Starting phenix.real_space_refine on Sun Feb 18 21:52:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg2_33805/02_2024/7yg2_33805.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg2_33805/02_2024/7yg2_33805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg2_33805/02_2024/7yg2_33805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg2_33805/02_2024/7yg2_33805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg2_33805/02_2024/7yg2_33805.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg2_33805/02_2024/7yg2_33805.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2196 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 13078 2.51 5 N 3521 2.21 5 O 4079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 290": "OE1" <-> "OE2" Residue "M TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 362": "OE1" <-> "OE2" Residue "M TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 416": "OD1" <-> "OD2" Residue "C GLU 422": "OE1" <-> "OE2" Residue "C PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 508": "OE1" <-> "OE2" Residue "C GLU 525": "OE1" <-> "OE2" Residue "D GLU 498": "OE1" <-> "OE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 553": "OD1" <-> "OD2" Residue "E ASP 453": "OD1" <-> "OD2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "E TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 541": "OE1" <-> "OE2" Residue "F ASP 417": "OD1" <-> "OD2" Residue "F PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 483": "OD1" <-> "OD2" Residue "F GLU 526": "OE1" <-> "OE2" Residue "F TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 453": "OD1" <-> "OD2" Residue "G GLU 468": "OE1" <-> "OE2" Residue "H ASP 376": "OD1" <-> "OD2" Residue "H ASP 483": "OD1" <-> "OD2" Residue "K PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 416": "OD1" <-> "OD2" Residue "K ASP 453": "OD1" <-> "OD2" Residue "K GLU 468": "OE1" <-> "OE2" Residue "K PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 532": "OE1" <-> "OE2" Residue "L GLU 398": "OE1" <-> "OE2" Residue "L ASP 416": "OD1" <-> "OD2" Residue "L ASP 483": "OD1" <-> "OD2" Residue "L GLU 508": "OE1" <-> "OE2" Residue "L TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 570": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20783 Number of models: 1 Model: "" Number of chains: 23 Chain: "M" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2257 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 9, 'TRANS': 261} Chain breaks: 2 Chain: "A" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1769 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 18, 'TRANS': 209} Chain: "C" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1779 Classifications: {'peptide': 230} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "F" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain breaks: 1 Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain breaks: 1 Chain: "K" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1737 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain breaks: 1 Chain: "L" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1761 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain breaks: 1 Chain: "J" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain breaks: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.69, per 1000 atoms: 0.51 Number of scatterers: 20783 At special positions: 0 Unit cell: (87.74, 175.48, 194.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4079 8.00 N 3521 7.00 C 13078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS M 162 " - pdb=" SG CYS M 334 " distance=2.03 Simple disulfide: pdb=" SG CYS M 168 " - pdb=" SG CYS M 323 " distance=2.03 Simple disulfide: pdb=" SG CYS M 358 " - pdb=" SG CYS M 446 " distance=2.03 Simple disulfide: pdb=" SG CYS M 372 " - pdb=" SG CYS M 393 " distance=2.03 Simple disulfide: pdb=" SG CYS M 441 " - pdb=" SG CYS M 444 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.04 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 575 " - pdb=" SG CYS J 14 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG I 1 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 7.82 Conformation dependent library (CDL) restraints added in 3.5 seconds 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5058 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 53 sheets defined 19.2% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'M' and resid 164 through 171 removed outlier: 3.531A pdb=" N CYS M 168 " --> pdb=" O THR M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 210 Processing helix chain 'M' and resid 216 through 223 Processing helix chain 'M' and resid 228 through 249 Processing helix chain 'M' and resid 252 through 272 Processing helix chain 'M' and resid 279 through 297 removed outlier: 3.635A pdb=" N LYS M 283 " --> pdb=" O THR M 279 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE M 286 " --> pdb=" O SER M 282 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N THR M 287 " --> pdb=" O LYS M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 313 Processing helix chain 'M' and resid 313 through 330 removed outlier: 3.504A pdb=" N VAL M 317 " --> pdb=" O ASN M 313 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA M 328 " --> pdb=" O GLY M 324 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN M 329 " --> pdb=" O TYR M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 373 removed outlier: 3.525A pdb=" N PHE M 373 " --> pdb=" O LYS M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 421 removed outlier: 3.556A pdb=" N THR M 409 " --> pdb=" O ASN M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 432 through 440 Processing helix chain 'M' and resid 451 through 456 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.646A pdb=" N GLY A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.729A pdb=" N GLU B 388 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 removed outlier: 3.757A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 467 Processing helix chain 'B' and resid 524 