LYS cc_start: 0.9295 (ptpt) cc_final: 0.8997 (ptpp) REVERT: C 330 THR cc_start: 0.8774 (p) cc_final: 0.8529 (p) REVERT: C 349 ARG cc_start: 0.8381 (mtp85) cc_final: 0.7858 (mtp85) REVERT: C 366 GLU cc_start: 0.7819 (mp0) cc_final: 0.7399 (mp0) REVERT: C 442 MET cc_start: 0.7611 (tmm) cc_final: 0.7269 (tmm) REVERT: C 450 ASP cc_start: 0.8309 (m-30) cc_final: 0.7559 (t0) REVERT: C 508 MET cc_start: 0.1649 (mtt) cc_final: 0.0680 (mtt) REVERT: C 563 PHE cc_start: 0.9127 (m-80) cc_final: 0.8870 (m-10) REVERT: C 611 MET cc_start: 0.7484 (mmp) cc_final: 0.6857 (mmm) REVERT: C 683 SER cc_start: 0.7562 (m) cc_final: 0.7242 (p) REVERT: D 219 MET cc_start: 0.8241 (tpp) cc_final: 0.8032 (tpp) REVERT: D 244 TYR cc_start: 0.8087 (p90) cc_final: 0.7591 (p90) REVERT: D 306 LEU cc_start: 0.9492 (tp) cc_final: 0.9280 (tt) REVERT: D 312 LYS cc_start: 0.9266 (ptpp) cc_final: 0.8836 (ptpp) REVERT: D 352 SER cc_start: 0.9116 (m) cc_final: 0.8906 (p) REVERT: D 465 ARG cc_start: 0.6209 (mmt90) cc_final: 0.5767 (mmm160) REVERT: D 543 LYS cc_start: 0.9263 (mmtp) cc_final: 0.8481 (mmmm) REVERT: D 546 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8748 (mp0) REVERT: D 562 ILE cc_start: 0.9576 (tp) cc_final: 0.9314 (mm) REVERT: D 578 GLU cc_start: 0.7489 (mp0) cc_final: 0.6856 (mp0) REVERT: D 678 MET cc_start: 0.7186 (ptp) cc_final: 0.6759 (ptp) REVERT: D 689 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7487 (tm-30) REVERT: D 690 ILE cc_start: 0.8870 (mm) cc_final: 0.8267 (mm) REVERT: D 700 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7740 (ttm110) REVERT: E 204 ASP cc_start: 0.7299 (t70) cc_final: 0.7080 (t0) REVERT: E 218 GLU cc_start: 0.9070 (pp20) cc_final: 0.8593 (pp20) REVERT: E 244 TYR cc_start: 0.8010 (p90) cc_final: 0.7466 (p90) REVERT: E 287 ARG cc_start: 0.8623 (mmm160) cc_final: 0.8158 (mmm-85) REVERT: E 288 LYS cc_start: 0.8906 (mtmm) cc_final: 0.8249 (mttt) REVERT: E 312 LYS cc_start: 0.9112 (tptt) cc_final: 0.8706 (ptpp) REVERT: E 332 MET cc_start: 0.9151 (mmm) cc_final: 0.8842 (mmt) REVERT: E 366 GLU cc_start: 0.8121 (mp0) cc_final: 0.7644 (mp0) REVERT: E 388 MET cc_start: 0.4407 (mtp) cc_final: 0.4070 (mtt) REVERT: E 486 LYS cc_start: 0.8198 (mttt) cc_final: 0.7741 (mmtt) REVERT: E 542 ILE cc_start: 0.9304 (mm) cc_final: 0.8849 (tp) REVERT: E 568 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8381 (tm-30) REVERT: E 601 ILE cc_start: 0.8777 (mt) cc_final: 0.8534 (mt) REVERT: E 642 LEU cc_start: 0.8577 (mt) cc_final: 0.8215 (pt) REVERT: F 205 ASP cc_start: 0.8493 (m-30) cc_final: 0.8066 (t0) REVERT: F 225 ARG cc_start: 0.9168 (mmm-85) cc_final: 0.8752 (tpp80) REVERT: F 278 LEU cc_start: 0.8972 (mt) cc_final: 0.8069 (mt) REVERT: F 287 ARG cc_start: 0.8327 (mmm-85) cc_final: 0.7949 (mmm-85) REVERT: F 288 LYS cc_start: 0.9396 (mptt) cc_final: 0.8827 (mmmt) REVERT: F 450 ASP cc_start: 0.8157 (m-30) cc_final: 0.7585 (t0) REVERT: F 499 HIS cc_start: 0.7653 (m90) cc_final: 0.7361 (m-70) REVERT: F 503 PHE cc_start: 0.6889 (t80) cc_final: 0.6512 (t80) REVERT: F 543 LYS cc_start: 0.9342 (mptt) cc_final: 0.9096 (mmtm) REVERT: F 546 GLU cc_start: 0.8819 (mp0) cc_final: 0.8514 (mp0) REVERT: F 549 THR cc_start: 0.6265 (p) cc_final: 0.6039 (p) REVERT: F 550 MET cc_start: 0.5160 (mmp) cc_final: 0.4842 (mmp) REVERT: F 689 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7858 (tm-30) outliers start: 1 outliers final: 0 residues processed: 645 average time/residue: 0.3997 time to fit residues: 389.6937 Evaluate side-chains 522 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.2980 chunk 268 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 252 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS A 533 ASN A 602 ASN ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 340 HIS ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 602 ASN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 327 GLN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.115280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.095023 restraints weight = 77350.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098100 restraints weight = 45976.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.100165 restraints weight = 31230.298| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25518 Z= 0.194 Angle : 0.692 10.767 34482 Z= 0.343 Chirality : 0.045 0.185 3894 Planarity : 0.005 0.096 4524 Dihedral : 8.201 112.567 3480 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 3150 helix: -0.22 (0.13), residues: 1584 sheet: -1.66 (0.29), residues: 282 loop : 0.06 (0.20), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 476 HIS 0.008 0.001 HIS F 735 PHE 0.021 0.001 PHE B 576 TYR 0.013 0.001 TYR C 244 ARG 0.019 0.001 ARG B 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6869.78 seconds wall clock time: 123 minutes 55.73 seconds (7435.73 seconds total)