Starting phenix.real_space_refine on Fri Aug 9 06:46:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/08_2024/7mdo_23776.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/08_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_23776/08_2024/7mdo_23776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/08_2024/7mdo_23776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/08_2024/7mdo_23776.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/08_2024/7mdo_23776.cif" } 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 13.06, per 1000 atoms: 0.52 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: 13.03 Conformation dependent library (CDL) restraints added in 6.5 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... Secondary structure from input PDB file: 157 helices and 13 sheets defined 53.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.503A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 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 228 through 233 removed outlier: 3.793A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.611A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.671A pdb=" N MET A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 276' Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.750A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 333 removed outlier: 3.642A pdb=" N ASP A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.644A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 526 through 534 removed outlier: 4.040A pdb=" N ALA A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 579 through 582 removed outlier: 3.563A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 649 through 663 removed outlier: 3.784A pdb=" N LYS A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 683 through 703 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 750 through 763 removed outlier: 4.008A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 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 228 through 233 removed outlier: 3.741A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 removed outlier: 3.567A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.817A pdb=" N MET B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 276 " --> pdb=" O GLU B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 276' Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.525A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.758A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.656A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.703A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 526 through 536 removed outlier: 3.725A pdb=" N ALA B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 579 through 582 removed outlier: 3.624A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 649 through 663 removed outlier: 3.710A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 677 Processing helix chain 'B' and resid 683 through 703 Processing helix chain 'B' and resid 732 through 741 Processing helix chain 'B' and resid 750 through 763 removed outlier: 3.897A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE B 758 " --> pdb=" O LYS B 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.552A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 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 228 through 233 removed outlier: 3.737A pdb=" N ALA C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 removed outlier: 3.610A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.630A pdb=" N MET C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 276 " --> pdb=" O GLU C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 276' Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.565A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.773A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 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 373 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 407 through 425 removed outlier: 3.559A pdb=" N LYS C 425 " --> pdb=" O GLN C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 482 through 493 removed outlier: 3.552A pdb=" N GLU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 499 Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 526 through 535 removed outlier: 3.870A pdb=" N ALA C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 555 through 569 Processing helix chain 'C' and resid 579 through 582 removed outlier: 3.641A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 579 through 582' Processing helix chain 'C' and resid 599 through 608 Processing helix chain 