Starting phenix.real_space_refine on Mon Apr 8 08:45:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/04_2024/8on7_16981_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/04_2024/8on7_16981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/04_2024/8on7_16981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/04_2024/8on7_16981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/04_2024/8on7_16981_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/04_2024/8on7_16981_updated.pdb" } resolution = 2.5 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= 0.002 sd= 0.033 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 108 5.16 5 C 8289 2.51 5 N 2169 2.21 5 O 2466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 134": "OD1" <-> "OD2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13032 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4204 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 29, 'TRANS': 495} Chain breaks: 1 Chain: "B" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4204 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 29, 'TRANS': 495} Chain breaks: 1 Chain: "C" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4204 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 29, 'TRANS': 495} Chain breaks: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 3} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 3} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 3} Chain: "G" 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: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" 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: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 7.78, per 1000 atoms: 0.60 Number of scatterers: 13032 At special positions: 0 Unit cell: (107.31, 109.354, 135.926, 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 108 16.00 O 2466 8.00 N 2169 7.00 C 8289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 401 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 381 " distance=2.04 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 360 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 401 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 381 " distance=2.04 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 360 " - pdb=" SG CYS C 368 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 444 " " NAG A 603 " - " ASN A 460 " " NAG B 601 " - " ASN B 392 " " NAG B 602 " - " ASN B 444 " " NAG B 603 " - " ASN B 460 " " NAG C 601 " - " ASN C 392 " " NAG C 602 " - " ASN C 444 " " NAG C 603 " - " ASN C 460 " " NAG G 1 " - " ASN A 180 " " NAG H 1 " - " ASN A 299 " " NAG I 1 " - " ASN B 180 " " NAG J 1 " - " ASN B 299 " " NAG K 1 " - " ASN C 180 " " NAG L 1 " - " ASN C 299 " Time building additional restraints: 5.97 Conformation dependent library (CDL) restraints added in 2.3 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 9 sheets defined 42.0% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 28 through 57 Processing helix chain 'A' and resid 87 through 99 Processing helix chain 'A' and resid 103 through 106 Processing helix chain 'A' and resid 113 through 132 removed outlier: 3.628A pdb=" N LYS A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 146 through 152 Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.260A pdb=" N LEU A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 315 through 331 Processing helix chain 'A' and resid 358 through 361 Processing helix chain 'A' and resid 366 through 391 removed outlier: 4.603A pdb=" N THR A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LYS A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 399 removed outlier: 3.580A pdb=" N CYS A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 464 through 470 removed outlier: 4.613A pdb=" N LYS A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'A' and resid 513 through 527 Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 28 through 57 Processing helix chain 'B' and resid 87 through 99 Processing helix chain 'B' and resid 103 through 106 Processing helix chain 'B' and resid 113 through 132 removed outlier: 3.628A pdb=" N LYS B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 146 through 152 Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.260A pdb=" N LEU B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 315 through 331 Processing helix chain 'B' and resid 358 through 361 Processing helix chain 'B' and resid 366 through 391 removed outlier: 4.603A pdb=" N THR B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LYS B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 399 removed outlier: 3.580A pdb=" N CYS B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 464 through 470 removed outlier: 4.613A pdb=" N LYS B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 508 Processing helix chain 'B' and resid 513 through 527 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 28 through 57 Processing helix chain 'C' and resid 87 through 99 Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 113 through 132 removed outlier: 3.628A pdb=" N LYS C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Proline residue: C 127 - end of helix Processing helix chain 'C' and resid 137 through 143 Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.260A pdb=" N LEU C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'C' and resid 358 through 361 Processing helix chain 'C' and resid 366 through 391 removed outlier: 4.603A pdb=" N THR C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LYS C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 399 removed outlier: 3.579A pdb=" N CYS C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 440 through 443 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 464 through 470 removed outlier: 4.613A pdb=" N LYS C 469 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 Processing helix chain 'C' and resid 513 through 527 Processing sheet with id= A, first strand: chain 'A' and resid 61 through 68 Processing sheet with id= B, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.777A pdb=" N ASN A 195 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN A 81 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 169 through 174 removed outlier: 6.531A pdb=" N ILE A 222 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS A 172 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER A 220 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR A 174 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY A 218 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 61 through 68 Processing sheet with id= E, first strand: chain 'B' and resid 185 through 190 removed outlier: 6.778A pdb=" N ASN B 195 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN B 81 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 169 through 174 removed outlier: 6.531A pdb=" N ILE B 222 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS B 172 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER B 220 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR B 174 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY B 218 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 61 through 68 Processing sheet with id= H, first strand: chain 'C' and resid 185 through 190 removed outlier: 6.777A pdb=" N ASN C 195 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN C 81 " --> pdb=" O ASN C 195 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 169 through 174 removed outlier: 6.530A pdb=" N ILE C 222 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS C 172 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER C 220 " --> pdb=" O CYS C 172 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR C 174 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY C 218 " --> pdb=" O TYR C 174 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1656 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: 3.88 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4179 1.35 - 1.47: 3312 1.47 - 1.59: 5709 1.59 - 1.71: 0 1.71 - 1.83: 162 Bond restraints: 13362 Sorted