Starting phenix.real_space_refine on Sat Sep 28 05:23:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vym_43667/09_2024/8vym_43667.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vym_43667/09_2024/8vym_43667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vym_43667/09_2024/8vym_43667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vym_43667/09_2024/8vym_43667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vym_43667/09_2024/8vym_43667.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vym_43667/09_2024/8vym_43667.cif" } resolution = 3.4 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 11520 2.51 5 N 3040 2.21 5 O 3656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18289 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3591 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 431} Chain breaks: 6 Chain: "B" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3461 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 414} Chain breaks: 6 Chain: "C" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3574 Classifications: {'peptide': 440} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 429} Chain breaks: 6 Chain: "D" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 944 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "F" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "G" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 944 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 802 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "J" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 944 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "K" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1017 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" 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: "T" 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: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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: "Y" 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: "Z" 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: 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.89, per 1000 atoms: 0.70 Number of scatterers: 18289 At special positions: 0 Unit cell: (139.978, 142.477, 154.142, 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 73 16.00 O 3656 8.00 N 3040 7.00 C 11520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 250 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 507 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 250 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 391 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 801 " - " ASN A 341 " " NAG A 802 " - " ASN A 409 " " NAG A 803 " - " ASN A 417 " " NAG A 804 " - " ASN A 405 " " NAG B 801 " - " ASN B 286 " " NAG B 802 " - " ASN B 341 " " NAG B 803 " - " ASN B 409 " " NAG B 804 " - " ASN B 405 " " NAG C 801 " - " ASN C 341 " " NAG C 802 " - " ASN C 409 " " NAG L 1 " - " ASN A 281 " " NAG M 1 " - " ASN A 286 " " NAG N 1 " - " ASN A 383 " " NAG O 1 " - " ASN A 302 " " NAG P 1 " - " ASN A 208 " " NAG Q 1 " - " ASN B 281 " " NAG R 1 " - " ASN B 383 " " NAG S 1 " - " ASN B 302 " " NAG T 1 " - " ASN B 417 " " NAG U 1 " - " ASN B 208 " " NAG V 1 " - " ASN C 208 " " NAG W 1 " - " ASN C 281 " " NAG X 1 " - " ASN C 286 " " NAG Y 1 " - " ASN C 302 " " NAG Z 1 " - " ASN C 383 " " NAG a 1 " - " ASN C 417 " Time building additional restraints: 5.13 Conformation dependent library (CDL) restraints added in 2.2 seconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4186 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 45 sheets defined 17.0% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.542A pdb=" N LEU A 389 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 407 Processing helix chain 'A' and resid 479 through 524 removed outlier: 3.561A pdb=" N GLU A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.556A pdb=" N ILE A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 675 Processing helix chain 'A' and resid 679 through 694 removed outlier: 3.557A pdb=" N VAL A 694 " --> pdb=" O TYR A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 338 through 342 removed outlier: 3.547A pdb=" N ASN B 341 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 408 removed outlier: 3.661A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 522 removed outlier: 4.044A pdb=" N ALA B 500 " --> pdb=" O ASN B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 668 through 674 Processing helix chain 'B' and resid 679 through 692 Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 392 through 405 Processing helix chain 'C' and resid 479 through 522 removed outlier: 4.207A pdb=" N GLN C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 668 through 675 Processing helix chain 'C' and resid 679 through 692 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 27A through 30 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.759A pdb=" N GLU H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 352 removed outlier: 5.473A pdb=" N PHE A 348 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LYS A 130 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 352 removed outlier: 5.473A pdb=" N PHE A 348 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LYS A 130 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 169 Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 215 removed outlier: 6.900A pdb=" N LYS A 139 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASP A 335 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 306 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 318 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG A 320 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 186 Processing sheet with id=AA6, first strand: chain 'A' and resid 188 through 191 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 359 removed outlier: 3.871A pdb=" N PHE A 375 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 540 Processing sheet with id=AA9, first strand: chain 'B' and resid 373 through 378 removed outlier: 3.745A pdb=" N PHE B 375 " --> pdb=" O PHE B 366 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHE B 348 