'C' and resid 649 through 663 removed outlier: 3.674A pdb=" N LYS C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 677 Processing helix chain 'C' and resid 683 through 703 Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 750 through 763 removed outlier: 3.981A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 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 228 through 233 removed outlier: 3.834A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 removed outlier: 3.629A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.609A pdb=" N MET D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER D 276 " --> pdb=" O GLU D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 276' Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.754A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.671A pdb=" N ASP D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 407 through 425 removed outlier: 3.599A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 482 through 493 Processing helix chain 'D' and resid 493 through 499 Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 526 through 535 removed outlier: 3.893A pdb=" N ALA D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 555 through 569 Processing helix chain 'D' and resid 578 through 582 removed outlier: 3.656A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 608 Processing helix chain 'D' and resid 649 through 663 removed outlier: 3.782A pdb=" N LYS D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 677 Processing helix chain 'D' and resid 683 through 703 Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 750 through 763 removed outlier: 3.944A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.576A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 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 228 through 233 removed outlier: 3.800A pdb=" N ALA E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 removed outlier: 3.586A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 276 removed outlier: 3.831A pdb=" N MET E 275 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER E 276 " --> pdb=" O GLU E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 272 through 276' Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.572A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.770A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 326 Processing helix chain 'E' and resid 327 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 373 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 407 through 425 removed outlier: 3.641A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 482 through 493 Processing helix chain 'E' and resid 493 through 499 Processing helix chain 'E' and resid 499 through 506 Processing helix chain 'E' and resid 526 through 535 removed outlier: 3.866A pdb=" N ALA E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 555 through 569 Processing helix chain 'E' and resid 579 through 582 removed outlier: 3.604A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 579 through 582' Processing helix chain 'E' and resid 599 through 608 Processing helix chain 'E' and resid 649 through 663 removed outlier: 3.676A pdb=" N LYS E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 676 Processing helix chain 'E' and resid 683 through 703 Processing helix chain 'E' and resid 732 through 741 Processing helix chain 'E' and resid 750 through 763 removed outlier: 3.911A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE E 758 " --> pdb=" O LYS E 754 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 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 228 through 233 removed outlier: 3.602A pdb=" N ALA F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 removed outlier: 3.615A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 276 removed outlier: 3.689A pdb=" N MET F 275 " --> pdb=" O PRO F 272 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER F 276 " --> pdb=" O GLU F 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 272 through 276' Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.570A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.777A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 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 373 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 407 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 438 through 445 Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 493 through 499 Processing helix chain 'F' and resid 499 through 506 Processing helix chain 'F' and resid 526 through 535 removed outlier: 3.911A pdb=" N