by residual: bond pdb=" N GLN C 344 " pdb=" CA GLN C 344 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.59e+00 bond pdb=" N GLN B 344 " pdb=" CA GLN B 344 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.47e+00 bond pdb=" N GLN A 344 " pdb=" CA GLN A 344 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.46e+00 bond pdb=" N ILE A 347 " pdb=" CA ILE A 347 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.24e-02 6.50e+03 6.80e+00 bond pdb=" N ILE C 347 " pdb=" CA ILE C 347 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.24e-02 6.50e+03 6.70e+00 ... (remaining 13357 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.76: 384 105.76 - 112.85: 6818 112.85 - 119.95: 4771 119.95 - 127.05: 5958 127.05 - 134.14: 165 Bond angle restraints: 18096 Sorted by residual: angle pdb=" N ASN B 346 " pdb=" CA ASN B 346 " pdb=" C ASN B 346 " ideal model delta sigma weight residual 113.20 108.20 5.00 1.21e+00 6.83e-01 1.71e+01 angle pdb=" N ASN C 346 " pdb=" CA ASN C 346 " pdb=" C ASN C 346 " ideal model delta sigma weight residual 113.20 108.21 4.99 1.21e+00 6.83e-01 1.70e+01 angle pdb=" N ASN A 346 " pdb=" CA ASN A 346 " pdb=" C ASN A 346 " ideal model delta sigma weight residual 113.20 108.21 4.99 1.21e+00 6.83e-01 1.70e+01 angle pdb=" CA PHE F 612 " pdb=" CB PHE F 612 " pdb=" CG PHE F 612 " ideal model delta sigma weight residual 113.80 117.45 -3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CA PHE D 612 " pdb=" CB PHE D 612 " pdb=" CG PHE D 612 " ideal model delta sigma weight residual 113.80 117.45 -3.65 1.00e+00 1.00e+00 1.33e+01 ... (remaining 18091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 7632 17.56 - 35.12: 540 35.12 - 52.67: 102 52.67 - 70.23: 36 70.23 - 87.79: 15 Dihedral angle restraints: 8325 sinusoidal: 3678 harmonic: 4647 Sorted by residual: dihedral pdb=" CA GLY B 294 " pdb=" C GLY B 294 " pdb=" N PRO B 295 " pdb=" CA PRO B 295 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY C 294 " pdb=" C GLY C 294 " pdb=" N PRO C 295 " pdb=" CA PRO C 295 " ideal model delta harmonic sigma weight residual -180.00 -160.79 -19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY A 294 " pdb=" C GLY A 294 " pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 8322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1392 0.040 - 0.080: 388 0.080 - 0.120: 182 0.120 - 0.160: 18 0.160 - 0.200: 6 Chirality restraints: 1986 Sorted by residual: chirality pdb=" CA MET A 229 " pdb=" N MET A 229 " pdb=" C MET A 229 " pdb=" CB MET A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA MET C 229 " pdb=" N MET C 229 " pdb=" C MET C 229 " pdb=" CB MET C 229 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA MET B 229 " pdb=" N MET B 229 " pdb=" C MET B 229 " pdb=" CB MET B 229 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 1983 not shown) Planarity restraints: 2343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 342 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C PRO A 342 " -0.051 2.00e-02 2.50e+03 pdb=" O PRO A 342 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 343 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 342 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C PRO C 342 " -0.050 2.00e-02 2.50e+03 pdb=" O PRO C 342 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU C 343 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 342 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" C PRO B 342 " -0.050 2.00e-02 2.50e+03 pdb=" O PRO B 342 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU B 343 " 0.017 2.00e-02 2.50e+03 ... (remaining 2340 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 127 2.68 - 3.23: 12349 3.23 - 3.79: 20259 3.79 - 4.34: 28874 4.34 - 4.90: 46452 Nonbonded interactions: 108061 Sorted by model distance: nonbonded pdb=" O ASP C 302 " pdb=" OD1 ASP C 302 " model vdw 2.122 3.040 nonbonded pdb=" O ASP A 302 " pdb=" OD1 ASP A 302 " model vdw 2.123 3.040 nonbonded pdb=" O ASP B 302 " pdb=" OD1 ASP B 302 " model vdw 2.123 3.040 nonbonded pdb=" O ASP A 308 " pdb=" OD1 ASP A 308 " model vdw 2.191 3.040 nonbonded pdb=" O ASP C 308 " pdb=" OD1 ASP C 308 " model vdw 2.191 3.040 ... (remaining 108056 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.990 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.780 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:14.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 : 0.004 0.035 13362 Z= 0.253 Angle : 0.714 8.648 18096 Z= 0.391 Chirality : 0.045 0.200 1986 Planarity : 0.005 0.044 2328 Dihedral : 13.287 87.791 5253 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.21 % Allowed : 4.48 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.21), residues: 1569 helix: 1.27 (0.20), residues: 666 sheet: 1.70 (0.29), residues: 267 loop : 0.51 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 34 HIS 0.006 0.001 HIS C 376 PHE 0.023 0.002 PHE C 10 TYR 0.018 0.001 TYR B 118 ARG 0.005 0.001 ARG E 611 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 462 time to evaluate : 1.576 Fit side-chains REVERT: A 31 ARG cc_start: 0.6652 (ttm170) cc_final: 0.6353 (ttm170) REVERT: A 50 SER cc_start: 0.7408 (t) cc_final: 0.6962 (p) REVERT: A 66 GLU cc_start: 0.8248 (pt0) cc_final: 0.7900 (pt0) REVERT: A 111 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 120 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7673 (mtmt) REVERT: A 125 TYR cc_start: 0.8118 (m-80) cc_final: 0.7865 (m-80) REVERT: A 200 LYS cc_start: 0.8133 (mttt) cc_final: 0.7894 (mmtp) REVERT: A 216 GLU cc_start: 0.7817 (mp0) cc_final: 0.7615 (mp0) REVERT: A 273 TYR cc_start: 0.8314 (m-80) cc_final: 0.7994 (m-80) REVERT: A 302 ASP cc_start: 0.7463 (t0) cc_final: 0.7189 (t0) REVERT: A 347 ILE cc_start: 0.7612 (mt) cc_final: 0.7214 (tp) REVERT: A 353 ASP cc_start: 0.7400 (p0) cc_final: 0.7138 (p0) REVERT: A 359 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6670 (mt-10) REVERT: A 388 LYS cc_start: 0.7616 (mtmt) cc_final: 0.7409 (mtmm) REVERT: A 391 LYS cc_start: 0.8040 (mptt) cc_final: 0.7746 (mmtm) REVERT: A 425 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7050 (mt-10) REVERT: A 438 LYS cc_start: 0.8124 (mttp) cc_final: 0.7920 (mttp) REVERT: A 445 LYS cc_start: 0.6808 (mtmt) cc_final: 0.6605 (mtmm) REVERT: B 16 MET cc_start: 0.7691 (mtp) cc_final: 0.7480 (mtm) REVERT: B 50 SER cc_start: 0.7790 (t) cc_final: 0.7247 (p) REVERT: B 51 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7048 (mt-10) REVERT: B 82 MET cc_start: 0.8625 (mtt) cc_final: 0.8263 (mtm) REVERT: B 111 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7485 (mt-10) REVERT: B 138 GLU cc_start: 0.7322 (mp0) cc_final: 0.6951 (mp0) REVERT: B 141 GLN cc_start: 0.8015 (mm110) cc_final: 0.7665 (mm-40) REVERT: B 235 GLU cc_start: 0.7934 (pt0) cc_final: 0.7696 (pt0) REVERT: B 326 TYR cc_start: 0.7648 (m-80) cc_final: 0.7176 (m-80) REVERT: B 347 ILE cc_start: 0.7773 (mt) cc_final: 0.7422 (tp) REVERT: B 360 CYS cc_start: 0.6970 (m) cc_final: 0.6707 (m) REVERT: B 362 PHE cc_start: 0.7976 (m-80) cc_final: 0.7754 (m-80) REVERT: B 388 LYS cc_start: 0.7449 (mtmt) cc_final: 0.7149 (mtmm) REVERT: B 391 LYS cc_start: 0.7650 (mptt) cc_final: 0.7352 (mmtp) REVERT: B 407 GLU cc_start: 0.7597 (tt0) cc_final: 0.7236 (tt0) REVERT: B 425 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7001 (mt-10) REVERT: B 427 ASP cc_start: 0.7643 (m-30) cc_final: 0.7416 (m-30) REVERT: C 16 MET cc_start: 0.7647 (mtp) cc_final: 0.7365 (mtm) REVERT: C 29 MET cc_start: 0.7060 (mmm) cc_final: 0.6671 (mmm) REVERT: C 51 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6975 (mt-10) REVERT: C 66 GLU cc_start: 0.8010 (pt0) cc_final: 0.7758 (pt0) REVERT: C 120 LYS cc_start: 0.7749 (mtmt) cc_final: 0.7423 (ttmm) REVERT: C 125 TYR cc_start: 0.7916 (m-80) cc_final: 0.7612 (m-80) REVERT: C 131 ASN cc_start: 0.8183 (m-40) cc_final: 0.7969 (m-40) REVERT: C 273 TYR cc_start: 0.8415 (m-80) cc_final: 0.8021 (m-80) REVERT: C 288 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7422 (mtp85) REVERT: C 301 SER cc_start: 0.7616 (t) cc_final: 0.7234 (p) REVERT: C 326 TYR cc_start: 