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS B 130 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 354 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLY B 124 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 356 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASP B 122 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 13.579A pdb=" N LEU B 121 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N GLN B 436 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU B 123 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLY B 433 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ASN B 417 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS B 435 " --> pdb=" O TYR B 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR B 415 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AB2, first strand: chain 'B' and resid 167 through 169 removed outlier: 7.000A pdb=" N LYS B 139 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASP B 335 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR B 318 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR B 304 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG B 320 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 184 through 185 Processing sheet with id=AB4, first strand: chain 'B' and resid 540 through 541 removed outlier: 3.545A pdb=" N GLY B 547 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 373 through 377 removed outlier: 5.505A pdb=" N PHE C 348 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS C 130 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 354 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY C 124 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU C 123 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 373 through 377 removed outlier: 5.505A pdb=" N PHE C 348 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS C 130 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 354 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY C 124 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU C 123 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 165 through 169 Processing sheet with id=AB8, first strand: chain 'C' and resid 223 through 224 removed outlier: 6.840A pdb=" N LYS C 139 " --> pdb=" O ASP C 335 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP C 335 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU C 316 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C 306 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR C 318 " --> pdb=" O THR C 304 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR C 304 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG C 320 " --> pdb=" O ASN C 302 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AC1, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AC2, first strand: chain 'C' and resid 214 through 215 Processing sheet with id=AC3, first strand: chain 'C' and resid 538 through 541 removed outlier: 4.208A pdb=" N ALA C 538 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.718A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN D 50 " --> pdb=" O TRP D 35A" (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP D 35A" --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR D 35 " --> pdb=" O ARG D 95 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.718A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN D 50 " --> pdb=" O TRP D 35A" (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP D 35A" --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR D 35 " --> pdb=" O ARG D 95 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.548A pdb=" N ALA E 11 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.548A pdb=" N ALA E 11 " --> pdb=" O THR E 105 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AD1, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.230A pdb=" N ALA F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.230A pdb=" N ALA F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR F 90 " --> pdb=" O VAL F 97 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.653A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP G 35A" --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR G 35 " --> pdb=" O ARG G 95 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.653A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP G 35A" --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR G 35 " --> pdb=" O ARG G 95 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 9 through 11 Processing sheet with id=AD8, first strand: chain 'H' and resid 18 through 24 Processing sheet with id=AD9, first strand: chain 'H' and resid 45 through 48 removed outlier: 6.269A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.428A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 9 through 12 Processing sheet with id=AE3, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.666A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP J 35A" --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR J 102 " --> pdb=" O THR J 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.666A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP J 35A" --> pdb=" O ASN J 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.653A pdb=" N TYR K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.769A pdb=" N VAL K 102 " --> pdb=" O LYS K 94 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER K 96 " --> pdb=" O MET K 100M" (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET K 100M" --> pdb=" O SER K 96 " (cutoff:3.500A) 815 hydrogen bonds defined for protein. 