ALA F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 555 through 569 Processing helix chain 'F' and resid 579 through 582 removed outlier: 3.678A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 579 through 582' Processing helix chain 'F' and resid 599 through 608 Processing helix chain 'F' and resid 649 through 663 removed outlier: 3.704A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 677 Processing helix chain 'F' and resid 683 through 703 Processing helix chain 'F' and resid 732 through 741 Processing helix chain 'F' and resid 750 through 763 removed outlier: 3.983A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE F 758 " --> pdb=" O LYS F 754 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 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) 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: 3.657A pdb=" N THR A 347 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.481A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 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) 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: 3.601A pdb=" N THR B 347 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.407A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 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: 3.705A pdb=" N THR C 347 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.532A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 270 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: 3.576A pdb=" N THR D 347 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 621 through 623 removed outlier: 5.600A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.526A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 265 through 270 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: 3.651A pdb=" N THR E 347 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.526A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 265 through 270 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) 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: 3.715A pdb=" N THR F 347 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.486A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1017 hydrogen bonds defined for protein. 3039 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: 9.84 Time building geometry restraints manager: 13.82 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: 6895 2.81 - 3.33: 23990 3.33 - 3.85: 42884 3.85 - 4.38: 49368 4.38 - 4.90: 79009 Nonbonded interactions: 202146 Sorted by model distance: nonbonded pdb=" O PRO F 246 " pdb=" OG1 THR F 249 " model vdw 2.283 3.040 nonbonded pdb=" O PRO C 246 " pdb=" OG1 THR C 249 " model vdw 2.286 3.040 nonbonded pdb=" O PRO B 246 " pdb=" OG1 THR B 249 " model vdw 2.291 3.040 nonbonded pdb=" O PRO E 246 " pdb=" OG1 THR E 249 " model vdw 2.293 3.040 nonbonded pdb=" O GLU F 546 " pdb=" OG1 THR F 549 " model vdw 2.303 3.040 ... (remaining 202141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.780 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: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 74.630 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.030 ------------------------------------------------------------------------------- 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= 0.301 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 : 2.872 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: 0.4181 time to fit residues: 587.3957 Evaluate side-chains 665 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 2.980 ------------------------------------------------------------------------------- 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: 2.9990 chunk 241 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 185 optimal weight: 0.0370 chunk 288 optimal weight: 8.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- 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 421 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 337 GLN C 421 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 337 GLN D 421 GLN D 602 ASN E 285 ASN E 401 ASN E 421 GLN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 285 ASN F 499 HIS F 533 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25518 Z= 0.246 Angle : 0.713 7.440 34482 Z= 0.367 Chirality : 0.045 0.164 3894 Planarity : 0.006 0.069 4524 Dihedral : 9.331 117.329 3480 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.07 % Allowed : 5.21 % Favored : 94.72 % 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: -1.42 (0.15), residues: 3150 helix: -0.89 (0.12), residues: 1584 sheet: -2.14 (0.28), residues: 306 