0.7532 (m-80) cc_final: 0.7026 (m-80) REVERT: C 353 ASP cc_start: 0.7460 (p0) cc_final: 0.7089 (p0) REVERT: C 355 ASN cc_start: 0.7312 (m110) cc_final: 0.7106 (m110) REVERT: C 363 THR cc_start: 0.7910 (m) cc_final: 0.7468 (p) REVERT: C 380 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7401 (mtmm) REVERT: C 391 LYS cc_start: 0.8025 (mptt) cc_final: 0.7749 (mmtp) REVERT: C 396 MET cc_start: 0.7841 (mmp) cc_final: 0.7616 (mmm) REVERT: C 399 CYS cc_start: 0.6685 (m) cc_final: 0.6110 (m) REVERT: C 409 SER cc_start: 0.8032 (m) cc_final: 0.7603 (p) REVERT: C 411 ASP cc_start: 0.7836 (m-30) cc_final: 0.7588 (m-30) REVERT: C 418 LYS cc_start: 0.8500 (tttm) cc_final: 0.8292 (tttm) REVERT: C 448 THR cc_start: 0.7353 (m) cc_final: 0.7077 (t) REVERT: C 457 LYS cc_start: 0.7892 (mtpp) cc_final: 0.7676 (mtpp) REVERT: C 468 MET cc_start: 0.8417 (mmm) cc_final: 0.8216 (mmm) REVERT: C 480 ASP cc_start: 0.7009 (m-30) cc_final: 0.6726 (m-30) outliers start: 3 outliers final: 0 residues processed: 462 average time/residue: 1.6182 time to fit residues: 799.6267 Evaluate side-chains 359 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0010 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 141 optimal weight: 0.0980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 108 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 482 ASN B 106 ASN B 108 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN C 106 ASN C 141 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 449 GLN C 463 ASN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13362 Z= 0.179 Angle : 0.581 12.608 18096 Z= 0.302 Chirality : 0.043 0.172 1986 Planarity : 0.005 0.049 2328 Dihedral : 5.234 36.199 2172 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.99 % Allowed : 11.73 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.21), residues: 1569 helix: 1.55 (0.21), residues: 690 sheet: 1.29 (0.29), residues: 270 loop : 0.54 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 349 HIS 0.005 0.001 HIS A 17 PHE 0.018 0.001 PHE A 10 TYR 0.015 0.001 TYR A 118 ARG 0.005 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 381 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.6898 (mmm) cc_final: 0.6670 (mmp) REVERT: A 16 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7413 (mtt) REVERT: A 21 LYS cc_start: 0.6602 (mmtp) cc_final: 0.6238 (mttt) REVERT: A 29 MET cc_start: 0.6857 (mmm) cc_final: 0.6490 (mmm) REVERT: A 31 ARG cc_start: 0.6661 (ttm170) cc_final: 0.6352 (ttm170) REVERT: A 50 SER cc_start: 0.7486 (t) cc_final: 0.7041 (p) REVERT: A 66 GLU cc_start: 0.8280 (pt0) cc_final: 0.7963 (pt0) REVERT: A 116 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7099 (mtm180) REVERT: A 216 GLU cc_start: 0.7830 (mp0) cc_final: 0.7626 (mp0) REVERT: A 271 GLU cc_start: 0.7687 (pt0) cc_final: 0.7274 (pt0) REVERT: A 273 TYR cc_start: 0.8433 (m-80) cc_final: 0.8166 (m-80) REVERT: A 302 ASP cc_start: 0.7642 (t0) cc_final: 0.7133 (t0) REVERT: A 303 LYS cc_start: 0.8172 (ptmm) cc_final: 0.7623 (ptpp) REVERT: A 347 ILE cc_start: 0.7579 (mt) cc_final: 0.7218 (tp) REVERT: A 359 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6704 (mt-10) REVERT: A 391 LYS cc_start: 0.8006 (mptt) cc_final: 0.7748 (mmtm) REVERT: A 409 SER cc_start: 0.8519 (t) cc_final: 0.8228 (m) REVERT: A 425 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 438 LYS cc_start: 0.8114 (mttp) cc_final: 0.7902 (mttp) REVERT: A 465 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 490 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: B 16 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7063 (mtm) REVERT: B 50 SER cc_start: 0.7812 (t) cc_final: 0.7297 (p) REVERT: B 116 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7083 (mtm180) REVERT: B 121 LYS cc_start: 0.7967 (mtpp) cc_final: 0.7548 (tttm) REVERT: B 138 GLU cc_start: 0.7370 (mp0) cc_final: 0.6985 (mp0) REVERT: B 164 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7828 (mm-40) REVERT: B 271 GLU cc_start: 0.7742 (pt0) cc_final: 0.7432 (pt0) REVERT: B 302 ASP cc_start: 0.7567 (t0) cc_final: 0.7067 (t0) REVERT: B 303 LYS cc_start: 0.8287 (ptmm) cc_final: 0.7723 (ptpp) REVERT: B 321 MET cc_start: 0.7234 (mtt) cc_final: 0.7030 (mtt) REVERT: B 326 TYR cc_start: 0.7647 (m-80) cc_final: 0.7159 (m-80) REVERT: B 347 ILE cc_start: 0.7812 (mt) cc_final: 0.7430 (tp) REVERT: B 360 CYS cc_start: 0.6951 (m) cc_final: 0.6727 (m) REVERT: B 388 LYS cc_start: 0.7396 (mtmt) cc_final: 0.7169 (mtmm) REVERT: B 391 LYS cc_start: 0.7650 (mptt) cc_final: 0.7389 (mmtp) REVERT: B 407 GLU cc_start: 0.7785 (tt0) cc_final: 0.7253 (tt0) REVERT: B 425 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6961 (mt-10) REVERT: B 427 ASP cc_start: 0.7656 (m-30) cc_final: 0.7430 (m-30) REVERT: C 7 MET cc_start: 0.6726 (mmm) cc_final: 0.6519 (mpm) REVERT: C 29 MET cc_start: 0.7120 (mmm) cc_final: 0.6731 (mmm) REVERT: C 44 MET cc_start: 0.7259 (mmm) cc_final: 0.6867 (mmm) REVERT: C 116 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6923 (mtm180) REVERT: C 273 TYR cc_start: 0.8500 (m-80) cc_final: 0.8140 (m-80) REVERT: C 301 SER cc_start: 0.7716 (t) cc_final: 0.7467 (p) REVERT: C 316 MET cc_start: 0.7537 (mtm) cc_final: 0.6829 (ptp) REVERT: C 326 TYR cc_start: 0.7578 (m-80) cc_final: 0.7182 (m-80) REVERT: C 353 ASP cc_start: 0.7389 (p0) cc_final: 0.7164 (p0) REVERT: C 359 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6539 (mt-10) REVERT: C 363 THR cc_start: 0.7834 (m) cc_final: 0.7376 (p) REVERT: C 380 LYS cc_start: 0.7383 (mtmt) cc_final: 0.7162 (mtmm) REVERT: C 386 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7810 (ttpt) REVERT: C 391 LYS cc_start: 0.8014 (mptt) cc_final: 0.7759 (mmtp) REVERT: C 396 MET cc_start: 0.7883 (mmp) cc_final: 0.7597 (mmm) REVERT: C 399 CYS cc_start: 0.6733 (m) cc_final: 0.6175 (m) REVERT: C 407 GLU cc_start: 0.7682 (tt0) cc_final: 0.7469 (tt0) REVERT: C 409 SER cc_start: 0.8408 (m) cc_final: 0.8099 (p) REVERT: C 411 ASP cc_start: 0.7969 (m-30) cc_final: 0.7747 (m-30) REVERT: C 468 MET cc_start: 0.8479 (mmm) cc_final: 0.8246 (mmm) REVERT: C 480 ASP cc_start: 0.7001 (m-30) cc_final: 0.6745 (m-30) REVERT: C 489 SER cc_start: 0.8102 (m) cc_final: 0.7837 (m) outliers start: 42 outliers final: 7 residues processed: 397 average time/residue: 1.6248 time to fit residues: 689.9584 Evaluate side-chains 382 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 368 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.0370 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 126 optimal weight: 0.0870 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 482 ASN B 106 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 482 ASN C 106 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13362 Z= 0.183 Angle : 0.569 13.074 18096 Z= 0.293 Chirality : 0.043 0.256 1986 Planarity : 0.004 0.051 2328 Dihedral : 5.089 31.062 2172 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.34 % Allowed : 12.86 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1569 helix: 1.66 (0.21), residues: 690 sheet: 1.32 (0.30), residues: 270 loop : 0.46 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 349 HIS 0.004 0.001 HIS A 260 PHE 0.011 0.001 PHE C 188 TYR 0.014 0.001 TYR C 118 ARG 0.003 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 362 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6851 (mmm) cc_final: 0.6622 (mmp) REVERT: A 16 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7441 (mtt) REVERT: A 29 MET cc_start: 0.6893 (mmm) cc_final: 0.6520 (mmm) REVERT: A 31 ARG cc_start: 0.6540 (ttm170) cc_final: 0.6227 (ttm170) REVERT: A 50 SER cc_start: 0.7515 (t) cc_final: 0.7083 (p) REVERT: A 51 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6884 (mt-10) REVERT: A 95 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7645 (mtt-85) REVERT: A 119 MET cc_start: 0.8344 (mmt) cc_final: 0.7900 (mmm) REVERT: A 156 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7387 (mm-30) REVERT: A 235 GLU cc_start: 0.7867 (pt0) cc_final: 0.7630 (pt0) REVERT: A 273 TYR cc_start: 0.8457 (m-80) cc_final: 0.8186 (m-80) REVERT: A 302 