through 531 removed outlier: 4.041A pdb=" N GLY B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 460 through 466 removed outlier: 3.779A pdb=" N LEU C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 414 through 420 removed outlier: 3.530A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 467 Processing helix chain 'D' and resid 524 through 531 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 415 through 421 Processing helix chain 'E' and resid 460 through 467 removed outlier: 3.519A pdb=" N ARG E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 Processing helix chain 'E' and resid 553 through 558 removed outlier: 3.912A pdb=" N LYS E 558 " --> pdb=" O LYS E 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 460 through 466 Processing helix chain 'F' and resid 524 through 530 Processing helix chain 'G' and resid 353 through 361 Processing helix chain 'G' and resid 414 through 419 Processing helix chain 'G' and resid 460 through 466 removed outlier: 3.642A pdb=" N LEU G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 529 Processing helix chain 'G' and resid 553 through 558 Processing helix chain 'H' and resid 353 through 360 Processing helix chain 'H' and resid 414 through 421 removed outlier: 3.886A pdb=" N GLY H 421 " --> pdb=" O ASP H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 466 Processing helix chain 'H' and resid 524 through 530 Processing helix chain 'K' and resid 353 through 361 Processing helix chain 'K' and resid 414 through 421 removed outlier: 3.542A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 467 Processing helix chain 'K' and resid 525 through 531 removed outlier: 3.886A pdb=" N GLY K 531 " --> pdb=" O GLU K 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 360 Processing helix chain 'L' and resid 414 through 420 removed outlier: 3.901A pdb=" N TRP L 418 " --> pdb=" O CYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 467 removed outlier: 3.737A pdb=" N LEU L 464 " --> pdb=" O ALA L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 530 Processing helix chain 'J' and resid 64 through 69 Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.575A pdb=" N ARG A 346 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 350 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 363 through 364 removed outlier: 4.507A pdb=" N THR A 363 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 413 " --> pdb=" O THR A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 389 through 392 removed outlier: 6.679A pdb=" N TRP A 382 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 381 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 427 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 425 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.835A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 519 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 476 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 501 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.835A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 519 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 476 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.834A pdb=" N GLN A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 485 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 535 " --> pdb=" O MET A 489 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 563 removed outlier: 7.261A pdb=" N TYR A 562 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 566 through 568 Processing sheet with id=AA9, first strand: chain 'B' and resid 346 through 348 removed outlier: 4.051A pdb=" N LEU B 368 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 382 through 383 removed outlier: 3.737A pdb=" N VAL B 428 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 453 through 456 removed outlier: 3.530A pdb=" N THR B 477 " --> pdb=" O ASP B 453 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 453 through 456 removed outlier: 3.530A pdb=" N THR B 477 " --> pdb=" O ASP B 453 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AB5, first strand: chain 'C' and resid 379 through 384 removed outlier: 4.144A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 429 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 381 " --> pdb=" O THR C 427 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 424 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 441 " --> pdb=" O PHE C 424 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.834A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.834A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB9, first strand: chain 'C' and resid 565 through 567 removed outlier: 3.629A pdb=" N VAL D 567 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU D 566 " --> pdb=" O VAL E 567 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 424 through 428 removed outlier: 3.812A pdb=" N VAL D 428 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU D 437 " --> pdb=" O VAL D 428 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 455 through 457 removed outlier: 3.677A pdb=" N LEU D 475 " --> pdb=" O TYR D 455 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 519 " --> pdb=" O CYS D 474 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 501 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 455 through 457 removed outlier: 3.677A pdb=" N LEU D 475 " --> pdb=" O TYR D 455 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AC5, first strand: chain 'D' and resid 535 through 539 removed outlier: 3.525A pdb=" N VAL D 538 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR D 548 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 424 through 427 Processing sheet with id=AC7, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.991A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.991A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AD1, first strand: chain 'F' and resid 363 through 365 removed outlier: 4.319A pdb=" N THR F 363 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA F 411 " --> pdb=" O