loop : -0.38 (0.19), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 454 HIS 0.006 0.002 HIS E 735 PHE 0.021 0.002 PHE E 506 TYR 0.019 0.002 TYR B 244 ARG 0.013 0.001 ARG E 465 *********************** 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 731 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 729 time to evaluate : 2.808 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: A 203 TYR cc_start: 0.8047 (m-10) cc_final: 0.7276 (m-10) REVERT: A 222 LEU cc_start: 0.9000 (tp) cc_final: 0.8590 (tp) REVERT: A 239 ARG cc_start: 0.7554 (mtp-110) cc_final: 0.7057 (mtm180) REVERT: A 312 LYS cc_start: 0.9126 (tptt) cc_final: 0.8924 (tptt) REVERT: A 349 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8181 (ttm-80) REVERT: A 395 ASP cc_start: 0.8070 (m-30) cc_final: 0.7774 (m-30) REVERT: A 450 ASP cc_start: 0.8398 (p0) cc_final: 0.8139 (t0) REVERT: A 484 ASP cc_start: 0.8037 (p0) cc_final: 0.7078 (p0) REVERT: A 486 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8214 (mmtt) REVERT: A 524 LYS cc_start: 0.8641 (ptpt) cc_final: 0.8420 (pttt) REVERT: A 526 LEU cc_start: 0.8199 (mt) cc_final: 0.7895 (mp) REVERT: A 543 LYS cc_start: 0.9264 (mmtp) cc_final: 0.9027 (mmtt) REVERT: A 634 LEU cc_start: 0.7454 (tp) cc_final: 0.7149 (tp) REVERT: A 678 MET cc_start: 0.6633 (ptp) cc_final: 0.6086 (ptt) REVERT: A 689 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7589 (tm-30) REVERT: A 690 ILE cc_start: 0.9014 (mm) cc_final: 0.8524 (mm) REVERT: B 199 ASN cc_start: 0.8629 (m110) cc_final: 0.8384 (p0) REVERT: B 225 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8175 (ttt180) REVERT: B 260 ASN cc_start: 0.8871 (m-40) cc_final: 0.7974 (m110) REVERT: B 291 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 309 ILE cc_start: 0.9253 (mp) cc_final: 0.9033 (mt) REVERT: B 312 LYS cc_start: 0.9402 (ptpt) cc_final: 0.9107 (ptpp) REVERT: B 403 THR cc_start: 0.8700 (p) cc_final: 0.8322 (t) REVERT: B 410 ASP cc_start: 0.8501 (p0) cc_final: 0.8296 (p0) REVERT: B 508 MET cc_start: 0.0770 (mtt) cc_final: -0.0028 (mtt) REVERT: B 543 LYS cc_start: 0.9157 (mmtp) cc_final: 0.8532 (mmtm) REVERT: B 546 GLU cc_start: 0.8942 (mp0) cc_final: 0.8492 (mp0) REVERT: B 565 LYS cc_start: 0.9345 (mptt) cc_final: 0.9114 (mmmt) REVERT: B 651 LYS cc_start: 0.9155 (ptpt) cc_final: 0.8787 (ptpt) REVERT: B 689 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 690 ILE cc_start: 0.8620 (mm) cc_final: 0.8128 (mm) REVERT: B 700 ARG cc_start: 0.8948 (ttp-170) cc_final: 0.8629 (ttm170) REVERT: B 757 MET cc_start: 0.7494 (tmm) cc_final: 0.7244 (tmm) REVERT: C 219 MET cc_start: 0.8260 (tpp) cc_final: 0.7849 (tpp) REVERT: C 244 TYR cc_start: 0.8091 (p90) cc_final: 0.7800 (p90) REVERT: C 252 THR cc_start: 0.8693 (p) cc_final: 0.8356 (p) REVERT: C 267 PHE cc_start: 0.8213 (t80) cc_final: 0.7650 (t80) REVERT: C 287 ARG cc_start: 0.8435 (mtm110) cc_final: 0.7740 (mtm110) REVERT: C 306 LEU cc_start: 0.9556 (tt) cc_final: 0.9255 (tt) REVERT: C 312 LYS cc_start: 0.9086 (ptpt) cc_final: 0.8677 (ptpt) REVERT: C 442 MET cc_start: 0.7773 (tmm) cc_final: 0.7411 (tmm) REVERT: C 449 MET cc_start: 0.8568 (mmm) cc_final: 0.8280 (mmm) REVERT: C 450 ASP cc_start: 0.8509 (p0) cc_final: 0.8287 (t0) REVERT: C 508 MET cc_start: 0.2486 (mtt) cc_final: 0.1752 (mtt) REVERT: C 543 LYS cc_start: 0.9096 (mmtp) cc_final: 0.8571 (mmtp) REVERT: C 546 GLU cc_start: 0.8959 (mp0) cc_final: 0.8576 (mp0) REVERT: C 550 MET cc_start: 0.5249 (mmp) cc_final: 0.4969 (mmp) REVERT: C 560 ARG cc_start: 0.8375 (mtp-110) cc_final: 0.7722 (mtp-110) REVERT: C 577 ASP cc_start: 0.7349 (p0) cc_final: 0.6540 (p0) REVERT: D 203 TYR cc_start: 0.8134 (m-10) cc_final: 0.7613 (m-10) REVERT: D 205 ASP cc_start: 0.8246 (t70) cc_final: 0.8032 (t70) REVERT: D 218 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8181 (tm-30) REVERT: D 219 MET cc_start: 0.8462 (tpp) cc_final: 0.8132 (tpp) REVERT: D 221 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7663 (tm-30) REVERT: D 222 LEU cc_start: 0.8889 (tp) cc_final: 0.8425 (tp) REVERT: D 306 LEU cc_start: 0.9436 (tt) cc_final: 0.9231 (tp) REVERT: D 312 LYS cc_start: 0.9015 (ptpp) cc_final: 0.8596 (ptpp) REVERT: D 392 ASP cc_start: 0.7376 (p0) cc_final: 0.7094 (p0) REVERT: D 395 ASP cc_start: 0.8435 (m-30) cc_final: 0.7976 (p0) REVERT: D 404 HIS cc_start: 0.8160 (p90) cc_final: 0.7781 (p90) REVERT: D 449 MET cc_start: 0.8294 (mmm) cc_final: 0.8072 (mmm) REVERT: D 508 MET cc_start: 0.1048 (mtt) cc_final: 0.0488 (mtt) REVERT: D 543 LYS cc_start: 0.9189 (mmtp) cc_final: 0.8287 (mmmm) REVERT: D 546 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8644 (mp0) REVERT: D 611 MET cc_start: 0.7696 (mmp) cc_final: 0.7469 (mmm) REVERT: D 678 MET cc_start: 0.7337 (ptp) cc_final: 0.6548 (ptt) REVERT: D 689 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7643 (tm-30) REVERT: D 690 ILE cc_start: 0.8941 (mm) cc_final: 0.8348 (mm) REVERT: D 700 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7749 (ttm170) REVERT: D 757 MET cc_start: 0.7209 (ppp) cc_final: 0.6980 (ppp) REVERT: E 204 ASP cc_start: 0.7181 (p0) cc_final: 0.6879 (t0) REVERT: E 278 LEU cc_start: 0.8429 (pp) cc_final: 0.8073 (pp) REVERT: E 281 GLU cc_start: 0.8706 (mp0) cc_final: 0.8270 (mp0) REVERT: E 287 ARG cc_start: 0.8659 (mmm160) cc_final: 0.8148 (mmm-85) REVERT: E 306 LEU cc_start: 0.9422 (tt) cc_final: 0.9145 (tp) REVERT: E 332 MET cc_start: 0.9006 (mmm) cc_final: 0.8286 (mmm) REVERT: E 411 LEU cc_start: 0.8919 (mp) cc_final: 0.8676 (mp) REVERT: E 449 MET cc_start: 0.8585 (mmm) cc_final: 0.8316 (mmm) REVERT: E 478 ASP cc_start: 0.7083 (m-30) cc_final: 0.6211 (t0) REVERT: E 484 ASP cc_start: 0.8866 (p0) cc_final: 0.8641 (p0) REVERT: E 508 MET cc_start: 0.0045 (mtt) cc_final: -0.0371 (mtt) REVERT: E 529 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8435 (mmmt) REVERT: E 542 ILE cc_start: 0.8964 (tp) cc_final: 0.8652 (tp) REVERT: E 560 ARG cc_start: 0.8580 (mtp-110) cc_final: 0.8217 (mtp180) REVERT: E 601 ILE cc_start: 0.8801 (mt) cc_final: 0.8585 (mt) REVERT: E 611 MET cc_start: 0.7806 (mmp) cc_final: 0.7591 (mmm) REVERT: E 643 ILE cc_start: 0.8411 (tp) cc_final: 0.7941 (pt) REVERT: E 662 ARG cc_start: 0.8527 (ttt90) cc_final: 0.8093 (tmm160) REVERT: E 757 MET cc_start: 0.7407 (ttp) cc_final: 0.7105 (ppp) REVERT: F 222 LEU cc_start: 0.9067 (tp) cc_final: 0.8812 (tp) REVERT: F 287 ARG cc_start: 0.8238 (mmm160) cc_final: 0.7774 (mmm-85) REVERT: F 306 LEU cc_start: 0.9480 (tt) cc_final: 0.9206 (tt) REVERT: F 312 LYS cc_start: 0.8871 (tptt) cc_final: 0.8653 (tppt) REVERT: F 332 MET cc_start: 0.8376 (tpt) cc_final: 0.8007 (tpp) REVERT: F 395 ASP cc_start: 0.7869 (m-30) cc_final: 0.7355 (p0) REVERT: F 449 MET cc_start: 0.8347 (mmm) cc_final: 0.8137 (mmm) REVERT: F 494 GLN cc_start: 0.7673 (tp-100) cc_final: 0.7440 (tp40) REVERT: F 499 HIS cc_start: 0.7897 (m90) cc_final: 0.7541 (m-70) REVERT: F 543 LYS cc_start: 0.9076 (mmtp) cc_final: 0.8263 (mptt) REVERT: F 546 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8471 (mp0) REVERT: F 550 MET cc_start: 0.6208 (mmp) cc_final: 0.5625 (mmp) REVERT: F 560 ARG cc_start: 0.8746 (mtp-110) cc_final: 0.8344 (mtp-110) REVERT: F 606 THR cc_start: 0.9412 (p) cc_final: 0.9174 (p) REVERT: F 692 GLN cc_start: 0.8056 (tp-100) cc_final: 0.7827 (tp40) REVERT: F 696 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7989 (mmmt) outliers start: 2 outliers final: 0 residues processed: 730 average time/residue: 0.4212 time to fit residues: 452.7169 Evaluate side-chains 578 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 578 time to evaluate : 3.079 ------------------------------------------------------------------------------- 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: 5.9990 chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 79 optimal weight: 0.2980 chunk 289 optimal weight: 3.9990 chunk 312 optimal weight: 20.0000 chunk 257 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 602 ASN F 602 ASN F 660 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25518 Z= 0.277 Angle : 0.724 8.380 34482 Z= 0.373 Chirality : 0.046 0.163 3894 Planarity : 0.006 0.074 4524 Dihedral : 9.194 119.902 3480 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % 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: -1.08 (0.15), residues: 3150 helix: -0.55 (0.12), residues: 1578 sheet: -2.17 (0.28), residues: 306 loop : -0.27 (0.20), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 476 HIS 0.009 0.002 HIS A 735 PHE 0.027 0.002 PHE C 742 TYR 0.028 0.002 TYR C 203 ARG 0.021 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 696 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 694 time to evaluate : 2.901 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: A 203 TYR cc_start: 0.7821 (m-10) cc_final: 0.7091 (m-10) REVERT: A 222 LEU cc_start: 0.9047 (tp) cc_final: 0.8704 (tp) REVERT: A 239 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.7019 (mtm180) REVERT: A 312 LYS cc_start: 0.9186 (tptt) cc_final: 0.8942 (tptt) REVERT: A 332 MET cc_start: 0.9184 (mmm) cc_final: 0.8933 (mmt) REVERT: A 349 ARG cc_start: 0.8716 (ttm170) cc_final: 0.8458 (ttm-80) REVERT: A 365 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8169 (mmm-85) REVERT: A 395 ASP