ASP cc_start: 0.7639 (t0) cc_final: 0.7132 (t0) REVERT: A 303 LYS cc_start: 0.8162 (ptmm) cc_final: 0.7657 (ptpp) REVERT: A 347 ILE cc_start: 0.7639 (mt) cc_final: 0.7235 (tp) REVERT: A 409 SER cc_start: 0.8521 (t) cc_final: 0.7975 (p) REVERT: A 425 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 437 GLU cc_start: 0.7599 (tp30) cc_final: 0.7176 (tm-30) REVERT: A 438 LYS cc_start: 0.8092 (mttp) cc_final: 0.7772 (mttp) REVERT: A 465 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7725 (mm-30) REVERT: B 16 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7196 (mtt) REVERT: B 50 SER cc_start: 0.7832 (t) cc_final: 0.7361 (p) REVERT: B 82 MET cc_start: 0.8683 (mtm) cc_final: 0.8456 (mtt) REVERT: B 138 GLU cc_start: 0.7380 (mp0) cc_final: 0.6991 (mp0) REVERT: B 141 GLN cc_start: 0.8066 (mm110) cc_final: 0.7732 (mm-40) REVERT: B 164 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7832 (mm-40) REVERT: B 302 ASP cc_start: 0.7543 (t0) cc_final: 0.7053 (t0) REVERT: B 303 LYS cc_start: 0.8303 (ptmm) cc_final: 0.7723 (ptpp) REVERT: B 326 TYR cc_start: 0.7596 (m-80) cc_final: 0.7216 (m-80) REVERT: B 347 ILE cc_start: 0.7825 (mt) cc_final: 0.7458 (tp) REVERT: B 360 CYS cc_start: 0.6946 (m) cc_final: 0.6731 (m) REVERT: B 388 LYS cc_start: 0.7378 (mtmt) cc_final: 0.7161 (mtmm) REVERT: B 391 LYS cc_start: 0.7627 (mptt) cc_final: 0.7285 (mmtp) REVERT: B 399 CYS cc_start: 0.6898 (m) cc_final: 0.6517 (m) REVERT: B 407 GLU cc_start: 0.7793 (tt0) cc_final: 0.7106 (tt0) REVERT: B 425 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6954 (mt-10) REVERT: B 518 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6388 (mm-30) REVERT: C 29 MET cc_start: 0.7056 (mmm) cc_final: 0.6712 (mmm) REVERT: C 44 MET cc_start: 0.7268 (mmm) cc_final: 0.6843 (mmm) REVERT: C 49 MET cc_start: 0.7448 (mmm) cc_final: 0.7131 (mmm) REVERT: C 116 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6915 (mtm180) REVERT: C 120 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7571 (ttmm) REVERT: C 213 GLU cc_start: 0.7484 (pt0) cc_final: 0.7234 (pt0) REVERT: C 273 TYR cc_start: 0.8542 (m-80) cc_final: 0.8121 (m-80) REVERT: C 301 SER cc_start: 0.7693 (t) cc_final: 0.7426 (p) REVERT: C 316 MET cc_start: 0.7567 (mtm) cc_final: 0.6871 (ptp) REVERT: C 326 TYR cc_start: 0.7446 (m-80) cc_final: 0.7007 (m-80) REVERT: C 386 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7850 (ttpt) REVERT: C 391 LYS cc_start: 0.7922 (mptt) cc_final: 0.7661 (mmtp) REVERT: C 396 MET cc_start: 0.7873 (mmp) cc_final: 0.7547 (mmm) REVERT: C 399 CYS cc_start: 0.6739 (m) cc_final: 0.6210 (m) REVERT: C 409 SER cc_start: 0.8419 (m) cc_final: 0.8003 (p) REVERT: C 468 MET cc_start: 0.8560 (mmm) cc_final: 0.8330 (mmm) REVERT: C 480 ASP cc_start: 0.7029 (m-30) cc_final: 0.6810 (m-30) REVERT: C 489 SER cc_start: 0.8171 (m) cc_final: 0.7889 (m) outliers start: 47 outliers final: 15 residues processed: 379 average time/residue: 1.6587 time to fit residues: 670.9337 Evaluate side-chains 370 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 350 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 475 ASN A 482 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 HIS C 475 ASN C 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13362 Z= 0.164 Angle : 0.539 7.880 18096 Z= 0.275 Chirality : 0.042 0.161 1986 Planarity : 0.004 0.049 2328 Dihedral : 4.728 29.666 2172 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.91 % Allowed : 14.00 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1569 helix: 1.80 (0.21), residues: 687 sheet: 1.22 (0.30), residues: 273 loop : 0.33 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 349 HIS 0.003 0.001 HIS A 260 PHE 0.023 0.001 PHE A 10 TYR 0.013 0.001 TYR A 118 ARG 0.006 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 354 time to evaluate : 1.562 Fit side-chains REVERT: A 7 MET cc_start: 0.6891 (mmm) cc_final: 0.6655 (mmp) REVERT: A 16 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7362 (mtt) REVERT: A 29 MET cc_start: 0.6869 (mmm) cc_final: 0.6493 (mmm) REVERT: A 31 ARG cc_start: 0.6520 (ttm170) cc_final: 0.6200 (ttm170) REVERT: A 49 MET cc_start: 0.7395 (mmp) cc_final: 0.7176 (mmm) REVERT: A 50 SER cc_start: 0.7518 (t) cc_final: 0.7100 (p) REVERT: A 66 GLU cc_start: 0.8325 (pt0) cc_final: 0.7988 (pt0) REVERT: A 86 ASP cc_start: 0.7684 (t0) cc_final: 0.7311 (t0) REVERT: A 95 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7686 (mtt-85) REVERT: A 119 MET cc_start: 0.8357 (mmt) cc_final: 0.7928 (mmm) REVERT: A 216 GLU cc_start: 0.7826 (mp0) cc_final: 0.7624 (mp0) REVERT: A 271 GLU cc_start: 0.7677 (pt0) cc_final: 0.7269 (pt0) REVERT: A 273 TYR cc_start: 0.8465 (m-80) cc_final: 0.8237 (m-80) REVERT: A 302 ASP cc_start: 0.7653 (t0) cc_final: 0.7122 (t0) REVERT: A 303 LYS cc_start: 0.8115 (ptmm) cc_final: 0.7591 (ptpp) REVERT: A 347 ILE cc_start: 0.7649 (mt) cc_final: 0.7271 (tp) REVERT: A 380 LYS cc_start: 0.7188 (mtmt) cc_final: 0.6863 (mttp) REVERT: A 409 SER cc_start: 0.8579 (t) cc_final: 0.8061 (p) REVERT: A 425 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6973 (mt-10) REVERT: A 465 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7745 (mm-30) REVERT: A 518 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6308 (mm-30) REVERT: B 16 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7167 (mtm) REVERT: B 50 SER cc_start: 0.7800 (t) cc_final: 0.7365 (p) REVERT: B 138 GLU cc_start: 0.7336 (mp0) cc_final: 0.6947 (mp0) REVERT: B 164 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7825 (mm-40) REVERT: B 249 VAL cc_start: 0.8134 (m) cc_final: 0.7713 (p) REVERT: B 302 ASP cc_start: 0.7553 (t0) cc_final: 0.7096 (t0) REVERT: B 303 LYS cc_start: 0.8296 (ptmm) cc_final: 0.7718 (ptpp) REVERT: B 326 TYR cc_start: 0.7545 (m-80) cc_final: 0.7125 (m-80) REVERT: B 347 ILE cc_start: 0.7879 (mt) cc_final: 0.7561 (tp) REVERT: B 359 GLU cc_start: 0.6569 (mp0) cc_final: 0.6056 (mp0) REVERT: B 360 CYS cc_start: 0.6927 (m) cc_final: 0.6650 (m) REVERT: B 391 LYS cc_start: 0.7571 (mptt) cc_final: 0.7306 (mmtp) REVERT: B 399 CYS cc_start: 0.6990 (m) cc_final: 0.6606 (m) REVERT: B 407 GLU cc_start: 0.7805 (tt0) cc_final: 0.7140 (tt0) REVERT: B 425 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6950 (mt-10) REVERT: B 518 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6468 (mm-30) REVERT: C 29 MET cc_start: 0.7060 (mmm) cc_final: 0.6720 (mmm) REVERT: C 44 MET cc_start: 0.7281 (mmm) cc_final: 0.6861 (mmm) REVERT: C 49 MET cc_start: 0.7407 (mmm) cc_final: 0.7023 (mmm) REVERT: C 120 LYS cc_start: 0.7869 (mtmt) cc_final: 0.7637 (ttmm) REVERT: C 156 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7346 (mm-30) REVERT: C 234 ASP cc_start: 0.7907 (p0) cc_final: 0.7679 (p0) REVERT: C 235 GLU cc_start: 0.8033 (pt0) cc_final: 0.7244 (pm20) REVERT: C 273 TYR cc_start: 0.8565 (m-80) cc_final: 0.8154 (m-80) REVERT: C 301 SER cc_start: 0.7670 (t) cc_final: 0.7386 (p) REVERT: C 316 MET cc_start: 0.7579 (mtm) cc_final: 0.6902 (ptp) REVERT: C 326 TYR cc_start: 0.7398 (m-80) cc_final: 0.6956 (m-80) REVERT: C 359 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6394 (tp30) REVERT: C 386 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7831 (ttpt) REVERT: C 391 LYS cc_start: 0.7883 (mptt) cc_final: 0.7628 (mmtp) REVERT: C 396 MET cc_start: 0.7824 (mmp) cc_final: 0.7501 (mmm) REVERT: C 399 CYS cc_start: 0.6699 (m) cc_final: 0.6228 (m) REVERT: C 409 SER cc_start: 0.8435 (m) cc_final: 0.8202 (p) REVERT: C 437 GLU cc_start: 0.7507 (tp30) cc_final: 0.7273 (tm-30) REVERT: C 453 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7392 (mt-10) REVERT: C 468 MET cc_start: 0.8554 (mmm) cc_final: 0.8303 (mmm) REVERT: C 480 ASP cc_start: 0.7028 (m-30) cc_final: 0.6795 (m-30) REVERT: C 489 SER cc_start: 0.8177 (m) cc_final: 0.7890 (m) outliers start: 41 outliers final: 15 residues processed: 371 average time/residue: 1.6942 time to fit residues: 671.0554 Evaluate side-chains 351 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 333 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 490 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 