LEU F 365 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 389 through 391 removed outlier: 7.175A pdb=" N TRP F 382 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER F 381 " --> pdb=" O THR F 427 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR F 427 " --> pdb=" O SER F 381 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.655A pdb=" N THR F 473 " --> pdb=" O LEU F 457 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.655A pdb=" N THR F 473 " --> pdb=" O LEU F 457 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD6, first strand: chain 'F' and resid 565 through 567 removed outlier: 6.196A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL G 567 " --> pdb=" O LEU H 566 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU K 566 " --> pdb=" O ASN H 563 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER H 565 " --> pdb=" O LEU K 566 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER K 565 " --> pdb=" O LEU L 566 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N MET L 568 " --> pdb=" O SER K 565 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL K 567 " --> pdb=" O MET L 568 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL J 41 " --> pdb=" O VAL L 567 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU J 34 " --> pdb=" O ARG J 20 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG J 20 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE J 17 " --> pdb=" O LEU J 7 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 347 through 349 Processing sheet with id=AD8, first strand: chain 'G' and resid 379 through 383 removed outlier: 3.534A pdb=" N THR G 379 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER G 381 " --> pdb=" O THR G 427 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR G 427 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR G 425 " --> pdb=" O THR G 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 455 through 457 removed outlier: 4.896A pdb=" N THR G 471 " --> pdb=" O VAL G 523 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL G 523 " --> pdb=" O THR G 471 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N THR G 473 " --> pdb=" O LEU G 521 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU G 521 " --> pdb=" O THR G 473 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU G 475 " --> pdb=" O SER G 519 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER G 519 " --> pdb=" O LEU G 475 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR G 477 " --> pdb=" O ALA G 517 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA G 517 " --> pdb=" O THR G 477 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE G 479 " --> pdb=" O TYR G 515 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 501 " --> pdb=" O ILE G 520 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 455 through 457 removed outlier: 4.896A pdb=" N THR G 471 " --> pdb=" O VAL G 523 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL G 523 " --> pdb=" O THR G 471 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N THR G 473 " --> pdb=" O LEU G 521 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU G 521 " --> pdb=" O THR G 473 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU G 475 " --> pdb=" O SER G 519 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER G 519 " --> pdb=" O LEU G 475 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR G 477 " --> pdb=" O ALA G 517 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA G 517 " --> pdb=" O THR G 477 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE G 479 " --> pdb=" O TYR G 515 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AE3, first strand: chain 'H' and resid 346 through 349 removed outlier: 4.036A pdb=" N LEU H 368 " --> pdb=" O PHE H 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 379 through 383 removed outlier: 4.364A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR H 429 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN H 439 " --> pdb=" O CYS H 426 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL H 428 " --> pdb=" O LEU H 437 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU H 437 " --> pdb=" O VAL H 428 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.935A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.935A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AE8, first strand: chain 'K' and resid 348 through 350 removed outlier: 3.755A pdb=" N ILE K 350 " --> pdb=" O THR K 366 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR K 366 " --> pdb=" O ILE K 350 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 379 through 383 removed outlier: 3.589A pdb=" N THR K 379 " --> pdb=" O THR K 429 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.516A pdb=" N THR K 477 " --> pdb=" O ASP K 453 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.516A pdb=" N THR K 477 " --> pdb=" O ASP K 453 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 493 through 494 removed outlier: 3.915A pdb=" N MET K 489 " --> pdb=" O THR K 535 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR K 535 " --> pdb=" O MET K 489 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 381 through 383 removed outlier: 4.012A pdb=" N PHE L 424 " --> pdb=" O ILE L 441 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE L 441 " --> pdb=" O PHE L 424 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.979A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE L 520 " --> pdb=" O VAL L 501 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL L 501 " --> pdb=" O ILE L 520 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.979A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET L 506 " --> pdb=" O PHE L 516 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 485 through 489 removed outlier: 3.832A pdb=" N PHE L 485 " --> pdb=" O ALA L 539 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR L 534 " --> pdb=" O VAL L 552 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL L 538 " --> pdb=" O THR L 548 