cc_start: 0.8023 (m-30) cc_final: 0.7479 (p0) REVERT: A 449 MET cc_start: 0.8282 (mmm) cc_final: 0.7973 (mmm) REVERT: A 524 LYS cc_start: 0.8378 (ptpt) cc_final: 0.7899 (ptpt) REVERT: A 526 LEU cc_start: 0.8444 (mt) cc_final: 0.8168 (mp) REVERT: A 560 ARG cc_start: 0.8509 (mtp180) cc_final: 0.7951 (mtp-110) REVERT: A 561 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8550 (mm-30) REVERT: A 678 MET cc_start: 0.6658 (ptp) cc_final: 0.6135 (ptt) REVERT: A 689 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 690 ILE cc_start: 0.9099 (mm) cc_final: 0.8593 (mm) REVERT: A 757 MET cc_start: 0.7306 (ppp) cc_final: 0.6875 (ppp) REVERT: B 205 ASP cc_start: 0.8381 (t70) cc_final: 0.8036 (t0) REVERT: B 217 LYS cc_start: 0.8527 (mppt) cc_final: 0.8250 (mmtp) REVERT: B 225 ARG cc_start: 0.8519 (mmm-85) cc_final: 0.8098 (ttt180) REVERT: B 312 LYS cc_start: 0.9471 (ptpt) cc_final: 0.9086 (ptpp) REVERT: B 449 MET cc_start: 0.8393 (mmm) cc_final: 0.7937 (mmm) REVERT: B 508 MET cc_start: 0.0423 (mtt) cc_final: 0.0210 (mtt) REVERT: B 543 LYS cc_start: 0.9175 (mmtp) cc_final: 0.8550 (mmtm) REVERT: B 546 GLU cc_start: 0.8963 (mp0) cc_final: 0.8473 (mp0) REVERT: B 550 MET cc_start: 0.5889 (mmp) cc_final: 0.5441 (ttm) REVERT: B 559 VAL cc_start: 0.8979 (t) cc_final: 0.8371 (t) REVERT: B 564 ASP cc_start: 0.9134 (m-30) cc_final: 0.8901 (m-30) REVERT: B 651 LYS cc_start: 0.9240 (ptpt) cc_final: 0.8880 (ptpt) REVERT: B 662 ARG cc_start: 0.8378 (ttt90) cc_final: 0.8141 (tpt170) REVERT: B 678 MET cc_start: 0.7627 (ptp) cc_final: 0.6785 (ptt) REVERT: B 689 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 690 ILE cc_start: 0.8778 (mm) cc_final: 0.8505 (mm) REVERT: B 700 ARG cc_start: 0.8854 (ttp-170) cc_final: 0.8539 (ttm170) REVERT: C 222 LEU cc_start: 0.9226 (mm) cc_final: 0.8909 (tp) REVERT: C 306 LEU cc_start: 0.9557 (tt) cc_final: 0.9193 (tt) REVERT: C 312 LYS cc_start: 0.8997 (ptpt) cc_final: 0.8708 (ptpt) REVERT: C 349 ARG cc_start: 0.8336 (mtp85) cc_final: 0.7975 (mtp85) REVERT: C 365 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7510 (ttm110) REVERT: C 442 MET cc_start: 0.7761 (tmm) cc_final: 0.7424 (tmm) REVERT: C 449 MET cc_start: 0.8627 (mmm) cc_final: 0.8400 (mmm) REVERT: C 543 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8415 (mmtm) REVERT: C 546 GLU cc_start: 0.8890 (mp0) cc_final: 0.8465 (mp0) REVERT: C 550 MET cc_start: 0.5117 (mmp) cc_final: 0.4721 (mmp) REVERT: C 560 ARG cc_start: 0.8492 (mtp-110) cc_final: 0.7814 (mtp-110) REVERT: C 562 ILE cc_start: 0.9619 (tp) cc_final: 0.8985 (mm) REVERT: C 577 ASP cc_start: 0.7715 (p0) cc_final: 0.7328 (p0) REVERT: D 219 MET cc_start: 0.8464 (tpp) cc_final: 0.8159 (tpp) REVERT: D 221 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7588 (tm-30) REVERT: D 222 LEU cc_start: 0.8832 (tp) cc_final: 0.8356 (tp) REVERT: D 281 GLU cc_start: 0.8750 (mp0) cc_final: 0.8472 (mp0) REVERT: D 283 GLU cc_start: 0.7992 (pp20) cc_final: 0.7766 (tm-30) REVERT: D 287 ARG cc_start: 0.8552 (mtm110) cc_final: 0.7910 (mtm110) REVERT: D 306 LEU cc_start: 0.9440 (tt) cc_final: 0.9182 (tp) REVERT: D 312 LYS cc_start: 0.9283 (ptpp) cc_final: 0.8896 (ptpp) REVERT: D 392 ASP cc_start: 0.7503 (p0) cc_final: 0.7271 (p0) REVERT: D 404 HIS cc_start: 0.8197 (p90) cc_final: 0.7837 (p90) REVERT: D 508 MET cc_start: 0.1356 (mtt) cc_final: 0.0637 (mtt) REVERT: D 543 LYS cc_start: 0.9127 (mmtp) cc_final: 0.8352 (mmmm) REVERT: D 546 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8593 (mp0) REVERT: D 678 MET cc_start: 0.7334 (ptp) cc_final: 0.6580 (ptt) REVERT: D 690 ILE cc_start: 0.9012 (mm) cc_final: 0.8429 (mm) REVERT: D 700 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7895 (ttm170) REVERT: E 204 ASP cc_start: 0.7373 (p0) cc_final: 0.7002 (t0) REVERT: E 219 MET cc_start: 0.9070 (tpp) cc_final: 0.8868 (tpp) REVERT: E 222 LEU cc_start: 0.9157 (tp) cc_final: 0.8942 (tp) REVERT: E 281 GLU cc_start: 0.8824 (mp0) cc_final: 0.8621 (mp0) REVERT: E 287 ARG cc_start: 0.8692 (mmm160) cc_final: 0.8323 (mmm-85) REVERT: E 306 LEU cc_start: 0.9380 (tt) cc_final: 0.9135 (tp) REVERT: E 332 MET cc_start: 0.9087 (mmm) cc_final: 0.8627 (mmm) REVERT: E 411 LEU cc_start: 0.9147 (mp) cc_final: 0.8761 (mm) REVERT: E 494 GLN cc_start: 0.8252 (tp40) cc_final: 0.8020 (mm110) REVERT: E 560 ARG cc_start: 0.8502 (mtp-110) cc_final: 0.8160 (mtp180) REVERT: E 565 LYS cc_start: 0.9192 (mtpp) cc_final: 0.8936 (mtpp) REVERT: E 577 ASP cc_start: 0.8080 (p0) cc_final: 0.7204 (p0) REVERT: E 601 ILE cc_start: 0.8803 (mt) cc_final: 0.8541 (mt) REVERT: E 651 LYS cc_start: 0.9128 (ptpt) cc_final: 0.8264 (pttp) REVERT: F 