2103 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: 6.41 Time building geometry restraints manager: 5.87 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: 5741 1.34 - 1.46: 4343 1.46 - 1.58: 8497 1.58 - 1.70: 0 1.70 - 1.81: 112 Bond restraints: 18693 Sorted by residual: bond pdb=" C ASP C 122 " pdb=" O ASP C 122 " ideal model delta sigma weight residual 1.235 1.227 0.008 1.22e-02 6.72e+03 4.02e-01 bond pdb=" C LYS A 518 " pdb=" O LYS A 518 " ideal model delta sigma weight residual 1.236 1.244 -0.007 1.15e-02 7.56e+03 3.72e-01 bond pdb=" N ASP D 100A" pdb=" CA ASP D 100A" ideal model delta sigma weight residual 1.457 1.465 -0.008 1.29e-02 6.01e+03 3.57e-01 bond pdb=" C ARG C 511 " pdb=" O ARG C 511 " ideal model delta sigma weight residual 1.236 1.243 -0.007 1.15e-02 7.56e+03 3.53e-01 bond pdb=" C TRP J 36 " pdb=" O TRP J 36 " ideal model delta sigma weight residual 1.236 1.243 -0.007 1.20e-02 6.94e+03 3.40e-01 ... (remaining 18688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 24530 1.03 - 2.06: 634 2.06 - 3.09: 146 3.09 - 4.12: 41 4.12 - 5.15: 6 Bond angle restraints: 25357 Sorted by residual: angle pdb=" C TRP J 35A" pdb=" N GLY J 35B" pdb=" CA GLY J 35B" ideal model delta sigma weight residual 121.03 117.05 3.98 1.51e+00 4.39e-01 6.94e+00 angle pdb=" N PHE D 100 " pdb=" CA PHE D 100 " pdb=" C PHE D 100 " ideal model delta sigma weight residual 110.80 115.62 -4.82 2.13e+00 2.20e-01 5.12e+00 angle pdb=" C ASN B 281 " pdb=" N GLY B 282 " pdb=" CA GLY B 282 " ideal model delta sigma weight residual 121.41 117.09 4.32 1.96e+00 2.60e-01 4.87e+00 angle pdb=" C SER B 438 " pdb=" N LEU B 439 " pdb=" CA LEU B 439 " ideal model delta sigma weight residual 121.54 125.75 -4.21 1.91e+00 2.74e-01 4.85e+00 angle pdb=" C ASN B 284 " pdb=" N ARG B 285 " pdb=" CA ARG B 285 " ideal model delta sigma weight residual 121.66 117.88 3.78 1.76e+00 3.23e-01 4.61e+00 ... (remaining 25352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 10933 16.76 - 33.52: 548 33.52 - 50.27: 89 50.27 - 67.03: 75 67.03 - 83.79: 5 Dihedral angle restraints: 11650 sinusoidal: 5146 harmonic: 6504 Sorted by residual: dihedral pdb=" CA TYR C 261 " pdb=" C TYR C 261 " pdb=" N PRO C 262 " pdb=" CA PRO C 262 " ideal model delta harmonic sigma weight residual 0.00 18.04 -18.04 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASN B 208 " pdb=" CB ASN B 208 " pdb=" CG ASN B 208 " pdb=" OD1 ASN B 208 " ideal model delta sinusoidal sigma weight residual 120.00 -176.98 -63.02 2 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CA ARG B 662 " pdb=" CB ARG B 662 " pdb=" CG ARG B 662 " pdb=" CD ARG B 662 " ideal model delta sinusoidal sigma weight residual -60.00 -119.06 59.06 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 11647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2496 0.056 - 0.113: 354 0.113 - 0.169: 56 0.169 - 0.226: 3 0.226 - 0.282: 2 Chirality restraints: 2911 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 208 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN B 208 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN C 208 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2908 not shown) Planarity restraints: 3201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 331 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" C VAL A 331 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL A 331 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 332 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 479 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C LEU B 479 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU B 479 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 480 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 267 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ALA C 267 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA C 267 " 0.014 2.00e-02 2.50e+03 pdb=" N THR C 268 " 0.013 2.00e-02 2.50e+03 ... (remaining 3198 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2679 2.76 - 3.30: 16707 3.30 - 3.83: 30121 3.83 - 4.37: 34890 4.37 - 4.90: 61506 Nonbonded interactions: 145903 Sorted by model distance: nonbonded pdb=" O LYS B 518 " pdb=" OG SER B 521 " model vdw 2.230 3.040 nonbonded pdb=" ND2 ASN D 97 " pdb=" OD2 ASP D 101 " model vdw 2.239 3.120 nonbonded pdb=" NE2 HIS K 35 " pdb=" OD2 ASP K 95 " model vdw 2.239 3.120 nonbonded pdb=" O ASN B 284 " pdb=" OG SER B 288 " model vdw 2.241 3.040 nonbonded pdb=" O ASP G 30 " pdb=" OG1 THR G 33 " model vdw 2.255 3.040 ... (remaining 145898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 103 through 147 or resid 165 through 190 or resid 198 thro \ ugh 438 or resid 470 or resid 474 or resid 476 through 548 or resid 550 through \ 640 or resid 642 through 693 or resid 803 through 804)) selection = (chain 'B' and (resid 103 through 113 or resid 120 through 229 or resid 244 thro \ ugh 439 or resid 441 through 548 or resid 640 through 693 or resid 803 through 8 \ 04)) selection = (chain 'C' and (resid 103 through 147 or resid 165 through 190 or resid 198 thro \ ugh 438 or resid 470 or resid 474 or resid 476 through 548 or resid 550 or resid \ 640 or resid 642 through 693 or resid 801 through 802)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'R' selection = chain 'V' selection = chain 'W' } 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: 17.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 1.380 Set scattering table: 0.000 Process input model: 44.460 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18693 Z= 0.114 Angle : 0.442 5.151 25357 Z= 0.237 Chirality : 0.042 0.282 2911 Planarity : 0.004 0.051 3175 Dihedral : 11.249 83.789 7413 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 0.66 % Allowed : 4.03 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: -0.34 (0.18), residues: 2160 helix: 1.78 (0.28), residues: 306 sheet: 0.10 (0.21), residues: 650 loop : -0.95 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 47 HIS 0.002 0.000 HIS B 365 PHE 0.016 0.001 PHE D 100 TYR 0.015 0.001 TYR F 49 ARG 0.012 0.000 ARG B 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 465 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7548 (tp) cc_final: 0.7189 (tt) REVERT: A 184 GLN cc_start: 0.8527 (mt0) cc_final: 0.8195 (mm110) REVERT: A 407 SER cc_start: 0.8887 (m) cc_final: 0.8653 (p) REVERT: B 184 GLN cc_start: 0.7098 (mm-40) cc_final: 0.6796 (mm-40) REVERT: B 186 TYR cc_start: 0.6463 (m-80) cc_final: 0.6178 (m-80) REVERT: B 412 TYR cc_start: 0.8502 (m-80) cc_final: 0.8283 (m-80) REVERT: B 545 VAL cc_start: 0.8609 (p) cc_final: 0.8323 (p) REVERT: C 217 ASP cc_start: 0.8050 (t0) cc_final: 0.7674 (t70) REVERT: C 436 GLN cc_start: 0.8076 (mt0) cc_final: 0.7774 (mt0) REVERT: C 542 MET cc_start: 0.7211 (ptp) cc_final: 0.6497 (ptm) REVERT: C 687 PHE cc_start: 0.8215 (t80) cc_final: 0.7219 (m-10) REVERT: C 691 LYS cc_start: 0.8254 (mtmt) cc_final: 0.7877 (mttp) REVERT: D 108 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6975 (mt) REVERT: E 21 ILE cc_start: 0.8515 (mt) cc_final: 0.8213 (tp) REVERT: E 92 ASP cc_start: 0.8275 (t70) cc_final: 0.8041 (t0) REVERT: E 96 TRP cc_start: 0.8818 (t-100) cc_final: 0.8477 (t-100) REVERT: F 87 TYR cc_start: 0.8817 (m-80) cc_final: 0.8288 (m-80) REVERT: I 79 ARG cc_start: 0.7560 (mmt90) cc_final: 0.7324 (mmt90) REVERT: I 87 TYR cc_start: 0.8614 (m-80) cc_final: 0.8371 (m-80) REVERT: J 70 SER cc_start: 0.8124 (p) cc_final: 0.7776 (t) REVERT: K 12 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8468 (mmmt) REVERT: K 19 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7935 (tttm) REVERT: K 62 ASN cc_start: 0.8755 (t0) cc_final: 0.8481 (t0) REVERT: K 68 THR cc_start: 0.8122 (m) cc_final: 0.7863 (p) REVERT: K 77 THR cc_start: 0.8783 (m) cc_final: 0.8482 (p) REVERT: K 84 SER cc_start: 0.8878 (m) cc_final: 0.8612 (t) outliers start: 13 outliers final: 1 residues processed: 475 average time/residue: 0.3549 time to fit residues: 241.6339 Evaluate side-chains 326 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 324 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 202 HIS A 264 HIS A 380 GLN A 669 GLN B 178 HIS B 202 HIS B 222 HIS B 380 GLN B 510 GLN B 669 GLN C 136 HIS C 202 HIS C 380 GLN C 669 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN E 17 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 37 GLN F 53 GLN H 6 GLN H 38 GLN H 51 ASN I 37 GLN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN K 3 GLN K 39 GLN K 64 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 18693 Z= 0.422 Angle : 0.632 7.980 25357 Z= 0.334 Chirality : 0.047 0.394 2911 Planarity : 0.005 0.076 3175 Dihedral : 8.442 58.117 3380 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.79 % Rotamer: Outliers : 2.40 % Allowed : 9.60 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: -0.14 (0.18), residues: 2160 helix: 2.26 (0.26), residues: 308 sheet: 0.15 (0.21), residues: 632 loop : -0.85 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 47 HIS 0.005 0.001 HIS B 177 PHE 0.022 0.002 PHE J 99 TYR 0.036 0.002 TYR E 49 ARG 0.007 0.001 ARG B 685 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 320 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7448 (tp) cc_final: 0.7153 (tt) REVERT: A 184 GLN cc_start: 0.8507 (mt0) cc_final: 0.8155 (mm110) REVERT: A 407 SER cc_start: 0.8891 (m) cc_final: 0.8605 (p) REVERT: A 517 PHE cc_start: 0.8371 (m-10) cc_final: 0.8134 (m-10) REVERT: A 648 MET cc_start: 0.8596 (tpt) cc_final: 0.8249 (tpt) REVERT: B 384 MET cc_start: 0.9093 (tpp) cc_final: 0.8642 (tpt) REVERT: B 646 ASP cc_start: 0.8617 (p0) cc_final: 0.8395 (p0) REVERT: C 542 MET cc_start: 0.7160 (ptp) cc_final: 0.5794 (tpt) REVERT: C 687 PHE cc_start: 0.8336 (t80) cc_final: 0.6808 (m-10) REVERT: D 82 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7574 (mtm180) REVERT: D 108 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7106 (mt) REVERT: E 21 ILE cc_start: 0.8551 (mt) cc_final: 0.8260 (tp) REVERT: E 51 ASN cc_start: 0.8081 (m-40) cc_final: 0.7827 (m110) REVERT: E 66 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7336 (ttpt) REVERT: E 92 ASP cc_start: 0.8331 (t70) cc_final: 0.8112 (t70) REVERT: E 96 TRP cc_start: 0.8893 (t-100) cc_final: 0.8573 (t-100) REVERT: F 85 GLU cc_start: 0.8335 (tt0) cc_final: 0.7909 (tt0) REVERT: F 87 TYR cc_start: 0.8758 (m-80) cc_final: 0.8006 (m-80) REVERT: G 64 LYS cc_start: 0.8018 (tttp) cc_final: 0.7797 (tttp) REVERT: I 27 ASN cc_start: 0.7707 (t0) cc_final: 0.7171 (t0) REVERT: I 29 GLU cc_start: 0.7659 (tt0) cc_final: 0.7426 (tt0) REVERT: I 87 TYR cc_start: 0.8681 (m-80) cc_final: 0.8287 (m-80) REVERT: J 70 SER cc_start: 0.8188 (p) cc_final: 0.7831 (m) outliers start: 47 outliers final: 29 residues processed: 348 average time/residue: 0.3388 time to fit residues: 170.7647 Evaluate side-chains 315 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 285 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 39 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 157 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 184 GLN A 432 GLN C 264 HIS D 50 ASN E 17 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 53 GLN I 51 ASN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 64 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18693 Z= 0.320 Angle : 0.564 7.577 25357 Z= 0.297 Chirality : 0.046 0.316 2911 Planarity : 0.004 0.070 3175 Dihedral : 7.786 59.530 3380 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.40 % Allowed : 11.75 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: -0.02 (0.18), residues: 2160 helix: 2.43 (0.26), residues: 306 sheet: 0.30 (0.21), residues: 611 loop : -0.81 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 47 HIS 0.003 0.001 HIS B 178 PHE 0.021 0.002 PHE A 687 TYR 0.024 0.001 TYR E 49 ARG 0.008 0.001 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 296 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7355 (tp) cc_final: 0.7091 (tt) REVERT: A 184 GLN cc_start: 0.8488 (mt0) cc_final: 0.8130 (mm110) REVERT: A 407 SER cc_start: 0.8869 (m) cc_final: 0.8556 (p) REVERT: A 517 PHE cc_start: 0.8348 (m-10) cc_final: 0.8126 (m-10) REVERT: A 648 MET cc_start: 0.8582 (tpt) cc_final: 0.7822 (tpt) REVERT: A 687 PHE cc_start: 0.8238 (t80) cc_final: 0.8021 (t80) REVERT: B 184 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7449 (mm110) REVERT: B 384 MET cc_start: 0.9111 (tpp) cc_final: 0.8681 (tpt) REVERT: C 542 MET cc_start: 0.7123 (ptp) cc_final: 0.5751 (tpt) REVERT: C 687 PHE cc_start: 0.8363 (t80) cc_final: 0.6791 (m-10) REVERT: D 66 ARG cc_start: 0.8516 (mtm110) cc_final: 0.8216 (ttp-170) REVERT: D 82 ARG cc_start: 0.7871 (mtm110) cc_final: 0.7096 (mtm180) REVERT: D 108 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7111 (mt) REVERT: E 21 ILE cc_start: 0.8578 (mt) cc_final: 0.8233 (tp) REVERT: E 38 GLN cc_start: 0.7967 (tt0) cc_final: 0.7680 (pt0) REVERT: E 92 ASP cc_start: 0.8321 (t70) cc_final: 0.8104 (t70) REVERT: E 96 TRP cc_start: 0.8928 (t-100) cc_final: 0.8525 (t-100) REVERT: F 54 ARG cc_start: 0.8640 (mtm110) cc_final: 0.8414 (mtm110) REVERT: G 64 LYS cc_start: 0.8061 (tttp) cc_final: 0.7792 (tttp) REVERT: G 66 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7830 (mtp85) REVERT: G 105 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7387 (mtm110) REVERT: H 48 MET cc_start: 0.8319 (mmt) cc_final: 0.8055 (mmm) REVERT: J 70 SER cc_start: 0.8163 (p) cc_final: 0.7796 (m) REVERT: J 91 TYR cc_start: 0.8288 (m-80) cc_final: 0.8009 (m-80) REVERT: J 100 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7521 (t0) outliers start: 47 outliers final: 31 residues processed: 328 average time/residue: 0.3530 time to fit residues: 167.9866 Evaluate side-chains 314 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 281 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 48 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 197 optimal weight: 0.0060 chunk 208 optimal weight: 0.0670 chunk 103 optimal weight: 10.0000 chunk 186 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 overall best weight: 0.8316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS E 17 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN F 6 GLN F 53 GLN I 51 ASN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18693 Z= 0.235 Angle : 0.532 7.347 25357 Z= 0.278 Chirality : 0.044 0.283 2911 Planarity : 0.004 0.052 3175 Dihedral : 7.343 59.872 3379 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.20 % Allowed : 12.26 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.11 (0.18), residues: 2160 helix: 2.57 (0.27), residues: 307 sheet: 0.40 (0.21), residues: 608 loop : -0.76 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 47 HIS 0.006 0.001 HIS B 178 PHE 0.016 0.001 PHE G 78 TYR 0.025 0.001 TYR E 49 ARG 0.016 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 298 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7311 (tp) cc_final: 0.7053 (tt) REVERT: A 184 GLN cc_start: 0.8495 (mt0) cc_final: 0.8113 (mm110) REVERT: A 362 ASP cc_start: 0.9065 (t0) cc_final: 0.8379 (m-30) REVERT: A 407 SER cc_start: 0.8817 (m) cc_final: 0.8497 (p) REVERT: A 517 PHE cc_start: 0.8292 (m-10) cc_final: 0.8076 (m-10) REVERT: A 687 PHE cc_start: 0.8246 (t80) cc_final: 0.8022 (t80) REVERT: B 184 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7264 (mm-40) REVERT: B 384 MET cc_start: 0.9089 (tpp) cc_final: 0.8664 (tpt) REVERT: B 646 ASP cc_start: 0.8623 (p0) cc_final: 0.8420 (p0) REVERT: C 542 MET cc_start: 0.7029 (ptp) cc_final: 0.5692 (tpt) REVERT: C 687 PHE cc_start: 0.8357 (t80) cc_final: 0.6731 (m-10) REVERT: D 59 TYR cc_start: 0.7553 (m-80) cc_final: 0.7227 (m-80) REVERT: D 66 ARG cc_start: 0.8490 (mtm110) cc_final: 0.8209 (ttp-170) REVERT: D 82 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7096 (mtm180) REVERT: D 108 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7118 (mt) REVERT: E 21 ILE cc_start: 0.8551 (mt) cc_final: 0.8244 (tp) REVERT: E 31 ASN cc_start: 0.8513 (m110) cc_final: 0.8174 (m110) REVERT: E 38 GLN cc_start: 0.7906 (tt0) cc_final: 0.7647 (pt0) REVERT: E 61 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7698 (mtm110) REVERT: E 79 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7768 (mtm180) REVERT: E 96 TRP cc_start: 0.8931 (t-100) cc_final: 0.8347 (t-100) REVERT: F 54 ARG cc_start: 0.8660 (mtm110) cc_final: 0.8453 (mtm110) REVERT: F 81 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8342 (tm-30) REVERT: G 5 GLN cc_start: 0.8717 (tt0) cc_final: 0.8383 (tm-30) REVERT: G 64 LYS cc_start: 0.8153 (tttp) cc_final: 0.7870 (tttp) REVERT: G 72 ASP cc_start: 0.7115 (t0) cc_final: 0.6549 (t0) REVERT: G 89 VAL cc_start: 0.8755 (m) cc_final: 0.8461 (p) REVERT: H 48 MET cc_start: 0.8253 (mmt) cc_final: 0.7961 (mmm) REVERT: I 27 ASN cc_start: 0.7653 (t0) cc_final: 0.6881 (t0) REVERT: I 87 TYR cc_start: 0.8786 (m-80) cc_final: 0.8412 (m-80) REVERT: J 70 SER cc_start: 0.8198 (p) cc_final: 0.7834 (m) REVERT: J 91 TYR cc_start: 0.8291 (m-80) cc_final: 0.8065 (m-80) REVERT: J 100 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7426 (t0) REVERT: K 3 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8052 (pp30) REVERT: K 100 TYR cc_start: 0.8939 (m-80) cc_final: 0.8728 (m-80) outliers start: 43 outliers final: 31 residues processed: 324 average time/residue: 0.3436 time to fit residues: 161.6938 Evaluate side-chains 314 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 280 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS C 469 HIS E 17 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN F 6 GLN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 18693 Z= 0.433 Angle : 0.605 9.116 25357 Z= 0.317 Chirality : 0.047 0.419 2911 Planarity : 0.004 0.061 3175 Dihedral : 7.516 57.264 3379 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.06 % Allowed : 11.70 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: -0.15 (0.18), residues: 2160 helix: 2.07 (0.27), residues: 313 sheet: 0.25 (0.20), residues: 627 loop : -0.89 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 47 HIS 0.008 0.001 HIS B 178 PHE 0.018 0.002 PHE G 78 TYR 0.022 0.002 TYR E 49 ARG 0.010 0.001 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 297 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8061 (m-30) cc_final: 0.7744 (m-30) REVERT: A 147 LEU cc_start: 0.7294 (tp) cc_final: 0.7052 (tt) REVERT: A 184 GLN cc_start: 0.8512 (mt0) cc_final: 0.8051 (mm110) REVERT: A 407 SER cc_start: 0.8875 (m) cc_final: 0.8516 (p) REVERT: A 517 PHE cc_start: 0.8325 (m-10) cc_final: 0.8100 (m-10) REVERT: A 687 PHE cc_start: 0.8278 (t80) cc_final: 0.7970 (t80) REVERT: B 184 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7420 (mm-40) REVERT: B 227 VAL cc_start: 0.8870 (m) cc_final: 0.8520 (p) REVERT: B 534 ASN cc_start: 0.7962 (t0) cc_final: 0.7577 (t0) REVERT: C 358 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8710 (p) REVERT: C 432 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8079 (tp40) REVERT: C 542 MET cc_start: 0.7060 (ptp) cc_final: 0.5706 (tpt) REVERT: C 687 PHE cc_start: 0.8401 (t80) cc_final: 0.6724 (m-10) REVERT: D 66 ARG cc_start: 0.8451 (mtm110) cc_final: 0.8077 (ttp-170) REVERT: D 108 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7245 (mt) REVERT: E 21 ILE cc_start: 0.8599 (mt) cc_final: 0.8201 (tp) REVERT: E 31 ASN cc_start: 0.8577 (m110) cc_final: 0.8229 (m110) REVERT: E 38 GLN cc_start: 0.8004 (tt0) cc_final: 0.7688 (pt0) REVERT: E 79 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7774 (mtm180) REVERT: E 96 TRP cc_start: 0.8987 (t-100) cc_final: 0.8398 (t-100) REVERT: F 81 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8320 (tm-30) REVERT: F 94 ASN cc_start: 0.9045 (t0) cc_final: 0.8817 (t0) REVERT: G 66 ARG cc_start: 0.8224 (mtp85) cc_final: 0.8007 (mtp85) REVERT: G 72 ASP cc_start: 0.7201 (t0) cc_final: 0.6705 (t0) REVERT: G 76 ASN cc_start: 0.8653 (t0) cc_final: 0.8248 (t0) REVERT: J 38 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8369 (ptm160) REVERT: J 70 SER cc_start: 0.8084 (p) cc_final: 0.7734 (m) REVERT: K 3 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8117 (pp30) REVERT: K 64 GLN cc_start: 0.8455 (tp40) cc_final: 0.7802 (mm110) outliers start: 60 outliers final: 41 residues processed: 334 average time/residue: 0.3296 time to fit residues: 161.6682 Evaluate side-chains 326 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 281 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain G residue 1 GLN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 122 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 208 optimal weight: 0.4980 chunk 173 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 264 HIS E 17 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN F 6 GLN F 53 GLN I 38 GLN J 39 GLN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18693 Z= 0.189 Angle : 0.521 6.949 25357 Z= 0.272 Chirality : 0.044 0.372 2911 Planarity : 0.004 0.046 3175 Dihedral : 7.204 59.987 3379 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.84 % Allowed : 13.64 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.08 (0.18), residues: 2160 helix: 2.55 (0.27), residues: 307 sheet: 0.38 (0.21), residues: 617 loop : -0.78 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 174 HIS 0.004 0.001 HIS B 178 PHE 0.013 0.001 PHE A 266 TYR 0.026 0.001 TYR E 49 ARG 0.010 0.000 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 291 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7315 (tp) cc_final: 0.7103 (tt) REVERT: A 184 GLN cc_start: 0.8496 (mt0) cc_final: 0.7968 (mm110) REVERT: A 361 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8294 (pm20) REVERT: A 407 SER cc_start: 0.8739 (m) cc_final: 0.8425 (p) REVERT: A 687 PHE cc_start: 0.8261 (t80) cc_final: 0.8005 (t80) REVERT: B 384 MET cc_start: 0.9269 (tpt) cc_final: 0.8659 (tpt) REVERT: B 534 ASN cc_start: 0.7888 (t0) cc_final: 0.7530 (t0) REVERT: B 545 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8600 (m) REVERT: C 542 MET cc_start: 0.7006 (ptp) cc_final: 0.5645 (tpt) REVERT: C 687 PHE cc_start: 0.8375 (t80) cc_final: 0.6683 (m-10) REVERT: D 82 ARG cc_start: 0.7858 (mtm110) cc_final: 0.7220 (mtm180) REVERT: D 108 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7218 (mt) REVERT: E 21 ILE cc_start: 0.8583 (mt) cc_final: 0.8176 (tp) REVERT: E 79 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7703 (mtm180) REVERT: E 96 TRP cc_start: 0.8914 (t-100) cc_final: 0.8333 (t-100) REVERT: F 54 ARG cc_start: 0.8700 (mtm110) cc_final: 0.8498 (mtm110) REVERT: F 81 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8349 (tm-30) REVERT: F 94 ASN cc_start: 0.9013 (t0) cc_final: 0.8812 (t0) REVERT: G 5 GLN cc_start: 0.8892 (tt0) cc_final: 0.8553 (tm-30) REVERT: H 48 MET cc_start: 0.8182 (mmt) cc_final: 0.7852 (mmm) REVERT: I 27 ASN cc_start: 0.7896 (t0) cc_final: 0.6988 (t0) REVERT: J 38 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8344 (ptm160) REVERT: J 70 SER cc_start: 0.8064 (p) cc_final: 0.7713 (m) REVERT: J 77 GLN cc_start: 0.8722 (pt0) cc_final: 0.8328 (pm20) REVERT: J 100 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7433 (t0) REVERT: K 3 GLN cc_start: 0.8376 (pt0) cc_final: 0.8084 (pp30) REVERT: K 64 GLN cc_start: 0.8457 (tp40) cc_final: 0.8226 (tp40) outliers start: 36 outliers final: 26 residues processed: 315 average time/residue: 0.3246 time to fit residues: 151.0139 Evaluate side-chains 309 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 280 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 175 optimal weight: 0.1980 chunk 116 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS D 39 GLN E 17 GLN E 51 ASN F 53 GLN I 38 GLN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18693 Z= 0.304 Angle : 0.554 7.768 25357 Z= 0.289 Chirality : 0.045 0.343 2911 Planarity : 0.004 0.049 3175 Dihedral : 7.208 58.532 3379 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.20 % Allowed : 13.53 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.08 (0.18), residues: 2160 helix: 2.43 (0.27), residues: 308 sheet: 0.46 (0.21), residues: 614 loop : -0.79 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 174 HIS 0.008 0.001 HIS B 178 PHE 0.032 0.001 PHE B 687 TYR 0.025 0.001 TYR E 49 ARG 0.011 0.000 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 283 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8062 (m-30) cc_final: 0.7744 (m-30) REVERT: A 147 LEU cc_start: 0.7359 (tp) cc_final: 0.7136 (tt) REVERT: A 184 GLN cc_start: 0.8520 (mt0) cc_final: 0.7888 (mm110) REVERT: A 361 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8392 (pm20) REVERT: A 407 SER cc_start: 0.8783 (m) cc_final: 0.8439 (p) REVERT: A 687 PHE cc_start: 0.8259 (t80) cc_final: 0.8004 (t80) REVERT: B 534 ASN cc_start: 0.7936 (t0) cc_final: 0.7522 (t0) REVERT: B 545 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8414 (m) REVERT: C 432 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8073 (tp40) REVERT: C 524 ASN cc_start: 0.8157 (t0) cc_final: 0.7827 (t0) REVERT: C 542 MET cc_start: 0.6992 (ptp) cc_final: 0.5627 (tpt) REVERT: C 687 PHE cc_start: 0.8398 (t80) cc_final: 0.6685 (m-10) REVERT: D 66 ARG cc_start: 0.8441 (mtm110) cc_final: 0.8113 (ttp-170) REVERT: E 21 ILE cc_start: 0.8594 (mt) cc_final: 0.8187 (tp) REVERT: E 79 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7706 (mtm180) REVERT: E 96 TRP cc_start: 0.8955 (t-100) cc_final: 0.8317 (t-100) REVERT: F 81 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8376 (tm-30) REVERT: F 85 GLU cc_start: 0.8552 (tt0) cc_final: 0.8272 (tt0) REVERT: F 94 ASN cc_start: 0.9018 (t0) cc_final: 0.8815 (t0) REVERT: G 5 GLN cc_start: 0.9042 (tt0) cc_final: 0.8628 (tm-30) REVERT: G 38 ARG cc_start: 0.8597 (ttp-170) cc_final: 0.8377 (ttp80) REVERT: G 76 ASN cc_start: 0.8843 (t0) cc_final: 0.8525 (t0) REVERT: H 48 MET cc_start: 0.8254 (mmt) cc_final: 0.7919 (mmm) REVERT: I 27 ASN cc_start: 0.7943 (t0) cc_final: 0.7000 (t0) REVERT: I 87 TYR cc_start: 0.8757 (m-80) cc_final: 0.8405 (m-80) REVERT: J 38 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8326 (ptm160) REVERT: J 70 SER cc_start: 0.8093 (p) cc_final: 0.7695 (m) REVERT: J 77 GLN cc_start: 0.8743 (pt0) cc_final: 0.8250 (pm20) REVERT: K 3 GLN cc_start: 0.8400 (pt0) cc_final: 0.8124 (pp30) REVERT: K 64 GLN cc_start: 0.8450 (tp40) cc_final: 0.8235 (tp40) outliers start: 43 outliers final: 33 residues processed: 310 average time/residue: 0.3513 time to fit residues: 163.9016 Evaluate side-chains 309 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 274 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain G residue 1 GLN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain J residue 1 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 100 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS E 17 GLN F 53 GLN G 39 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18693 Z= 0.215 Angle : 0.524 11.089 25357 Z= 0.272 Chirality : 0.044 0.394 2911 Planarity : 0.004 0.050 3175 Dihedral : 7.026 59.003 3377 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.99 % Allowed : 14.15 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.17 (0.18), residues: 2160 helix: 2.59 (0.27), residues: 308 sheet: 0.49 (0.21), residues: 611 loop : -0.74 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 174 HIS 0.008 0.001 HIS B 178 PHE 0.033 0.001 PHE B 687 TYR 0.027 0.001 TYR E 49 ARG 0.012 0.000 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 290 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7277 (tp) cc_final: 0.7067 (tt) REVERT: A 173 MET cc_start: 0.7893 (tpt) cc_final: 0.7401 (tpt) REVERT: A 184 GLN cc_start: 0.8543 (mt0) cc_final: 0.7936 (mm110) REVERT: A 311 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7739 (ptm-80) REVERT: A 361 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8460 (pm20) REVERT: A 407 SER cc_start: 0.8699 (m) cc_final: 0.8382 (p) REVERT: A 687 PHE cc_start: 0.8274 (t80) cc_final: 0.8011 (t80) REVERT: B 384 MET cc_start: 0.9272 (tpt) cc_final: 0.8651 (tpt) REVERT: B 534 ASN cc_start: 0.7901 (t0) cc_final: 0.7518 (t0) REVERT: B 545 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8364 (m) REVERT: C 217 ASP cc_start: 0.7729 (t70) cc_final: 0.7397 (t0) REVERT: C 524 ASN cc_start: 0.8080 (t0) cc_final: 0.7796 (t0) REVERT: C 687 PHE cc_start: 0.8384 (t80) cc_final: 0.6661 (m-10) REVERT: D 66 ARG cc_start: 0.8343 (mtm110) cc_final: 0.7998 (ttp-170) REVERT: D 108 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7240 (mt) REVERT: E 21 ILE cc_start: 0.8568 (mt) cc_final: 0.8259 (tp) REVERT: E 31 ASN cc_start: 0.8607 (m110) cc_final: 0.8310 (m110) REVERT: E 79 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7759 (mtm180) REVERT: E 96 TRP cc_start: 0.8910 (t-100) cc_final: 0.8296 (t-100) REVERT: F 81 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8383 (tm-30) REVERT: F 85 GLU cc_start: 0.8513 (tt0) cc_final: 0.8245 (tt0) REVERT: G 76 ASN cc_start: 0.8864 (t0) cc_final: 0.8558 (t0) REVERT: G 105 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7730 (ptp90) REVERT: I 27 ASN cc_start: 0.7993 (t0) cc_final: 0.7142 (t0) REVERT: I 87 TYR cc_start: 0.8735 (m-80) cc_final: 0.8377 (m-80) REVERT: J 70 SER cc_start: 0.8008 (p) cc_final: 0.7612 (m) REVERT: J 77 GLN cc_start: 0.8711 (pt0) cc_final: 0.8166 (pm20) REVERT: J 100 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7466 (t0) REVERT: K 3 GLN cc_start: 0.8400 (pt0) cc_final: 0.8128 (pp30) REVERT: K 13 ASN cc_start: 0.8289 (m-40) cc_final: 0.7658 (p0) REVERT: K 64 GLN cc_start: 0.8459 (tp40) cc_final: 0.8257 (tp40) outliers start: 39 outliers final: 32 residues processed: 316 average time/residue: 0.3305 time to fit residues: 153.8448 Evaluate side-chains 311 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 276 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 100 TYR Chi-restraints excluded: chain K residue 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 152 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN F 53 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18693 Z= 0.211 Angle : 0.528 11.480 25357 Z= 0.273 Chirality : 0.044 0.416 2911 Planarity : 0.004 0.053 3175 Dihedral : 6.909 57.822 3377 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.35 % Allowed : 13.64 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.23 (0.18), residues: 2160 helix: 2.62 (0.27), residues: 308 sheet: 0.52 (0.21), residues: 626 loop : -0.70 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 174 HIS 0.007 0.001 HIS B 178 PHE 0.035 0.001 PHE B 687 TYR 0.027 0.001 TYR E 49 ARG 0.012 0.000 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 282 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7332 (tp) cc_final: 0.7078 (tt) REVERT: A 173 MET cc_start: 0.7892 (tpt) cc_final: 0.7420 (tpt) REVERT: A 184 GLN cc_start: 0.8520 (mt0) cc_final: 0.7858 (mm110) REVERT: A 189 TYR cc_start: 0.6760 (t80) cc_final: 0.6518 (t80) REVERT: A 311 ARG cc_start: 0.8105 (ptm160) cc_final: 0.7783 (ptm-80) REVERT: A 361 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8451 (pm20) REVERT: A 407 SER cc_start: 0.8716 (m) cc_final: 0.8386 (p) REVERT: A 687 PHE cc_start: 0.8250 (t80) cc_final: 0.7996 (t80) REVERT: B 384 MET cc_start: 0.9279 (tpt) cc_final: 0.8672 (tpt) REVERT: B 534 ASN cc_start: 0.7921 (t0) cc_final: 0.7489 (t0) REVERT: B 542 MET cc_start: 0.5875 (tmm) cc_final: 0.5674 (tmm) REVERT: B 545 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8143 (m) REVERT: C 217 ASP cc_start: 0.7753 (t70) cc_final: 0.7418 (t0) REVERT: C 432 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8074 (tp40) REVERT: C 524 ASN cc_start: 0.8078 (t0) cc_final: 0.7787 (t0) REVERT: C 542 MET cc_start: 0.6945 (ptp) cc_final: 0.5587 (tpt) REVERT: C 687 PHE cc_start: 0.8381 (t80) cc_final: 0.6661 (m-10) REVERT: D 66 ARG cc_start: 0.8387 (mtm110) cc_final: 0.7907 (ttp-170) REVERT: D 82 ARG cc_start: 0.7744 (mtm110) cc_final: 0.7431 (mtm180) REVERT: D 108 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7238 (mt) REVERT: E 21 ILE cc_start: 0.8557 (mt) cc_final: 0.8257 (tp) REVERT: E 31 ASN cc_start: 0.8571 (m110) cc_final: 0.8262 (m110) REVERT: E 79 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7769 (mtm180) REVERT: E 96 TRP cc_start: 0.8907 (t-100) cc_final: 0.8305 (t-100) REVERT: F 81 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8403 (tm-30) REVERT: F 85 GLU cc_start: 0.8504 (tt0) cc_final: 0.8248 (tt0) REVERT: G 76 ASN cc_start: 0.8948 (t0) cc_final: 0.8631 (t0) REVERT: G 105 ARG cc_start: 0.8158 (mtm110) cc_final: 0.7714 (ptp90) REVERT: I 27 ASN cc_start: 0.7982 (t0) cc_final: 0.7166 (t0) REVERT: J 70 SER cc_start: 0.7951 (p) cc_final: 0.7604 (m) REVERT: J 77 GLN cc_start: 0.8731 (pt0) cc_final: 0.8178 (pm20) REVERT: K 3 GLN cc_start: 0.8401 (pt0) cc_final: 0.8140 (pp30) REVERT: K 13 ASN cc_start: 0.8313 (m-40) cc_final: 0.7723 (p0) REVERT: K 28 THR cc_start: 0.8889 (m) cc_final: 0.8458 (p) REVERT: K 64 GLN cc_start: 0.8466 (tp40) cc_final: 0.8262 (tp40) outliers start: 46 outliers final: 35 residues processed: 313 average time/residue: 0.3231 time to fit residues: 149.7870 Evaluate side-chains 316 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 278 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 1 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 100 TYR Chi-restraints excluded: chain K residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 198 optimal weight: 0.2980 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 105 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN F 6 GLN F 53 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18693 Z= 0.252 Angle : 0.543 12.034 25357 Z= 0.281 Chirality : 0.045 0.429 2911 Planarity : 0.004 0.056 3175 Dihedral : 6.873 57.902 3377 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.09 % Allowed : 14.15 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.21 (0.18), residues: 2160 helix: 2.57 (0.27), residues: 308 sheet: 0.49 (0.21), residues: 623 loop : -0.69 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 47 HIS 0.007 0.001 HIS B 178 PHE 0.037 0.001 PHE B 687 TYR 0.026 0.001 TYR E 49 ARG 0.013 0.000 ARG F 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 277 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8016 (m-30) cc_final: 0.7702 (m-30) REVERT: A 173 MET cc_start: 0.7891 (tpt) cc_final: 0.7397 (tpt) REVERT: A 184 GLN cc_start: 0.8486 (mt0) cc_final: 0.7834 (mm110) REVERT: A 189 TYR cc_start: 0.6754 (t80) cc_final: 0.6524 (t80) REVERT: A 311 ARG cc_start: 0.8074 (ptm160) cc_final: 0.7765 (ptm-80) REVERT: A 361 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8461 (pm20) REVERT: A 407 SER cc_start: 0.8704 (m) cc_final: 0.8383 (p) REVERT: A 687 PHE cc_start: 0.8267 (t80) cc_final: 0.8010 (t80) REVERT: B 384 MET cc_start: 0.9276 (tpt) cc_final: 0.8679 (tpt) REVERT: B 534 ASN cc_start: 0.7946 (t0) cc_final: 0.7523 (t0) REVERT: B 542 MET cc_start: 0.5885 (tmm) cc_final: 0.5682 (tmm) REVERT: B 545 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8163 (m) REVERT: C 189 TYR cc_start: 0.6688 (t80) cc_final: 0.6466 (t80) REVERT: C 217 ASP cc_start: 0.7749 (t70) cc_final: 0.7428 (t0) REVERT: C 432 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8096 (tp40) REVERT: C 524 ASN cc_start: 0.8106 (t0) cc_final: 0.7804 (t0) REVERT: C 542 MET cc_start: 0.6916 (ptp) cc_final: 0.5591 (tpt) REVERT: D 66 ARG cc_start: 0.8386 (mtm110) cc_final: 0.7930 (ttp-170) REVERT: D 82 ARG cc_start: 0.7822 (mtm110) cc_final: 0.7530 (mtm180) REVERT: D 108 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7279 (mt) REVERT: E 21 ILE cc_start: 0.8560 (mt) cc_final: 0.8258 (tp) REVERT: E 31 ASN cc_start: 0.8568 (m110) cc_final: 0.8236 (m110) REVERT: E 79 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7755 (mtm180) REVERT: E 96 TRP cc_start: 0.8845 (t-100) cc_final: 0.8188 (t-100) REVERT: F 81 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8407 (tm-30) REVERT: G 76 ASN cc_start: 0.8955 (t0) cc_final: 0.8648 (t0) REVERT: G 105 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7679 (ptp90) REVERT: I 27 ASN cc_start: 0.8045 (t0) cc_final: 0.7200 (t0) REVERT: J 70 SER cc_start: 0.7959 (p) cc_final: 0.7612 (m) REVERT: J 77 GLN cc_start: 0.8729 (pt0) cc_final: 0.8155 (pm20) REVERT: K 3 GLN cc_start: 0.8407 (pt0) cc_final: 0.8147 (pp30) REVERT: K 13 ASN cc_start: 0.8305 (m-40) cc_final: 0.7724 (p0) REVERT: K 28 THR cc_start: 0.8898 (m) cc_final: 0.8472 (p) REVERT: K 64 GLN cc_start: 0.8461 (tp40) cc_final: 0.8256 (tp40) outliers start: 41 outliers final: 33 residues processed: 306 average time/residue: 0.2997 time to fit residues: 135.3690 Evaluate side-chains 307 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 271 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 25 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 176 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 249 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN F 6 GLN F 53 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.162627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117692 restraints weight = 28642.599| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.96 r_work: 0.3287 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18693 Z= 0.189 Angle : 0.529 12.244 25357 Z= 0.273 Chirality : 0.044 0.408 2911 Planarity : 0.004 0.057 3175 Dihedral : 6.762 58.036 3377 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.04 % Allowed : 14.35 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.28 (0.18), residues: 2160 helix: 2.68 (0.27), residues: 308 sheet: 0.53 (0.21), residues: 626 loop : -0.66 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 174 HIS 0.007 0.001 HIS B 178 PHE 0.038 0.001 PHE B 687 TYR 0.025 0.001 TYR E 49 ARG 0.014 0.000 ARG F 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4519.09 seconds wall clock time: 81 minutes 44.61 seconds (4904.61 seconds total)