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR L 548 " --> pdb=" O VAL L 538 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 110 through 116 removed outlier: 3.887A pdb=" N ALA J 111 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR J 126 " --> pdb=" O ALA J 111 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1842 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: 6.86 Time building geometry restraints manager: 8.42 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: 6747 1.34 - 1.46: 4867 1.46 - 1.58: 9534 1.58 - 1.70: 1 1.70 - 1.82: 142 Bond restraints: 21291 Sorted by residual: bond pdb=" C1 NAG G 601 " pdb=" O5 NAG G 601 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" C1 NAG H 601 " pdb=" O5 NAG H 601 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" CB PRO D 497 " pdb=" CG PRO D 497 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.45e+00 ... (remaining 21286 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.81: 937 106.81 - 113.64: 11989 113.64 - 120.47: 7582 120.47 - 127.31: 8250 127.31 - 134.14: 331 Bond angle restraints: 29089 Sorted by residual: angle pdb=" CA PRO D 497 " pdb=" N PRO D 497 " pdb=" CD PRO D 497 " ideal model delta sigma weight residual 112.00 105.15 6.85 1.40e+00 5.10e-01 2.40e+01 angle pdb=" N GLY A 531 " pdb=" CA GLY A 531 " pdb=" C GLY A 531 " ideal model delta sigma weight residual 111.36 116.91 -5.55 1.17e+00 7.31e-01 2.25e+01 angle pdb=" CA PRO E 497 " pdb=" N PRO E 497 " pdb=" CD PRO E 497 " ideal model delta sigma weight residual 112.00 105.89 6.11 1.40e+00 5.10e-01 1.90e+01 angle pdb=" C THR E 370 " pdb=" N ASP E 371 " pdb=" CA ASP E 371 " ideal model delta sigma weight residual 122.46 127.95 -5.49 1.41e+00 5.03e-01 1.51e+01 angle pdb=" C THR A 530 " pdb=" N GLY A 531 " pdb=" CA GLY A 531 " ideal model delta sigma weight residual 119.92 123.57 -3.65 9.60e-01 1.09e+00 1.45e+01 ... (remaining 29084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 12208 23.03 - 46.06: 798 46.06 - 69.08: 56 69.08 - 92.11: 34 92.11 - 115.14: 21 Dihedral angle restraints: 13117 sinusoidal: 5369 harmonic: 7748 Sorted by residual: dihedral pdb=" CB CYS D 367 " pdb=" SG CYS D 367 " pdb=" SG CYS D 426 " pdb=" CB CYS D 426 " ideal model delta sinusoidal sigma weight residual 93.00 162.63 -69.63 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS L 575 " pdb=" SG CYS L 575 " pdb=" SG CYS J 14 " pdb=" CB CYS J 14 " ideal model delta sinusoidal sigma weight residual -86.00 -153.39 67.39 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS F 367 " pdb=" SG CYS F 367 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual 93.00 34.82 58.18 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 13114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3092 0.085 - 0.170: 318 0.170 - 0.256: 4 0.256 - 0.341: 0 0.341 - 0.426: 1 Chirality restraints: 3415 Sorted by residual: chirality pdb=" C1 NAG K 601 " pdb=" ND2 ASN K 563 " pdb=" C2 NAG K 601 " pdb=" O5 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB VAL H 390 " pdb=" CA VAL H 390 " pdb=" CG1 VAL H 390 " pdb=" CG2 VAL H 390 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C1 NAG G 601 " pdb=" ND2 ASN G 563 " pdb=" C2 NAG G 601 " pdb=" O5 NAG G 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3412 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 496 " 0.093 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO E 497 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO E 497 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO E 497 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 496 " -0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO D 497 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO D 497 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 497 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 457 " -0.061 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO C 458 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 458 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 458 " -0.050 5.00e-02 4.00e+02 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1199 2.74 - 3.28: 20363 3.28 - 3.82: 33211 3.82 - 4.36: 38461 4.36 - 4.90: 66350 Nonbonded interactions: 159584 Sorted by model distance: nonbonded pdb=" O MET L 489 " pdb=" OG1 THR L 535 " model vdw 2.196 2.440 nonbonded pdb=" O ALA H 448 " pdb=" OG SER H 480 " model vdw 2.228 2.440 nonbonded pdb=" O ILE B 350 " pdb=" OG1 THR B 366 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASN L 563 " pdb=" ND2 ASN J 36 " model vdw 2.295 2.520 nonbonded pdb=" OG1 THR B 383 " pdb=" OG1 THR B 425 " model vdw 2.295 2.440 ... (remaining 159579 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' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 8.270 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 53.040 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 21291 Z= 0.199 Angle : 0.608 8.425 29089 Z= 0.315 Chirality : 0.046 0.426 3415 Planarity : 0.006 0.138 3712 Dihedral : 15.078 115.141 7978 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.43 (0.16), residues: 2592 helix: -0.34 (0.23), residues: 470 sheet: 0.28 (0.20), residues: 687 loop : -0.48 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 418 HIS 0.009 0.001 HIS K 430 PHE 0.029 0.002 PHE C 348 TYR 0.023 0.001 TYR B 500 ARG 0.014 0.001 ARG C 491 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 270 ILE cc_start: 0.7017 (mt) cc_final: 0.6814 (mt) REVERT: M 332 ASN cc_start: 0.6987 (t0) cc_final: 0.6765 (t0) REVERT: M 340 ILE cc_start: 0.7267 (tp) cc_final: 0.7052 (tp) REVERT: A 402 ASN cc_start: 0.3916 (p0) cc_final: 0.3569 (m110) REVERT: A 570 ASP cc_start: 0.7458 (t70) cc_final: 0.7196 (t0) REVERT: C 364 LYS cc_start: 0.7365 (pttp) cc_final: 0.6767 (mttt) REVERT: E 419 ASN cc_start: 0.8601 (m110) cc_final: 0.8339 (m110) REVERT: G 529 ASN cc_start: 0.6988 (m-40) cc_final: 0.6314 (m-40) REVERT: H 529 ASN cc_start: 0.7269 (m-40) cc_final: 0.7051 (m-40) REVERT: K 416 ASP cc_start: 0.8084 (p0) cc_final: 0.7710 (p0) REVERT: K 453 ASP cc_start: 0.5753 (p0) cc_final: 0.5498 (p0) REVERT: K 529 ASN cc_start: 0.7985 (m-40) cc_final: 0.7677 (m110) REVERT: L 451 ARG cc_start: 0.7639 (ptm-80) cc_final: 0.7396 (ttp-110) REVERT: L 461 ARG cc_start: 0.7096 (mmm-85) cc_final: 0.6864 (mmm160) REVERT: L 515 TYR cc_start: 0.7130 (m-80) cc_final: 0.6860 (m-80) REVERT: J 48 ASN cc_start: 0.7599 (m-40) cc_final: 0.7358 (m-40) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.3429 time to fit residues: 203.4921 Evaluate side-chains 297 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 203 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 235 optimal weight: 30.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 339 ASN A 400 HIS A 529 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN D 385 GLN E 439 GLN E 490 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 545 ASN F 463 GLN F 529 ASN G 487 GLN G 493 GLN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN K 400 HIS ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 21291 Z= 0.392 Angle : 0.669 9.043 29089 Z= 0.349 Chirality : 0.049 0.451 3415 Planarity : 0.005 0.070 3712 Dihedral : 8.716 110.883 3075 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.99 % Allowed : 10.74 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.45 (0.16), residues: 2592 helix: -0.01 (0.23), residues: 487 sheet: 0.06 (0.19), residues: 733 loop : -0.52 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 382 HIS 0.011 0.001 HIS E 518 PHE 0.025 0.003 PHE E 354 TYR 0.026 0.002 TYR M 337 ARG 0.006 0.001 ARG C 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 318 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 402 ASN cc_start: 0.3459 (p0) cc_final: 0.3157 (m-40) REVERT: B 419 ASN cc_start: 0.8487 (m110) cc_final: 0.8242 (p0) REVERT: B 541 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: C 506 MET cc_start: 0.7953 (mtm) cc_final: 0.7658 (mtp) REVERT: E 419 ASN cc_start: 0.8687 (m110) cc_final: 0.8405 (m110) REVERT: F 529 ASN cc_start: 0.7068 (m110) cc_final: 0.6724 (m-40) REVERT: G 455 TYR cc_start: 0.7808 (m-80) cc_final: 0.6969 (m-80) REVERT: G 554 LYS cc_start: 0.7264 (mppt) cc_final: 0.7011 (mttt) REVERT: H 529 ASN cc_start: 0.7698 (m-40) cc_final: 0.7392 (m-40) REVERT: K 414 CYS cc_start: 0.7777 (t) cc_final: 0.7166 (m) REVERT: L 515 TYR cc_start: 0.7185 (m-80) cc_final: 0.6961 (m-80) outliers start: 47 outliers final: 32 residues processed: 346 average time/residue: 0.3621 time to fit residues: 184.7236 Evaluate side-chains 303 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 270 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 311 THR Chi-restraints excluded: chain M residue 331 ASP Chi-restraints excluded: chain M residue 427 ASP Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 350 ILE Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain L residue 571 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 195 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 235 optimal weight: 20.0000 chunk 254 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 233 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN B 395 ASN B 439 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN C 487 GLN D 385 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN K 400 HIS ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21291 Z= 0.294 Angle : 0.581 8.715 29089 Z= 0.300 Chirality : 0.046 0.478 3415 Planarity : 0.005 0.068 3712 Dihedral : 7.698 103.391 3075 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.54 % Allowed : 13.20 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.47 (0.16), residues: 2592 helix: 0.23 (0.23), residues: 493 sheet: -0.09 (0.19), residues: 719 loop : -0.55 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 382 HIS 0.009 0.001 HIS L 518 PHE 0.021 0.002 PHE M 346 TYR 0.020 0.001 TYR M 337 ARG 0.011 0.001 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 290 time to evaluate : 2.313 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 402 ASN cc_start: 0.3255 (p0) cc_final: 0.2978 (m-40) REVERT: A 554 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8033 (mtpp) REVERT: A 570 ASP cc_start: 0.7615 (t0) cc_final: 0.7386 (t0) REVERT: D 506 MET cc_start: 0.7575 (mtm) cc_final: 0.7374 (mtp) REVERT: E 419 ASN cc_start: 0.8734 (m110) cc_final: 0.8396 (m110) REVERT: G 364 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7313 (tppt) REVERT: G 455 TYR cc_start: 0.7878 (m-80) cc_final: 0.7015 (m-80) REVERT: H 529 ASN cc_start: 0.7886 (m-40) cc_final: 0.7642 (m-40) REVERT: K 414 CYS cc_start: 0.7830 (t) cc_final: 0.6925 (m) REVERT: K 553 ASP cc_start: 0.7420 (t0) cc_final: 0.7140 (t70) REVERT: L 515 TYR cc_start: 0.7251 (m-80) cc_final: 0.6889 (m-80) REVERT: L 519 SER cc_start: 0.7892 (OUTLIER) cc_final: 0.7119 (t) outliers start: 60 outliers final: 46 residues processed: 332 average time/residue: 0.3593 time to fit residues: 176.9398 Evaluate side-chains 304 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 257 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 331 ASP Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 427 ASP Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain G residue 406 SER Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 519 SER Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain L residue 571 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 250 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 529 ASN B 395 ASN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21291 Z= 0.240 Angle : 0.554 9.974 29089 Z= 0.284 Chirality : 0.045 0.462 3415 Planarity : 0.004 0.067 3712 Dihedral : 7.245 101.584 3075 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.13 % Allowed : 15.06 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.41 (0.16), residues: 2592 helix: 0.41 (0.24), residues: 491 sheet: -0.13 (0.19), residues: 730 loop : -0.52 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 382 HIS 0.028 0.001 HIS K 400 PHE 0.023 0.001 PHE M 346 TYR 0.029 0.001 TYR M 235 ARG 0.010 0.000 ARG M 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 287 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. REVERT: M 270 ILE cc_start: 0.7569 (mt) cc_final: 0.7353 (mt) REVERT: A 346 ARG cc_start: 0.5997 (tpm170) cc_final: 0.5553 (ptp-170) REVERT: A 402 ASN cc_start: 0.3173 (p0) cc_final: 0.2905 (m-40) REVERT: A 410 GLU cc_start: 0.6218 (tm-30) cc_final: 0.5864 (tm-30) REVERT: B 419 ASN cc_start: 0.8337 (m-40) cc_final: 0.8113 (p0) REVERT: D 562 TYR cc_start: 0.8057 (m-80) cc_final: 0.7834 (m-80) REVERT: E 419 ASN cc_start: 0.8714 (m110) cc_final: 0.8446 (m110) REVERT: G 455 TYR cc_start: 0.7872 (m-80) cc_final: 0.7143 (m-80) REVERT: G 467 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7406 (mmm-85) REVERT: H 529 ASN cc_start: 0.7968 (m-40) cc_final: 0.7717 (m110) REVERT: K 414 CYS cc_start: 0.7855 (t) cc_final: 0.7119 (m) REVERT: K 483 ASP cc_start: 0.7106 (t70) cc_final: 0.6497 (t0) REVERT: K 529 ASN cc_start: 0.8324 (m-40) cc_final: 0.8104 (m110) REVERT: K 553 ASP cc_start: 0.7534 (t0) cc_final: 0.7330 (t0) REVERT: L 515 TYR cc_start: 0.7230 (m-80) cc_final: 0.6810 (m-80) REVERT: L 519 SER cc_start: 0.7873 (m) cc_final: 0.7025 (t) outliers start: 74 outliers final: 56 residues processed: 341 average time/residue: 0.3741 time to fit residues: 188.5887 Evaluate side-chains 322 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 266 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 427 ASP Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain G residue 406 SER Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain J residue 12 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 186 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 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 393 HIS A 529 ASN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 518 HIS ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 400 HIS K 419 ASN ** K 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 529 ASN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 493 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21291 Z= 0.207 Angle : 0.547 11.334 29089 Z= 0.277 Chirality : 0.045 0.444 3415 Planarity : 0.004 0.086 3712 Dihedral : 6.865 100.315 3075 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.21 % Allowed : 16.20 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.33 (0.16), residues: 2592 helix: 0.54 (0.24), residues: 493 sheet: -0.12 (0.19), residues: 713 loop : -0.47 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 382 HIS 0.008 0.001 HIS K 430 PHE 0.019 0.001 PHE H 424 TYR 0.038 0.001 TYR M 235 ARG 0.011 0.000 ARG M 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 288 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 340 ILE cc_start: 0.6971 (tp) cc_final: 0.6717 (tp) REVERT: A 402 ASN cc_start: 0.3226 (p0) cc_final: 0.2952 (m-40) REVERT: C 358 PHE cc_start: 0.8309 (t80) cc_final: 0.7837 (t80) REVERT: E 419 ASN cc_start: 0.8688 (m110) cc_final: 0.8397 (m110) REVERT: E 553 ASP cc_start: 0.7332 (m-30) cc_final: 0.7090 (m-30) REVERT: F 551 THR cc_start: 0.8143 (m) cc_final: 0.7935 (t) REVERT: G 414 CYS cc_start: 0.5795 (OUTLIER) cc_final: 0.5269 (t) REVERT: G 455 TYR cc_start: 0.7787 (m-80) cc_final: 0.7006 (m-80) REVERT: H 375 TYR cc_start: 0.4154 (t80) cc_final: 0.3900 (t80) REVERT: H 529 ASN cc_start: 0.7991 (m-40) cc_final: 0.7735 (m110) REVERT: K 414 CYS cc_start: 0.7864 (t) cc_final: 0.7068 (m) REVERT: K 483 ASP cc_start: 0.7182 (t70) cc_final: 0.6634 (t0) REVERT: L 515 TYR cc_start: 0.7233 (m-80) cc_final: 0.6799 (m-80) outliers start: 76 outliers final: 60 residues processed: 347 average time/residue: 0.3657 time to fit residues: 191.0440 Evaluate side-chains 323 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 262 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 427 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 414 CYS Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain J residue 12 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 0.8980 chunk 225 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 490 GLN A 529 ASN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 400 HIS K 400 HIS ** K 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21291 Z= 0.219 Angle : 0.567 12.976 29089 Z= 0.286 Chirality : 0.045 0.433 3415 Planarity : 0.004 0.071 3712 Dihedral : 6.605 99.753 3075 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.68 % Allowed : 16.75 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.31 (0.16), residues: 2592 helix: 0.64 (0.24), residues: 492 sheet: -0.09 (0.19), residues: 729 loop : -0.50 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 382 HIS 0.008 0.001 HIS L 518 PHE 0.019 0.001 PHE G 405 TYR 0.038 0.001 TYR M 235 ARG 0.011 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 280 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. REVERT: M 300 ASN cc_start: 0.8404 (t0) cc_final: 0.8148 (t0) REVERT: M 340 ILE cc_start: 0.6981 (tp) cc_final: 0.6746 (tp) REVERT: A 402 ASN cc_start: 0.3230 (p0) cc_final: 0.2958 (m-40) REVERT: A 410 GLU cc_start: 0.6148 (tm-30) cc_final: 0.5811 (tm-30) REVERT: B 419 ASN cc_start: 0.8321 (m-40) cc_final: 0.8115 (p0) REVERT: C 358 PHE cc_start: 0.8325 (t80) cc_final: 0.7895 (t80) REVERT: D 506 MET cc_start: 0.7453 (mtm) cc_final: 0.7245 (mtp) REVERT: E 419 ASN cc_start: 0.8699 (m110) cc_final: 0.8412 (m110) REVERT: F 551 THR cc_start: 0.8151 (m) cc_final: 0.7938 (t) REVERT: G 414 CYS cc_start: 0.5873 (OUTLIER) cc_final: 0.5215 (t) REVERT: H 370 THR cc_start: -0.0521 (OUTLIER) cc_final: -0.0936 (p) REVERT: H 529 ASN cc_start: 0.8015 (m-40) cc_final: 0.7790 (m-40) REVERT: K 483 ASP cc_start: 0.7305 (t70) cc_final: 0.6798 (t0) REVERT: K 549 GLU cc_start: 0.7967 (pm20) cc_final: 0.7670 (pm20) REVERT: L 451 ARG cc_start: 0.8055 (ttp-110) cc_final: 0.7741 (ptm160) REVERT: L 515 TYR cc_start: 0.7271 (m-80) cc_final: 0.6792 (m-80) REVERT: L 519 SER cc_start: 0.7808 (m) cc_final: 0.7071 (t) outliers start: 87 outliers final: 68 residues processed: 345 average time/residue: 0.3387 time to fit residues: 175.7466 Evaluate side-chains 337 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 267 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 427 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 393 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 414 CYS Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain J residue 12 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 115 optimal weight: 0.0030 overall best weight: 2.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 326 GLN A 393 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN C 465 ASN E 487 GLN E 529 ASN F 463 GLN F 487 GLN ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 HIS ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 21291 Z= 0.448 Angle : 0.680 12.193 29089 Z= 0.351 Chirality : 0.049 0.482 3415 Planarity : 0.005 0.078 3712 Dihedral : 7.062 100.059 3075 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.10 % Allowed : 16.71 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.76 (0.16), residues: 2592 helix: 0.27 (0.23), residues: 490 sheet: -0.51 (0.18), residues: 735 loop : -0.71 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 382 HIS 0.015 0.001 HIS K 518 PHE 0.038 0.003 PHE G 405 TYR 0.043 0.002 TYR M 235 ARG 0.010 0.001 ARG C 461 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 294 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 300 ASN cc_start: 0.8466 (t0) cc_final: 0.8205 (t0) REVERT: A 402 ASN cc_start: 0.3078 (p0) cc_final: 0.2745 (m-40) REVERT: A 570 ASP cc_start: 0.7975 (t0) cc_final: 0.7715 (t0) REVERT: B 419 ASN cc_start: 0.8261 (m-40) cc_final: 0.8055 (p0) REVERT: B 518 HIS cc_start: 0.6392 (p90) cc_final: 0.6152 (p90) REVERT: D 350 ILE cc_start: 0.5696 (mm) cc_final: 0.5357 (mm) REVERT: D 568 MET cc_start: 0.7627 (mpp) cc_final: 0.7234 (mpp) REVERT: E 419 ASN cc_start: 0.8726 (m110) cc_final: 0.8394 (m110) REVERT: H 370 THR cc_start: -0.0453 (OUTLIER) cc_final: -0.0880 (p) REVERT: H 529 ASN cc_start: 0.7960 (m-40) cc_final: 0.7712 (m-40) REVERT: K 414 CYS cc_start: 0.8000 (t) cc_final: 0.7252 (m) REVERT: K 483 ASP cc_start: 0.7614 (t70) cc_final: 0.7218 (t0) REVERT: L 515 TYR cc_start: 0.7307 (m-80) cc_final: 0.6646 (m-80) REVERT: L 519 SER cc_start: 0.8022 (m) cc_final: 0.7320 (t) REVERT: L 553 ASP cc_start: 0.6806 (m-30) cc_final: 0.6527 (m-30) REVERT: J 4 ARG cc_start: 0.6843 (mmm-85) cc_final: 0.6342 (mtp180) REVERT: J 11 LYS cc_start: 0.7773 (tptt) cc_final: 0.7475 (mmtp) outliers start: 97 outliers final: 76 residues processed: 370 average time/residue: 0.3531 time to fit residues: 194.8483 Evaluate side-chains 348 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 271 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 331 ASP Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 427 ASP Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 393 HIS Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 480 SER Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain J residue 12 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.0470 chunk 158 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 400 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN F 463 GLN F 529 ASN ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21291 Z= 0.208 Angle : 0.586 12.703 29089 Z= 0.299 Chirality : 0.046 0.432 3415 Planarity : 0.004 0.079 3712 Dihedral : 6.547 99.157 3075 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.21 % Allowed : 17.89 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2592 helix: 0.44 (0.24), residues: 491 sheet: -0.38 (0.18), residues: 747 loop : -0.63 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 382 HIS 0.017 0.001 HIS L 518 PHE 0.015 0.002 PHE E 354 TYR 0.038 0.001 TYR M 235 ARG 0.012 0.001 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 290 time to evaluate : 2.236 Fit side-chains TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. REVERT: M 300 ASN cc_start: 0.8436 (t0) cc_final: 0.8183 (t0) REVERT: M 321 MET cc_start: 0.7820 (ttt) cc_final: 0.7461 (ptm) REVERT: A 402 ASN cc_start: 0.3154 (p0) cc_final: 0.2775 (m-40) REVERT: A 570 ASP cc_start: 0.7903 (t0) cc_final: 0.7665 (t0) REVERT: D 350 ILE cc_start: 0.5688 (mm) cc_final: 0.5357 (mm) REVERT: E 419 ASN cc_start: 0.8681 (m110) cc_final: 0.8416 (m110) REVERT: F 551 THR cc_start: 0.8336 (m) cc_final: 0.8120 (t) REVERT: H 370 THR cc_start: -0.0547 (OUTLIER) cc_final: -0.0966 (p) REVERT: H 529 ASN cc_start: 0.8065 (m-40) cc_final: 0.7840 (m-40) REVERT: H 567 VAL cc_start: 0.7725 (m) cc_final: 0.7478 (t) REVERT: K 414 CYS cc_start: 0.7951 (t) cc_final: 0.7059 (m) REVERT: K 483 ASP cc_start: 0.7467 (t70) cc_final: 0.7071 (t0) REVERT: K 491 ARG cc_start: 0.7914 (mpp-170) cc_final: 0.7525 (mpp-170) REVERT: L 453 ASP cc_start: 0.6581 (t0) cc_final: 0.6239 (t0) REVERT: L 515 TYR cc_start: 0.7260 (m-80) cc_final: 0.6752 (m-80) REVERT: L 534 TYR cc_start: 0.6971 (m-80) cc_final: 0.6734 (m-80) REVERT: J 117 TYR cc_start: 0.6368 (t80) cc_final: 0.6106 (t80) outliers start: 76 outliers final: 64 residues processed: 351 average time/residue: 0.3640 time to fit residues: 190.1495 Evaluate side-chains 334 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 269 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 427 ASP Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 393 HIS Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 480 SER Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 101 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.7980 chunk 239 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 182 optimal weight: 0.6980 chunk 71 optimal weight: 0.1980 chunk 210 optimal weight: 30.0000 chunk 220 optimal weight: 0.5980 chunk 231 optimal weight: 0.0070 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 400 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21291 Z= 0.177 Angle : 0.573 11.422 29089 Z= 0.292 Chirality : 0.045 0.403 3415 Planarity : 0.004 0.081 3712 Dihedral : 6.120 97.582 3075 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.92 % Allowed : 18.57 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.47 (0.16), residues: 2592 helix: 0.50 (0.24), residues: 490 sheet: -0.24 (0.18), residues: 749 loop : -0.58 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 382 HIS 0.012 0.001 HIS K 518 PHE 0.020 0.001 PHE H 424 TYR 0.036 0.001 TYR M 235 ARG 0.013 0.001 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 287 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 340 ILE cc_start: 0.7002 (tp) cc_final: 0.6778 (tp) REVERT: A 402 ASN cc_start: 0.3138 (p0) cc_final: 0.2765 (m-40) REVERT: A 570 ASP cc_start: 0.7752 (t0) cc_final: 0.7494 (t0) REVERT: B 451 ARG cc_start: 0.8283 (ptm-80) cc_final: 0.7973 (ptm-80) REVERT: D 350 ILE cc_start: 0.5548 (mm) cc_final: 0.5212 (mm) REVERT: D 506 MET cc_start: 0.7443 (mtm) cc_final: 0.7242 (mtp) REVERT: E 419 ASN cc_start: 0.8731 (m110) cc_final: 0.8465 (m110) REVERT: F 551 THR cc_start: 0.8238 (m) cc_final: 0.8025 (t) REVERT: G 414 CYS cc_start: 0.5873 (OUTLIER) cc_final: 0.5234 (t) REVERT: G 554 LYS cc_start: 0.6823 (mttt) cc_final: 0.6437 (mttp) REVERT: H 370 THR cc_start: -0.0554 (OUTLIER) cc_final: -0.0835 (p) REVERT: H 529 ASN cc_start: 0.8071 (m-40) cc_final: 0.7864 (m-40) REVERT: K 414 CYS cc_start: 0.7964 (t) cc_final: 0.7005 (m) REVERT: K 483 ASP cc_start: 0.7341 (t70) cc_final: 0.6918 (t0) REVERT: K 491 ARG cc_start: 0.7752 (mpp-170) cc_final: 0.7545 (mpp-170) REVERT: K 549 GLU cc_start: 0.7870 (pm20) cc_final: 0.7601 (pm20) REVERT: L 453 ASP cc_start: 0.6442 (t0) cc_final: 0.6232 (t0) REVERT: L 515 TYR cc_start: 0.7244 (m-80) cc_final: 0.6746 (m-80) REVERT: J 47 GLU cc_start: 0.7840 (mp0) cc_final: 0.7516 (mp0) REVERT: J 117 TYR cc_start: 0.6285 (t80) cc_final: 0.6015 (t80) REVERT: J 125 GLU cc_start: 0.7488 (tt0) cc_final: 0.7126 (tt0) outliers start: 69 outliers final: 59 residues processed: 340 average time/residue: 0.3528 time to fit residues: 180.0185 Evaluate side-chains 337 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 276 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 427 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 393 HIS Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 414 CYS Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 480 SER Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 101 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 0.9980 chunk 245 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 171 optimal weight: 0.2980 chunk 258 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 400 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21291 Z= 0.198 Angle : 0.574 8.966 29089 Z= 0.293 Chirality : 0.045 0.405 3415 Planarity : 0.004 0.078 3712 Dihedral : 5.950 96.855 3075 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.83 % Allowed : 18.82 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2592 helix: 0.57 (0.24), residues: 485 sheet: -0.19 (0.18), residues: 745 loop : -0.50 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 382 HIS 0.010 0.001 HIS K 518 PHE 0.025 0.001 PHE B 348 TYR 0.035 0.001 TYR M 235 ARG 0.013 0.001 ARG B 491 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 280 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 402 ASN cc_start: 0.3296 (p0) cc_final: 0.2956 (m-40) REVERT: A 570 ASP cc_start: 0.7699 (t0) cc_final: 0.7454 (t0) REVERT: B 451 ARG cc_start: 0.8290 (ptm-80) cc_final: 0.7990 (ptm-80) REVERT: D 350 ILE cc_start: 0.5546 (mm) cc_final: 0.5213 (mm) REVERT: D 506 MET cc_start: 0.7465 (mtm) cc_final: 0.7255 (mtp) REVERT: E 419 ASN cc_start: 0.8689 (m110) cc_final: 0.8424 (m110) REVERT: F 551 THR cc_start: 0.8270 (m) cc_final: 0.8047 (t) REVERT: H 370 THR cc_start: -0.0499 (OUTLIER) cc_final: -0.0808 (p) REVERT: H 529 ASN cc_start: 0.8079 (m-40) cc_final: 0.7857 (m-40) REVERT: K 414 CYS cc_start: 0.7971 (t) cc_final: 0.6999 (m) REVERT: K 483 ASP cc_start: 0.7321 (t70) cc_final: 0.6889 (t0) REVERT: K 491 ARG cc_start: 0.7754 (mpp-170) cc_final: 0.7532 (mpp-170) REVERT: L 453 ASP cc_start: 0.6584 (t0) cc_final: 0.6316 (t0) REVERT: L 515 TYR cc_start: 0.7264 (m-80) cc_final: 0.6733 (m-80) REVERT: L 534 TYR cc_start: 0.6792 (m-80) cc_final: 0.6556 (m-80) REVERT: J 125 GLU cc_start: 0.7511 (tt0) cc_final: 0.7141 (tt0) outliers start: 67 outliers final: 62 residues processed: 332 average time/residue: 0.3655 time to fit residues: 179.8242 Evaluate side-chains 335 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 272 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 276 MET Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 427 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 393 HIS Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 480 SER Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 529 ASN Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 101 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 20.0000 chunk 218 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 57 optimal weight: 0.6980 chunk 205 optimal weight: 0.0010 chunk 86 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 400 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.190660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.133871 restraints weight = 30879.800| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.03 r_work: 0.3536 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21291 Z= 0.221 Angle : 0.585 10.107 29089 Z= 0.298 Chirality : 0.045 0.411 3415 Planarity : 0.005 0.081 3712 Dihedral : 5.900 96.420 3075 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.92 % Allowed : 18.99 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2592 helix: 0.59 (0.24), residues: 485 sheet: -0.22 (0.18), residues: 757 loop : -0.49 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 382 HIS 0.020 0.001 HIS L 518 PHE 0.024 0.001 PHE B 348 TYR 0.036 0.001 TYR M 235 ARG 0.013 0.001 ARG B 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4854.66 seconds wall clock time: 88 minutes 57.40 seconds (5337.40 seconds total)