219 MET cc_start: 0.8649 (tpp) cc_final: 0.8396 (tpp) REVERT: F 267 PHE cc_start: 0.8222 (t80) cc_final: 0.7998 (t80) REVERT: F 287 ARG cc_start: 0.8279 (mmm160) cc_final: 0.7632 (mmm-85) REVERT: F 306 LEU cc_start: 0.9507 (tt) cc_final: 0.9190 (tt) REVERT: F 395 ASP cc_start: 0.8029 (m-30) cc_final: 0.7594 (p0) REVERT: F 449 MET cc_start: 0.8321 (mmm) cc_final: 0.8118 (mmm) REVERT: F 484 ASP cc_start: 0.8561 (p0) cc_final: 0.7976 (p0) REVERT: F 546 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8426 (mp0) REVERT: F 550 MET cc_start: 0.6040 (mmp) cc_final: 0.5458 (mmp) REVERT: F 560 ARG cc_start: 0.8660 (mtp-110) cc_final: 0.8286 (mtp-110) REVERT: F 578 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7745 (mm-30) REVERT: F 662 ARG cc_start: 0.8320 (ttt90) cc_final: 0.8010 (ttt90) REVERT: F 689 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7929 (tm-30) REVERT: F 757 MET cc_start: 0.7474 (ttt) cc_final: 0.7136 (ttp) outliers start: 2 outliers final: 0 residues processed: 696 average time/residue: 0.4142 time to fit residues: 428.2220 Evaluate side-chains 556 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 3.042 ------------------------------------------------------------------------------- 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: 0.9990 chunk 217 optimal weight: 0.4980 chunk 150 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 290 optimal weight: 0.9990 chunk 307 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 692 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 GLN C 499 HIS C 602 ASN D 602 ASN E 215 GLN E 421 GLN E 602 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25518 Z= 0.200 Angle : 0.692 15.598 34482 Z= 0.345 Chirality : 0.045 0.180 3894 Planarity : 0.005 0.078 4524 Dihedral : 9.017 119.902 3480 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -0.79 (0.15), residues: 3150 helix: -0.28 (0.13), residues: 1572 sheet: -2.09 (0.29), residues: 288 loop : -0.17 (0.20), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 454 HIS 0.007 0.001 HIS A 735 PHE 0.020 0.001 PHE A 742 TYR 0.012 0.002 TYR C 203 ARG 0.013 0.001 ARG C 465 *********************** 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 695 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 695 time to evaluate : 2.802 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: A 203 TYR cc_start: 0.7704 (m-10) cc_final: 0.7008 (m-10) REVERT: A 239 ARG cc_start: 0.7543 (mtp-110) cc_final: 0.7007 (mtm180) REVERT: A 312 LYS cc_start: 0.9171 (tptt) cc_final: 0.8937 (tptt) REVERT: A 332 MET cc_start: 0.9158 (mmm) cc_final: 0.8939 (mmt) REVERT: A 349 ARG cc_start: 0.8723 (ttm170) cc_final: 0.8512 (ttm-80) REVERT: A 499 HIS cc_start: 0.7223 (m170) cc_final: 0.6935 (m170) REVERT: A 526 LEU cc_start: 0.8351 (mt) cc_final: 0.8081 (mp) REVERT: A 560 ARG cc_start: 0.8731 (mtp180) cc_final: 0.8256 (mtp-110) REVERT: A 561 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8468 (mm-30) REVERT: A 678 MET cc_start: 0.6624 (ptp) cc_final: 0.6111 (ptt) REVERT: A 689 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 690 ILE cc_start: 0.9049 (mm) cc_final: 0.8544 (mm) REVERT: A 757 MET cc_start: 0.7273 (ppp) cc_final: 0.6875 (ppp) REVERT: B 205 ASP cc_start: 0.8349 (t70) cc_final: 0.8071 (t0) REVERT: B 222 LEU cc_start: 0.9138 (tp) cc_final: 0.8833 (tp) REVERT: B 225 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8226 (ttt180) REVERT: B 252 THR cc_start: 0.8807 (p) cc_final: 0.8587 (t) REVERT: B 312 LYS cc_start: 0.9452 (ptpt) cc_final: 0.9106 (ptpp) REVERT: B 332 MET cc_start: 0.9189 (mmm) cc_final: 0.8857 (mmm) REVERT: B 508 MET cc_start: 0.0476 (mtt) cc_final: 0.0199 (mtt) REVERT: B 543 LYS cc_start: 0.9169 (mmtp) cc_final: 0.8817 (mmtm) REVERT: B 550 MET cc_start: 0.5822 (mmp) cc_final: 0.5565 (ttm) REVERT: B 559 VAL cc_start: 0.8925 (t) cc_final: 0.8330 (t) REVERT: B 560 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.8201 (mtp-110) REVERT: B 561 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8670 (mm-30) REVERT: B 634 LEU cc_start: 0.7957 (tt) cc_final: 0.7486 (tt) REVERT: B 651 LYS cc_start: 0.9197 (ptpt) cc_final: 0.8830 (ptpt) REVERT: B 658 LYS cc_start: 0.7967 (tptp) cc_final: 0.7523 (tppt) REVERT: B 678 MET cc_start: 0.7570 (ptp) cc_final: 0.7355 (ptm) REVERT: B 689 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7602 (tm-30) REVERT: B 690 ILE cc_start: 0.8533 (mm) cc_final: 0.8088 (mm) REVERT: B 700 ARG cc_start: 0.8823 (ttp-170) cc_final: 0.8502 (ttm170) REVERT: C 217 LYS cc_start: 0.8376 (mtmm) cc_final: 0.7989 (mmmm) REVERT: C 222 LEU cc_start: 0.9185 (mm) cc_final: 