482 ASN B 108 ASN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13362 Z= 0.240 Angle : 0.552 7.350 18096 Z= 0.282 Chirality : 0.043 0.176 1986 Planarity : 0.004 0.047 2328 Dihedral : 4.648 29.004 2172 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.27 % Allowed : 14.64 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1569 helix: 1.75 (0.21), residues: 690 sheet: 1.16 (0.30), residues: 273 loop : 0.28 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 349 HIS 0.004 0.001 HIS A 260 PHE 0.018 0.001 PHE A 10 TYR 0.015 0.001 TYR C 118 ARG 0.007 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 348 time to evaluate : 1.596 Fit side-chains REVERT: A 7 MET cc_start: 0.6914 (mmm) cc_final: 0.6695 (mmp) REVERT: A 16 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7384 (mtt) REVERT: A 29 MET cc_start: 0.6882 (mmm) cc_final: 0.6501 (mmm) REVERT: A 31 ARG cc_start: 0.6533 (ttm170) cc_final: 0.6233 (ttm170) REVERT: A 49 MET cc_start: 0.7408 (mmp) cc_final: 0.7185 (mmm) REVERT: A 50 SER cc_start: 0.7564 (t) cc_final: 0.7152 (p) REVERT: A 66 GLU cc_start: 0.8327 (pt0) cc_final: 0.8005 (pt0) REVERT: A 82 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7047 (mmt) REVERT: A 86 ASP cc_start: 0.7676 (t0) cc_final: 0.7288 (t0) REVERT: A 95 ARG cc_start: 0.7928 (mtt180) cc_final: 0.7698 (mtt-85) REVERT: A 119 MET cc_start: 0.8451 (mmt) cc_final: 0.8017 (mmm) REVERT: A 271 GLU cc_start: 0.7682 (pt0) cc_final: 0.7287 (pt0) REVERT: A 302 ASP cc_start: 0.7699 (t0) cc_final: 0.7161 (t0) REVERT: A 303 LYS cc_start: 0.8121 (ptmm) cc_final: 0.7578 (ptpp) REVERT: A 311 GLU cc_start: 0.7051 (tp30) cc_final: 0.6832 (tp30) REVERT: A 347 ILE cc_start: 0.7630 (mt) cc_final: 0.7252 (tp) REVERT: A 373 MET cc_start: 0.6950 (mmm) cc_final: 0.6721 (mmp) REVERT: A 380 LYS cc_start: 0.7216 (mtmt) cc_final: 0.6943 (mtpp) REVERT: A 409 SER cc_start: 0.8580 (t) cc_final: 0.8078 (p) REVERT: A 425 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6983 (mt-10) REVERT: A 465 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7737 (mm-30) REVERT: A 518 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6479 (mm-30) REVERT: B 16 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7077 (mtm) REVERT: B 50 SER cc_start: 0.7801 (t) cc_final: 0.7366 (p) REVERT: B 51 GLU cc_start: 0.7234 (mt-10) cc_final: 0.7010 (mt-10) REVERT: B 135 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7248 (mt-10) REVERT: B 138 GLU cc_start: 0.7358 (mp0) cc_final: 0.6961 (mp0) REVERT: B 302 ASP cc_start: 0.7595 (t0) cc_final: 0.7153 (t0) REVERT: B 303 LYS cc_start: 0.8314 (ptmm) cc_final: 0.7738 (ptpp) REVERT: B 326 TYR cc_start: 0.7564 (m-80) cc_final: 0.7043 (m-80) REVERT: B 347 ILE cc_start: 0.7866 (mt) cc_final: 0.7552 (tp) REVERT: B 360 CYS cc_start: 0.6920 (m) cc_final: 0.6690 (m) REVERT: B 370 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6893 (mm-40) REVERT: B 388 LYS cc_start: 0.7552 (mtpp) cc_final: 0.7270 (mtpt) REVERT: B 391 LYS cc_start: 0.7554 (mptt) cc_final: 0.7273 (mmtp) REVERT: B 399 CYS cc_start: 0.7036 (m) cc_final: 0.6604 (m) REVERT: B 407 GLU cc_start: 0.7803 (tt0) cc_final: 0.7244 (tt0) REVERT: B 425 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6986 (mt-10) REVERT: B 480 ASP cc_start: 0.7120 (m-30) cc_final: 0.6861 (m-30) REVERT: B 488 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7807 (mt-10) REVERT: C 21 LYS cc_start: 0.6015 (mttt) cc_final: 0.5768 (mttt) REVERT: C 29 MET cc_start: 0.7059 (mmm) cc_final: 0.6717 (mmm) REVERT: C 44 MET cc_start: 0.7320 (mmm) cc_final: 0.6841 (mmm) REVERT: C 49 MET cc_start: 0.7419 (mmm) cc_final: 0.7039 (mmm) REVERT: C 116 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6882 (mtm180) REVERT: C 120 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7629 (ttmm) REVERT: C 156 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7284 (mm-30) REVERT: C 235 GLU cc_start: 0.8071 (pt0) cc_final: 0.7785 (pt0) REVERT: C 273 TYR cc_start: 0.8589 (m-80) cc_final: 0.8188 (m-80) REVERT: C 301 SER cc_start: 0.7651 (t) cc_final: 0.7320 (p) REVERT: C 326 TYR cc_start: 0.7477 (m-80) cc_final: 0.7012 (m-80) REVERT: C 359 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6483 (tp30) REVERT: C 386 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7824 (ttpt) REVERT: C 391 LYS cc_start: 0.7896 (mptt) cc_final: 0.7625 (mmtp) REVERT: C 396 MET cc_start: 0.7849 (mmp) cc_final: 0.7543 (mmm) REVERT: C 399 CYS cc_start: 0.6778 (m) cc_final: 0.6398 (m) REVERT: C 453 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7383 (mt-10) REVERT: C 468 MET cc_start: 0.8571 (mmm) cc_final: 0.8321 (mmm) REVERT: C 480 ASP cc_start: 0.7050 (m-30) cc_final: 0.6809 (m-30) REVERT: C 489 SER cc_start: 0.8179 (m) cc_final: 0.7868 (m) outliers start: 46 outliers final: 15 residues processed: 362 average time/residue: 1.6192 time to fit residues: 626.7405 Evaluate side-chains 372 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 351 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN C 152 ASN C 475 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13362 Z= 0.203 Angle : 0.539 7.646 18096 Z= 0.274 Chirality : 0.042 0.163 1986 Planarity : 0.004 0.046 2328 Dihedral : 4.555 28.449 2172 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.13 % Allowed : 15.35 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1569 helix: 1.79 (0.21), residues: 690 sheet: 1.13 (0.30), residues: 273 loop : 0.24 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 349 HIS 0.003 0.001 HIS A 260 PHE 0.016 0.001 PHE A 10 TYR 0.014 0.001 TYR A 118 ARG 0.005 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 368 time to evaluate : 1.570 Fit side-chains REVERT: A 7 MET cc_start: 0.6932 (mmm) cc_final: 0.6701 (mmp) REVERT: A 16 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7357 (mtt) REVERT: A 21 LYS cc_start: 0.6575 (mttt) cc_final: 0.6354 (mttt) REVERT: A 29 MET cc_start: 0.6875 (mmm) cc_final: 0.6492 (mmm) REVERT: A 31 ARG cc_start: 0.6524 (ttm170) cc_final: 0.6181 (ttm170) REVERT: A 49 MET cc_start: 0.7480 (mmp) cc_final: 0.7247 (mmm) REVERT: A 50 SER cc_start: 0.7557 (t) cc_final: 0.7167 (p) REVERT: A 66 GLU cc_start: 0.8334 (pt0) cc_final: 0.7985 (pt0) REVERT: A 86 ASP cc_start: 0.7661 (t0) cc_final: 0.7275 (t0) REVERT: A 95 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7722 (mtt-85) REVERT: A 119 MET cc_start: 0.8439 (mmt) cc_final: 0.8120 (mmt) REVERT: A 271 GLU cc_start: 0.7528 (pt0) cc_final: 0.7100 (pt0) REVERT: A 302 ASP cc_start: 0.7718 (t0) cc_final: 0.7171 (t0) REVERT: A 303 LYS cc_start: 0.8122 (ptmm) cc_final: 0.7584 (ptpp) REVERT: A 311 GLU cc_start: 0.7018 (tp30) cc_final: 0.6764 (tp30) REVERT: A 347 ILE cc_start: 0.7602 (mt) cc_final: 0.7244 (tp) REVERT: A 373 MET cc_start: 0.6927 (mmm) cc_final: 0.6714 (mmp) REVERT: A 380 LYS cc_start: 0.7155 (mtmt) cc_final: 0.6872 (mttp) REVERT: A 409 SER cc_start: 0.8581 (t) cc_final: 0.8090 (p) REVERT: A 425 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6965 (mt-10) REVERT: A 465 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7738 (mm-30) REVERT: A 518 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6376 (mm-30) REVERT: B 16 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7123 (mtm) REVERT: B 50 SER cc_start: 0.7797 (t) cc_final: 0.7371 (p) REVERT: B 51 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6980 (mt-10) REVERT: B 135 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7293 (mt-10) REVERT: B 138 GLU cc_start: 0.7368 (mp0) cc_final: 0.6962 (mp0) REVERT: B 302 ASP cc_start: 0.7593 (t0) cc_final: 0.7136 (t0) REVERT: B 303 LYS cc_start: 0.8315 (ptmm) cc_final: 0.7748 (ptpp) REVERT: B 326 TYR cc_start: 0.7519 (m-80) cc_final: 0.7006 (m-80) REVERT: B 347 ILE cc_start: 0.7848 (mt) cc_final: 0.7530 (tp) REVERT: B 360 CYS cc_start: 0.6907 (m) cc_final: 0.6668 (m) REVERT: B 370 GLN cc_start: 0.7169 (mm-40) cc_final: 0.6909 (mm-40) REVERT: B 391 LYS cc_start: 0.7543 (mptt) cc_final: 0.7264 (mmtp) REVERT: B 399 CYS cc_start: 0.7020 (m) cc_final: 0.6599 (m) REVERT: B 425 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6987 (mt-10) REVERT: B 480 ASP cc_start: 0.7112 (m-30) cc_final: 0.6837 (m-30) REVERT: B 485 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7832 (ttpp) REVERT: B 488 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 511 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7228 (mp) REVERT: B 518 GLU cc_start: 0.7147 (tp30) cc_final: 0.6517 (mm-30) REVERT: C 29 MET cc_start: 0.7124 (mmm) cc_final: 0.6754 (mmm) REVERT: C 44 MET cc_start: 0.7288 (mmm) cc_final: 0.6787 (mmm) REVERT: C 49 MET cc_start: 0.7426 (mmm) cc_final: 0.7008 (mmm) REVERT: C 120 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7620 (ttmm) REVERT: C 213 GLU cc_start: 0.7677 (pt0) cc_final: 0.7475 (pt0) REVERT: C 273 TYR cc_start: 0.8594 (m-80) cc_final: 0.8174 (m-80) REVERT: C 301 SER cc_start: 0.7652 (t) cc_final: 0.7280 (p) REVERT: C 326 TYR cc_start: 0.7445 (m-80) cc_final: 0.6943 (m-80) REVERT: C 359 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6767 (mt-10) REVERT: C 386 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7879 (mtpt) REVERT: C 391 LYS cc_start: 0.7870 (mptt) cc_final: 0.7599 (mmtp) REVERT: C 396 MET cc_start: 0.7847 (mmp) cc_final: 0.7545 (mmm) REVERT: C 399 CYS cc_start: 0.6771 (m) cc_final: 0.6297 (m) REVERT: C 468 MET cc_start: 0.8623 (mmm) cc_final: 0.8388 (mmm) REVERT: C 480 ASP cc_start: 0.7050 (m-30) cc_final: 0.6803 (m-30) REVERT: C 489 SER cc_start: 0.8031 (m) cc_final: 0.7756 (m) outliers start: 44 outliers final: 18 residues processed: 384 average time/residue: 1.6611 time to fit residues: 681.0312 Evaluate side-chains 359 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 335 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 482 ASN B 108 ASN B 141 GLN C 475 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13362 Z= 0.222 Angle : 0.547 8.024 18096 Z= 0.279 Chirality : 0.042 0.163 1986 Planarity : 0.004 0.045 2328 Dihedral : 4.533 28.354 2172 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.41 % Allowed : 15.14 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.21), residues: 1569 helix: 1.76 (0.21), residues: 690 sheet: 1.06 (0.30), residues: 273 loop : 0.21 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 349 HIS 0.003 0.001 HIS A 260 PHE 0.014 0.001 PHE A 10 TYR 0.014 0.001 TYR A 118 ARG 0.004 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 349 time to evaluate : 1.458 Fit side-chains REVERT: A 7 MET cc_start: 0.6938 (mmm) cc_final: 0.6709 (mmp) REVERT: A 16 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7383 (mtt) REVERT: A 29 MET cc_start: 0.7010 (mmm) cc_final: 0.6591 (mmm) REVERT: A 31 ARG cc_start: 0.6497 (ttm170) cc_final: 0.6141 (ttm170) REVERT: A 49 MET cc_start: 0.7486 (mmp) cc_final: 0.7254 (mmm) REVERT: A 50 SER cc_start: 0.7559 (t) cc_final: 0.7185 (p) REVERT: A 66 GLU cc_start: 0.8312 (pt0) cc_final: 0.7971 (pt0) REVERT: A 86 ASP cc_start: 0.7657 (t0) cc_final: 0.7278 (t0) REVERT: A 95 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7545 (mtt-85) REVERT: A 119 MET cc_start: 0.8444 (mmt) cc_final: 0.8113 (mmt) REVERT: A 271 GLU cc_start: 0.7599 (pt0) cc_final: 0.7192 (pt0) REVERT: A 302 ASP cc_start: 0.7717 (t0) cc_final: 0.7204 (t0) REVERT: A 303 LYS cc_start: 0.8133 (ptmm) cc_final: 0.7626 (ptpp) REVERT: A 311 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6680 (tp30) REVERT: A 347 ILE cc_start: 0.7584 (mt) cc_final: 0.7233 (tp) REVERT: A 373 MET cc_start: 0.6923 (mmm) cc_final: 0.6640 (mmp) REVERT: A 409 SER cc_start: 0.8569 (t) cc_final: 0.8094 (p) REVERT: A 425 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6977 (mt-10) REVERT: A 465 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7736 (mm-30) REVERT: B 16 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7136 (mtm) REVERT: B 50 SER cc_start: 0.7788 (t) cc_final: 0.7379 (p) REVERT: B 113 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6699 (mm-30) REVERT: B 138 GLU cc_start: 0.7382 (mp0) cc_final: 0.7000 (mp0) REVERT: B 141 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7890 (mm110) REVERT: B 156 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7119 (mm-30) REVERT: B 302 ASP cc_start: 0.7577 (t0) cc_final: 0.7128 (t0) REVERT: B 303 LYS cc_start: 0.8306 (ptmm) cc_final: 0.7740 (ptpp) REVERT: B 326 TYR cc_start: 0.7518 (m-80) cc_final: 0.7068 (m-80) REVERT: B 347 ILE cc_start: 0.7891 (mt) cc_final: 0.7573 (tp) REVERT: B 370 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6935 (mm-40) REVERT: B 391 LYS cc_start: 0.7526 (mptt) cc_final: 0.7242 (mmtp) REVERT: B 399 CYS cc_start: 0.7035 (m) cc_final: 0.6628 (m) REVERT: B 407 GLU cc_start: 0.7795 (tt0) cc_final: 0.7569 (tt0) REVERT: B 425 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7013 (mt-10) REVERT: B 437 GLU cc_start: 0.7736 (tp30) cc_final: 0.7183 (tm-30) REVERT: B 453 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7277 (mt-10) REVERT: B 466 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7263 (mm-30) REVERT: B 480 ASP cc_start: 0.7109 (m-30) cc_final: 0.6838 (m-30) REVERT: B 485 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7830 (ttpp) REVERT: B 511 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7231 (mp) REVERT: C 7 MET cc_start: 0.6887 (mmm) cc_final: 0.6580 (mpm) REVERT: C 29 MET cc_start: 0.7130 (mmm) cc_final: 0.6754 (mmm) REVERT: C 44 MET cc_start: 0.7297 (mmm) cc_final: 0.6784 (mmm) REVERT: C 49 MET cc_start: 0.7389 (mmm) cc_final: 0.7004 (mmm) REVERT: C 86 ASP cc_start: 0.7834 (t0) cc_final: 0.7625 (t0) REVERT: C 120 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7606 (ttmm) REVERT: C 156 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7297 (mm-30) REVERT: C 238 MET cc_start: 0.8269 (tpt) cc_final: 0.7990 (tpt) REVERT: C 273 TYR cc_start: 0.8585 (m-80) cc_final: 0.8147 (m-80) REVERT: C 293 ILE cc_start: 0.7841 (mm) cc_final: 0.7600 (mt) REVERT: C 301 SER cc_start: 0.7662 (t) cc_final: 0.7235 (p) REVERT: C 326 TYR cc_start: 0.7463 (m-80) cc_final: 0.6954 (m-80) REVERT: C 359 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6532 (tp30) REVERT: C 386 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7909 (ttpt) REVERT: C 391 LYS cc_start: 0.7876 (mptt) cc_final: 0.7592 (mmtp) REVERT: C 396 MET cc_start: 0.7849 (mmp) cc_final: 0.7557 (mmm) REVERT: C 399 CYS cc_start: 0.6787 (m) cc_final: 0.6318 (m) REVERT: C 453 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7428 (mt-10) REVERT: C 468 MET cc_start: 0.8619 (mmm) cc_final: 0.8396 (mmm) REVERT: C 480 ASP cc_start: 0.7061 (m-30) cc_final: 0.6827 (m-30) REVERT: C 489 SER cc_start: 0.8164 (m) cc_final: 0.7889 (m) outliers start: 48 outliers final: 19 residues processed: 367 average time/residue: 1.6342 time to fit residues: 642.0818 Evaluate side-chains 364 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 337 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 173 HIS A 482 ASN B 108 ASN B 141 GLN B 376 HIS C 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13362 Z= 0.191 Angle : 0.554 8.487 18096 Z= 0.282 Chirality : 0.042 0.243 1986 Planarity : 0.004 0.044 2328 Dihedral : 4.540 28.265 2172 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.99 % Allowed : 15.99 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.21), residues: 1569 helix: 1.76 (0.21), residues: 690 sheet: 1.03 (0.30), residues: 273 loop : 0.16 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 349 HIS 0.003 0.001 HIS A 260 PHE 0.014 0.001 PHE A 10 TYR 0.014 0.001 TYR A 118 ARG 0.010 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 337 time to evaluate : 1.524 Fit side-chains REVERT: A 7 MET cc_start: 0.6947 (mmm) cc_final: 0.6703 (mmp) REVERT: A 29 MET cc_start: 0.7001 (mmm) cc_final: 0.6585 (mmm) REVERT: A 31 ARG cc_start: 0.6487 (ttm170) cc_final: 0.6130 (ttm170) REVERT: A 49 MET cc_start: 0.7484 (mmp) cc_final: 0.7251 (mmm) REVERT: A 50 SER cc_start: 0.7572 (t) cc_final: 0.7210 (p) REVERT: A 86 ASP cc_start: 0.7650 (t0) cc_final: 0.7280 (t0) REVERT: A 95 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7538 (mtt-85) REVERT: A 119 MET cc_start: 0.8440 (mmt) cc_final: 0.8161 (mmt) REVERT: A 156 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7391 (mm-30) REVERT: A 302 ASP cc_start: 0.7698 (t0) cc_final: 0.7186 (t0) REVERT: A 303 LYS cc_start: 0.8095 (ptmm) cc_final: 0.7589 (ptpp) REVERT: A 329 GLU cc_start: 0.7504 (tt0) cc_final: 0.7167 (tt0) REVERT: A 347 ILE cc_start: 0.7573 (mt) cc_final: 0.7233 (tp) REVERT: A 373 MET cc_start: 0.6891 (mmm) cc_final: 0.6642 (mmp) REVERT: A 380 LYS cc_start: 0.6972 (mtmt) cc_final: 0.6719 (mttp) REVERT: A 409 SER cc_start: 0.8545 (t) cc_final: 0.8071 (p) REVERT: A 425 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6970 (mt-10) REVERT: A 437 GLU cc_start: 0.7611 (tp30) cc_final: 0.7076 (tm-30) REVERT: A 465 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 16 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7161 (mtm) REVERT: B 50 SER cc_start: 0.7787 (t) cc_final: 0.7386 (p) REVERT: B 113 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6695 (mm-30) REVERT: B 131 ASN cc_start: 0.7968 (m-40) cc_final: 0.7634 (m110) REVERT: B 138 GLU cc_start: 0.7395 (mp0) cc_final: 0.6994 (mp0) REVERT: B 141 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7711 (mm-40) REVERT: B 156 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7133 (mm-30) REVERT: B 302 ASP cc_start: 0.7574 (t0) cc_final: 0.7123 (t0) REVERT: B 303 LYS cc_start: 0.8308 (ptmm) cc_final: 0.7735 (ptpp) REVERT: B 326 TYR cc_start: 0.7514 (m-80) cc_final: 0.7025 (m-80) REVERT: B 347 ILE cc_start: 0.7883 (mt) cc_final: 0.7571 (tp) REVERT: B 370 GLN cc_start: 0.7050 (mm-40) cc_final: 0.6779 (mm-40) REVERT: B 391 LYS cc_start: 0.7524 (mptt) cc_final: 0.7237 (mmtp) REVERT: B 399 CYS cc_start: 0.7024 (m) cc_final: 0.6604 (m) REVERT: B 425 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7018 (mt-10) REVERT: B 437 GLU cc_start: 0.7740 (tp30) cc_final: 0.7180 (tm-30) REVERT: B 453 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7272 (mt-10) REVERT: B 466 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7286 (mm-30) REVERT: B 480 ASP cc_start: 0.7108 (m-30) cc_final: 0.6839 (m-30) REVERT: B 485 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7834 (ttpp) REVERT: B 511 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7188 (mp) REVERT: C 7 MET cc_start: 0.6895 (mmm) cc_final: 0.6587 (mpm) REVERT: C 29 MET cc_start: 0.7025 (mmm) cc_final: 0.6670 (mmm) REVERT: C 44 MET cc_start: 0.7292 (mmm) cc_final: 0.6750 (mmm) REVERT: C 49 MET cc_start: 0.7387 (mmm) cc_final: 0.7111 (mmm) REVERT: C 86 ASP cc_start: 0.7830 (t0) cc_final: 0.7624 (t0) REVERT: C 120 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7585 (ttmm) REVERT: C 156 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7269 (mm-30) REVERT: C 273 TYR cc_start: 0.8577 (m-80) cc_final: 0.8138 (m-80) REVERT: C 293 ILE cc_start: 0.7818 (mm) cc_final: 0.7587 (mt) REVERT: C 301 SER cc_start: 0.7662 (t) cc_final: 0.7211 (p) REVERT: C 326 TYR cc_start: 0.7421 (m-80) cc_final: 0.6900 (m-80) REVERT: C 355 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7056 (p0) REVERT: C 359 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6548 (tp30) REVERT: C 380 LYS cc_start: 0.7366 (mtmt) cc_final: 0.7134 (mttt) REVERT: C 386 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7832 (ttpt) REVERT: C 391 LYS cc_start: 0.7869 (mptt) cc_final: 0.7582 (mmtp) REVERT: C 396 MET cc_start: 0.7846 (mmp) cc_final: 0.7519 (mmm) REVERT: C 399 CYS cc_start: 0.6780 (m) cc_final: 0.6309 (m) REVERT: C 453 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7445 (mt-10) REVERT: C 468 MET cc_start: 0.8616 (mmm) cc_final: 0.8369 (mmm) REVERT: C 480 ASP cc_start: 0.7047 (m-30) cc_final: 0.6815 (m-30) REVERT: C 489 SER cc_start: 0.8126 (m) cc_final: 0.7851 (m) outliers start: 42 outliers final: 19 residues processed: 355 average time/residue: 1.5861 time to fit residues: 603.5638 Evaluate side-chains 360 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 334 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 523 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN B 108 ASN B 141 GLN C 475 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13362 Z= 0.228 Angle : 0.568 8.581 18096 Z= 0.289 Chirality : 0.043 0.179 1986 Planarity : 0.004 0.056 2328 Dihedral : 4.556 28.251 2172 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.84 % Allowed : 16.92 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1569 helix: 1.71 (0.21), residues: 690 sheet: 1.00 (0.30), residues: 273 loop : 0.12 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 349 HIS 0.003 0.001 HIS A 260 PHE 0.015 0.001 PHE B 140 TYR 0.014 0.001 TYR A 118 ARG 0.013 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 340 time to evaluate : 1.689 Fit side-chains REVERT: A 7 MET cc_start: 0.6954 (mmm) cc_final: 0.6707 (mmp) REVERT: A 29 MET cc_start: 0.7000 (mmm) cc_final: 0.6581 (mmm) REVERT: A 31 ARG cc_start: 0.6487 (ttm170) cc_final: 0.6136 (ttm170) REVERT: A 49 MET cc_start: 0.7493 (mmp) cc_final: 0.7256 (mmm) REVERT: A 50 SER cc_start: 0.7591 (t) cc_final: 0.7230 (p) REVERT: A 86 ASP cc_start: 0.7677 (t0) cc_final: 0.7275 (t0) REVERT: A 95 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7545 (mtt-85) REVERT: A 119 MET cc_start: 0.8441 (mmt) cc_final: 0.8151 (mmt) REVERT: A 156 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7384 (mm-30) REVERT: A 302 ASP cc_start: 0.7708 (t0) cc_final: 0.7203 (t0) REVERT: A 303 LYS cc_start: 0.8089 (ptmm) cc_final: 0.7585 (ptpp) REVERT: A 311 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6586 (mm-30) REVERT: A 329 GLU cc_start: 0.7518 (tt0) cc_final: 0.7187 (tt0) REVERT: A 347 ILE cc_start: 0.7645 (mt) cc_final: 0.7297 (tp) REVERT: A 373 MET cc_start: 0.6888 (mmm) cc_final: 0.6645 (mmp) REVERT: A 380 LYS cc_start: 0.6941 (mtmt) cc_final: 0.6710 (mttp) REVERT: A 409 SER cc_start: 0.8545 (t) cc_final: 0.8073 (p) REVERT: A 425 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6975 (mt-10) REVERT: A 437 GLU cc_start: 0.7662 (tp30) cc_final: 0.7108 (tm-30) REVERT: A 465 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7747 (mm-30) REVERT: B 16 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7155 (mtm) REVERT: B 50 SER cc_start: 0.7791 (t) cc_final: 0.7385 (p) REVERT: B 113 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6730 (mm-30) REVERT: B 131 ASN cc_start: 0.7968 (m-40) cc_final: 0.7637 (m110) REVERT: B 138 GLU cc_start: 0.7394 (mp0) cc_final: 0.7020 (mp0) REVERT: B 156 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7136 (mm-30) REVERT: B 302 ASP cc_start: 0.7584 (t0) cc_final: 0.7137 (t0) REVERT: B 303 LYS cc_start: 0.8303 (ptmm) cc_final: 0.7738 (ptpp) REVERT: B 326 TYR cc_start: 0.7521 (m-80) cc_final: 0.7017 (m-80) REVERT: B 347 ILE cc_start: 0.7906 (mt) cc_final: 0.7605 (tp) REVERT: B 366 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5848 (pm20) REVERT: B 370 GLN cc_start: 0.7044 (mm-40) cc_final: 0.6759 (mm-40) REVERT: B 391 LYS cc_start: 0.7517 (mptt) cc_final: 0.7224 (mmtp) REVERT: B 399 CYS cc_start: 0.7031 (m) cc_final: 0.6638 (m) REVERT: B 425 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7017 (mt-10) REVERT: B 437 GLU cc_start: 0.7740 (tp30) cc_final: 0.7216 (tm-30) REVERT: B 453 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7269 (mt-10) REVERT: B 466 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7284 (mm-30) REVERT: B 480 ASP cc_start: 0.7111 (m-30) cc_final: 0.6845 (m-30) REVERT: B 485 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7813 (ttpp) REVERT: B 511 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7215 (mp) REVERT: C 7 MET cc_start: 0.6836 (mmm) cc_final: 0.6557 (mpm) REVERT: C 29 MET cc_start: 0.7021 (mmm) cc_final: 0.6666 (mmm) REVERT: C 39 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6708 (mp) REVERT: C 44 MET cc_start: 0.7296 (mmm) cc_final: 0.6751 (mmm) REVERT: C 49 MET cc_start: 0.7390 (mmm) cc_final: 0.7110 (mmm) REVERT: C 86 ASP cc_start: 0.7777 (t0) cc_final: 0.7552 (t0) REVERT: C 100 ASP cc_start: 0.7548 (t0) cc_final: 0.7210 (t0) REVERT: C 120 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7604 (ttmm) REVERT: C 156 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7275 (mm-30) REVERT: C 238 MET cc_start: 0.8285 (tpt) cc_final: 0.8009 (tpt) REVERT: C 273 TYR cc_start: 0.8581 (m-80) cc_final: 0.8140 (m-80) REVERT: C 293 ILE cc_start: 0.7853 (mm) cc_final: 0.7641 (mt) REVERT: C 301 SER cc_start: 0.7646 (t) cc_final: 0.7302 (t) REVERT: C 326 TYR cc_start: 0.7444 (m-80) cc_final: 0.6935 (m-80) REVERT: C 355 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.7062 (p0) REVERT: C 359 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6566 (tp30) REVERT: C 380 LYS cc_start: 0.7170 (mtmt) cc_final: 0.6918 (mttt) REVERT: C 386 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7836 (ttpt) REVERT: C 391 LYS cc_start: 0.7872 (mptt) cc_final: 0.7582 (mmtp) REVERT: C 396 MET cc_start: 0.7767 (mmp) cc_final: 0.7471 (mmm) REVERT: C 399 CYS cc_start: 0.6793 (m) cc_final: 0.6324 (m) REVERT: C 463 ASN cc_start: 0.8086 (t0) cc_final: 0.7870 (t0) REVERT: C 468 MET cc_start: 0.8617 (mmm) cc_final: 0.8289 (mmm) REVERT: C 480 ASP cc_start: 0.7073 (m-30) cc_final: 0.6824 (m-30) REVERT: C 489 SER cc_start: 0.8120 (m) cc_final: 0.7853 (m) outliers start: 40 outliers final: 19 residues processed: 356 average time/residue: 1.5313 time to fit residues: 584.8233 Evaluate side-chains 364 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 336 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 523 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 143 optimal weight: 0.0670 chunk 123 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.0570 chunk 98 optimal weight: 1.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN B 108 ASN B 141 GLN C 475 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13362 Z= 0.162 Angle : 0.550 8.434 18096 Z= 0.277 Chirality : 0.042 0.161 1986 Planarity : 0.004 0.059 2328 Dihedral : 4.477 27.943 2172 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.06 % Allowed : 17.98 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.21), residues: 1569 helix: 1.82 (0.21), residues: 687 sheet: 0.98 (0.30), residues: 273 loop : 0.12 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 349 HIS 0.003 0.001 HIS C 260 PHE 0.013 0.001 PHE A 10 TYR 0.013 0.001 TYR A 118 ARG 0.014 0.000 ARG C 494 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 336 time to evaluate : 1.488 Fit side-chains REVERT: A 7 MET cc_start: 0.6960 (mmm) cc_final: 0.6710 (mmp) REVERT: A 29 MET cc_start: 0.6987 (mmm) cc_final: 0.6573 (mmm) REVERT: A 31 ARG cc_start: 0.6477 (ttm170) cc_final: 0.6159 (ttm170) REVERT: A 49 MET cc_start: 0.7475 (mmp) cc_final: 0.7256 (mmm) REVERT: A 50 SER cc_start: 0.7584 (t) cc_final: 0.7324 (p) REVERT: A 86 ASP cc_start: 0.7647 (t0) cc_final: 0.7277 (t0) REVERT: A 95 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7530 (mtt-85) REVERT: A 119 MET cc_start: 0.8413 (mmt) cc_final: 0.8166 (mmt) REVERT: A 271 GLU cc_start: 0.7505 (pt0) cc_final: 0.7162 (pt0) REVERT: A 302 ASP cc_start: 0.7686 (t0) cc_final: 0.7154 (t0) REVERT: A 303 LYS cc_start: 0.8068 (ptmm) cc_final: 0.7544 (ptpp) REVERT: A 347 ILE cc_start: 0.7639 (mt) cc_final: 0.7308 (tp) REVERT: A 373 MET cc_start: 0.6833 (mmm) cc_final: 0.6624 (mmp) REVERT: A 380 LYS cc_start: 0.6909 (mtmt) cc_final: 0.6702 (mttm) REVERT: A 391 LYS cc_start: 0.8228 (mppt) cc_final: 0.8002 (mmtp) REVERT: A 409 SER cc_start: 0.8546 (t) cc_final: 0.8079 (p) REVERT: A 425 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6972 (mt-10) REVERT: A 465 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 16 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7162 (mtm) REVERT: B 50 SER cc_start: 0.7785 (t) cc_final: 0.7378 (p) REVERT: B 53 LEU cc_start: 0.7076 (mt) cc_final: 0.6846 (mp) REVERT: B 82 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8266 (mtm) REVERT: B 113 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6721 (mm-30) REVERT: B 131 ASN cc_start: 0.7960 (m-40) cc_final: 0.7648 (m110) REVERT: B 138 GLU cc_start: 0.7380 (mp0) cc_final: 0.7019 (mp0) REVERT: B 156 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7132 (mm-30) REVERT: B 302 ASP cc_start: 0.7568 (t0) cc_final: 0.7115 (t0) REVERT: B 303 LYS cc_start: 0.8310 (ptmm) cc_final: 0.7735 (ptpp) REVERT: B 319 GLN cc_start: 0.7343 (mt0) cc_final: 0.7129 (mt0) REVERT: B 326 TYR cc_start: 0.7523 (m-80) cc_final: 0.7084 (m-80) REVERT: B 347 ILE cc_start: 0.7900 (mt) cc_final: 0.7615 (tp) REVERT: B 370 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6767 (mm-40) REVERT: B 399 CYS cc_start: 0.7003 (m) cc_final: 0.6629 (m) REVERT: B 425 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7007 (mt-10) REVERT: B 437 GLU cc_start: 0.7735 (tp30) cc_final: 0.7178 (tm-30) REVERT: B 453 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7254 (mt-10) REVERT: B 466 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7276 (mm-30) REVERT: B 480 ASP cc_start: 0.7089 (m-30) cc_final: 0.6825 (m-30) REVERT: B 485 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7827 (ttpp) REVERT: B 511 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7185 (mp) REVERT: C 7 MET cc_start: 0.6916 (mmm) cc_final: 0.6625 (mpm) REVERT: C 29 MET cc_start: 0.7012 (mmm) cc_final: 0.6657 (mmm) REVERT: C 44 MET cc_start: 0.7296 (mmm) cc_final: 0.6761 (mmm) REVERT: C 49 MET cc_start: 0.7383 (mmm) cc_final: 0.7105 (mmm) REVERT: C 86 ASP cc_start: 0.7777 (t0) cc_final: 0.7552 (t0) REVERT: C 120 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7580 (ttmm) REVERT: C 156 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7271 (mm-30) REVERT: C 273 TYR cc_start: 0.8567 (m-80) cc_final: 0.8149 (m-80) REVERT: C 293 ILE cc_start: 0.7853 (mm) cc_final: 0.7642 (mt) REVERT: C 301 SER cc_start: 0.7662 (t) cc_final: 0.7317 (t) REVERT: C 316 MET cc_start: 0.7547 (mtp) cc_final: 0.7263 (ptp) REVERT: C 326 TYR cc_start: 0.7395 (m-80) cc_final: 0.6899 (m-80) REVERT: C 355 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.7089 (p0) REVERT: C 359 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6554 (tp30) REVERT: C 380 LYS cc_start: 0.7153 (mtmt) cc_final: 0.6950 (mttt) REVERT: C 386 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7786 (ttpt) REVERT: C 391 LYS cc_start: 0.7846 (mptt) cc_final: 0.7600 (mptt) REVERT: C 396 MET cc_start: 0.7837 (mmp) cc_final: 0.7501 (mmm) REVERT: C 399 CYS cc_start: 0.6785 (m) cc_final: 0.6318 (m) REVERT: C 453 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7432 (mt-10) REVERT: C 463 ASN cc_start: 0.8081 (t0) cc_final: 0.7849 (t0) REVERT: C 468 MET cc_start: 0.8613 (mmm) cc_final: 0.8369 (mmm) REVERT: C 480 ASP cc_start: 0.7070 (m-30) cc_final: 0.6805 (m-30) REVERT: C 489 SER cc_start: 0.8149 (m) cc_final: 0.7872 (m) outliers start: 29 outliers final: 14 residues processed: 346 average time/residue: 1.6713 time to fit residues: 621.2093 Evaluate side-chains 353 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 333 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 chunk 18 optimal weight: 0.0470 chunk 34 optimal weight: 0.0870 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 127 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN B 108 ASN B 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.130555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118772 restraints weight = 17045.666| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.72 r_work: 0.3511 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13362 Z= 0.152 Angle : 0.537 8.778 18096 Z= 0.272 Chirality : 0.041 0.151 1986 Planarity : 0.004 0.052 2328 Dihedral : 4.360 27.224 2172 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.85 % Allowed : 18.05 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.21), residues: 1569 helix: 1.93 (0.21), residues: 681 sheet: 1.01 (0.30), residues: 273 loop : 0.12 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 349 HIS 0.003 0.001 HIS C 260 PHE 0.013 0.001 PHE A 10 TYR 0.013 0.001 TYR C 414 ARG 0.013 0.000 ARG C 494 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8655.15 seconds wall clock time: 154 minutes 13.60 seconds (9253.60 seconds total)