0.8854 (tp) REVERT: C 241 ILE cc_start: 0.9193 (pt) cc_final: 0.8964 (pt) REVERT: C 312 LYS cc_start: 0.8773 (ptpt) cc_final: 0.8522 (ptpt) REVERT: C 349 ARG cc_start: 0.8639 (mtp85) cc_final: 0.8118 (mtp85) REVERT: C 351 ASN cc_start: 0.8074 (p0) cc_final: 0.7219 (p0) REVERT: C 442 MET cc_start: 0.7694 (tmm) cc_final: 0.7386 (tmm) REVERT: C 449 MET cc_start: 0.8532 (mmm) cc_final: 0.8315 (mmm) REVERT: C 486 LYS cc_start: 0.8732 (mttt) cc_final: 0.8276 (mmmt) REVERT: C 508 MET cc_start: 0.1885 (mtt) cc_final: 0.1408 (mtt) REVERT: C 543 LYS cc_start: 0.9124 (mmtp) cc_final: 0.8390 (mmtp) REVERT: C 546 GLU cc_start: 0.8832 (mp0) cc_final: 0.8347 (mp0) REVERT: C 550 MET cc_start: 0.5123 (mmp) cc_final: 0.4398 (ttm) REVERT: C 560 ARG cc_start: 0.8500 (mtp-110) cc_final: 0.7941 (mtp-110) REVERT: D 218 GLU cc_start: 0.8758 (pp20) cc_final: 0.8127 (tm-30) REVERT: D 219 MET cc_start: 0.8465 (tpp) cc_final: 0.8029 (tpp) REVERT: D 221 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7696 (tm-30) REVERT: D 283 GLU cc_start: 0.8138 (pp20) cc_final: 0.7892 (tm-30) REVERT: D 287 ARG cc_start: 0.8540 (mtm110) cc_final: 0.7822 (mtm110) REVERT: D 305 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8308 (mm-30) REVERT: D 306 LEU cc_start: 0.9459 (tt) cc_final: 0.9237 (tp) REVERT: D 312 LYS cc_start: 0.9297 (ptpp) cc_final: 0.8870 (ptpp) REVERT: D 404 HIS cc_start: 0.8159 (p90) cc_final: 0.7863 (p90) REVERT: D 508 MET cc_start: 0.0765 (mtt) cc_final: 0.0301 (mtt) REVERT: D 529 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8257 (tptt) REVERT: D 543 LYS cc_start: 0.9154 (mmtp) cc_final: 0.8148 (mmmm) REVERT: D 546 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8539 (mp0) REVERT: D 562 ILE cc_start: 0.9240 (tp) cc_final: 0.8650 (tp) REVERT: D 678 MET cc_start: 0.7150 (ptp) cc_final: 0.6388 (ptt) REVERT: D 690 ILE cc_start: 0.8881 (mm) cc_final: 0.8374 (mm) REVERT: E 204 ASP cc_start: 0.7251 (p0) cc_final: 0.6921 (t0) REVERT: E 219 MET cc_start: 0.9142 (tpp) cc_final: 0.8762 (tpp) REVERT: E 287 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8160 (mmm-85) REVERT: E 306 LEU cc_start: 0.9399 (tt) cc_final: 0.9108 (tp) REVERT: E 332 MET cc_start: 0.9145 (mmm) cc_final: 0.8641 (mmm) REVERT: E 411 LEU cc_start: 0.9050 (mp) cc_final: 0.8655 (mm) REVERT: E 499 HIS cc_start: 0.7454 (m-70) cc_final: 0.7244 (m-70) REVERT: E 529 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8449 (mmmt) REVERT: E 542 ILE cc_start: 0.8872 (tp) cc_final: 0.8488 (tp) REVERT: E 560 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.8182 (mtp-110) REVERT: E 562 ILE cc_start: 0.9336 (tp) cc_final: 0.8691 (mt) REVERT: E 601 ILE cc_start: 0.8818 (mt) cc_final: 0.8555 (mt) REVERT: E 651 LYS cc_start: 0.9104 (ptpt) cc_final: 0.8243 (pttp) REVERT: E 662 ARG cc_start: 0.8566 (tpt170) cc_final: 0.8180 (tmm160) REVERT: E 757 MET cc_start: 0.6861 (ppp) cc_final: 0.6454 (ppp) REVERT: F 203 TYR cc_start: 0.7677 (m-10) cc_final: 0.7164 (m-80) REVERT: F 267 PHE cc_start: 0.8200 (t80) cc_final: 0.7970 (t80) REVERT: F 278 LEU cc_start: 0.9078 (mt) cc_final: 0.8852 (mm) REVERT: F 287 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7727 (mmm-85) REVERT: F 312 LYS cc_start: 0.9229 (ptpt) cc_final: 0.9002 (ptpp) REVERT: F 368 ASP cc_start: 0.8353 (t0) cc_final: 0.8102 (t0) REVERT: F 388 MET cc_start: 0.5133 (mtt) cc_final: 0.4787 (mtt) REVERT: F 484 ASP cc_start: 0.8511 (p0) cc_final: 0.7924 (p0) REVERT: F 486 LYS cc_start: 0.8418 (tttt) cc_final: 0.6365 (tttt) REVERT: F 499 HIS cc_start: 0.7758 (m90) cc_final: 0.7476 (m-70) REVERT: F 546 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8384 (mp0) REVERT: F 550 MET cc_start: 0.6070 (mmp) cc_final: 0.5518 (mmp) REVERT: F 560 ARG cc_start: 0.8648 (mtp-110) cc_final: 0.8352 (mtp-110) REVERT: F 561 GLU cc_start: 0.8987 (tp30) cc_final: 0.8747 (tp30) REVERT: F 578 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7706 (mm-30) REVERT: F 662 ARG cc_start: 0.8351 (ttt90) cc_final: 0.7993 (ttt90) REVERT: F 689 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7881 (tm-30) REVERT: F 757 MET cc_start: 0.7358 (ttt) cc_final: 0.7127 (ppp) outliers start: 0 outliers final: 0 residues processed: 695 average time/residue: 0.3996 time to fit residues: 419.0258 Evaluate side-chains 549 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 2.177 ------------------------------------------------------------------------------- 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: 6.9990 chunk 174 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 275 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: