Starting phenix.real_space_refine on Sat Aug 23 15:23:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8on7_16981/08_2025/8on7_16981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8on7_16981/08_2025/8on7_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/cci-nas-00/data/ceres_data/8on7_16981/08_2025/8on7_16981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8on7_16981/08_2025/8on7_16981.map" model { file = "/net/cci-nas-00/data/ceres_data/8on7_16981/08_2025/8on7_16981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8on7_16981/08_2025/8on7_16981.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13032 Number of models: 1 Model: "" Number of chains: 18 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: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} 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: 2.79, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, 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 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 459.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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... Secondary structure from input PDB file: 63 helices and 9 sheets defined 47.5% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 18 through 24 Processing helix chain 'A' and resid 27 through 58 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 112 through 124 removed outlier: 3.628A pdb=" N LYS A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.901A pdb=" N PHE A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.631A pdb=" N CYS A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 365 through 390 removed outlier: 4.603A pdb=" N THR A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 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 423 through 435 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 512 through 528 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 18 through 24 Processing helix chain 'B' and resid 27 through 58 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.628A pdb=" N LYS B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 136 through 144 Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.901A pdb=" N PHE B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.631A pdb=" N CYS B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 365 through 390 removed outlier: 4.603A pdb=" N THR B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 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 423 through 435 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'B' and resid 512 through 528 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 18 through 24 Processing helix chain 'C' and resid 27 through 58 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 112 through 124 removed outlier: 3.628A pdb=" N LYS C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 145 through 153 removed outlier: 3.901A pdb=" N PHE C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 314 through 332 removed outlier: 3.630A pdb=" N CYS C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 365 through 390 removed outlier: 4.603A pdb=" N THR C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 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 423 through 435 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 493 through 508 Processing helix chain 'C' and resid 512 through 528 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 removed outlier: 9.247A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU A 490 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 279 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY A 218 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR A 174 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER A 220 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS A 172 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 222 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 68 removed outlier: 9.247A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU A 490 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, first strand: chain 'B' and resid 61 through 68 removed outlier: 9.247A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU B 490 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE B 279 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY B 218 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR B 174 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER B 220 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS B 172 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 222 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 68 removed outlier: 9.247A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU B 490 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AA6, 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=AA7, first strand: chain 'C' and resid 61 through 68 removed outlier: 9.246A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU C 490 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE C 279 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY C 218 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR C 174 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER C 220 " --> pdb=" O CYS C 172 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS C 172 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE C 222 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 68 removed outlier: 9.246A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU C 490 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AA9, 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) 685 hydrogen bonds defined for protein. 1911 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: 1.82 Time building geometry restraints manager: 1.36 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: 4176 1.35 - 1.47: 3312 1.47 - 1.59: 5709 1.59 - 1.71: 0 1.71 - 1.83: 162 Bond restraints: 13359 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 13354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 17457 1.73 - 3.46: 537 3.46 - 5.19: 71 5.19 - 6.92: 19 6.92 - 8.65: 6 Bond angle restraints: 18090 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 18085 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: 2340 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 2337 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 127 2.68 - 3.23: 12279 3.23 - 3.79: 20203 3.79 - 4.34: 28672 4.34 - 4.90: 46440 Nonbonded interactions: 107721 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 107716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 0.680 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.460 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.790 ------------------------------------------------------------------------------- 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 0.109 13407 Z= 0.264 Angle : 0.735 9.082 18201 Z= 0.394 Chirality : 0.045 0.200 1986 Planarity : 0.005 0.044 2325 Dihedral : 13.287 87.791 5253 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.52 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG E 611 TYR 0.018 0.001 TYR B 118 PHE 0.023 0.002 PHE C 10 TRP 0.033 0.003 TRP B 34 HIS 0.006 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00385 (13359) covalent geometry : angle 0.71384 (18090) SS BOND : bond 0.00215 ( 24) SS BOND : angle 1.02601 ( 48) hydrogen bonds : bond 0.15082 ( 661) hydrogen bonds : angle 6.37183 ( 1911) Misc. bond : bond 0.10909 ( 3) link_BETA1-4 : bond 0.00599 ( 6) link_BETA1-4 : angle 1.62149 ( 18) link_NAG-ASN : bond 0.00249 ( 15) link_NAG-ASN : angle 3.39080 ( 45) *********************** 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 to be fit. rotamer outliers: 3 poor density : 462 time to evaluate : 0.343 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: 0.5926 time to fit residues: 292.8590 Evaluate side-chains 359 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.0770 chunk 149 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.127248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115426 restraints weight = 17255.748| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.73 r_work: 0.3463 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13407 Z= 0.137 Angle : 0.628 12.614 18201 Z= 0.325 Chirality : 0.044 0.232 1986 Planarity : 0.005 0.048 2325 Dihedral : 5.290 36.526 2172 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.99 % Allowed : 11.58 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.21), residues: 1569 helix: 1.54 (0.20), residues: 690 sheet: 1.41 (0.29), residues: 267 loop : 0.65 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 288 TYR 0.014 0.001 TYR C 118 PHE 0.018 0.001 PHE A 10 TRP 0.014 0.002 TRP B 34 HIS 0.005 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00310 (13359) covalent geometry : angle 0.60490 (18090) SS BOND : bond 0.00550 ( 24) SS BOND : angle 2.48192 ( 48) hydrogen bonds : bond 0.04580 ( 661) hydrogen bonds : angle 4.90215 ( 1911) Misc. bond : bond 0.00063 ( 3) link_BETA1-4 : bond 0.00605 ( 6) link_BETA1-4 : angle 1.37995 ( 18) link_NAG-ASN : bond 0.00319 ( 15) link_NAG-ASN : angle 2.30339 ( 45) *********************** 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 437 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 395 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7279 (mmm) cc_final: 0.7079 (mmm) REVERT: A 138 GLU cc_start: 0.7779 (mp0) cc_final: 0.7564 (mp0) REVERT: A 216 GLU cc_start: 0.7746 (mp0) cc_final: 0.7541 (mp0) REVERT: A 271 GLU cc_start: 0.7794 (pt0) cc_final: 0.7572 (pt0) REVERT: A 273 TYR cc_start: 0.8478 (m-80) cc_final: 0.8254 (m-80) REVERT: A 302 ASP cc_start: 0.8113 (t0) cc_final: 0.7680 (t0) REVERT: A 347 ILE cc_start: 0.8225 (mt) cc_final: 0.8019 (tp) REVERT: A 353 ASP cc_start: 0.7689 (p0) cc_final: 0.7375 (p0) REVERT: A 465 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7910 (mm-30) REVERT: B 121 LYS cc_start: 0.8303 (mtpp) cc_final: 0.8088 (tttm) REVERT: B 138 GLU cc_start: 0.7800 (mp0) cc_final: 0.7559 (mp0) REVERT: B 164 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8042 (mm-40) REVERT: B 256 ARG cc_start: 0.8550 (tpt170) cc_final: 0.8317 (tpt170) REVERT: B 293 ILE cc_start: 0.8569 (mm) cc_final: 0.8333 (mt) REVERT: B 302 ASP cc_start: 0.7903 (t0) cc_final: 0.7508 (t0) REVERT: B 326 TYR cc_start: 0.8848 (m-80) cc_final: 0.8584 (m-80) REVERT: B 360 CYS cc_start: 0.7211 (m) cc_final: 0.6970 (m) REVERT: C 213 GLU cc_start: 0.7718 (pt0) cc_final: 0.7462 (pt0) REVERT: C 273 TYR cc_start: 0.8557 (m-80) cc_final: 0.8305 (m-80) REVERT: C 326 TYR cc_start: 0.8693 (m-80) cc_final: 0.8452 (m-80) REVERT: C 353 ASP cc_start: 0.7530 (p0) cc_final: 0.7328 (p0) REVERT: C 363 THR cc_start: 0.8739 (m) cc_final: 0.8488 (p) REVERT: C 399 CYS cc_start: 0.7400 (m) cc_final: 0.7180 (m) REVERT: C 468 MET cc_start: 0.8813 (mmm) cc_final: 0.8573 (mmm) outliers start: 42 outliers final: 6 residues processed: 414 average time/residue: 0.6554 time to fit residues: 289.4777 Evaluate side-chains 341 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 335 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 511 ILE 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 94 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 136 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 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 449 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.127059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115334 restraints weight = 17556.356| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.71 r_work: 0.3466 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13407 Z= 0.136 Angle : 0.620 12.910 18201 Z= 0.315 Chirality : 0.044 0.227 1986 Planarity : 0.005 0.050 2325 Dihedral : 5.191 31.741 2172 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.56 % Allowed : 14.50 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.21), residues: 1569 helix: 1.68 (0.20), residues: 690 sheet: 1.30 (0.30), residues: 270 loop : 0.51 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 187 TYR 0.014 0.001 TYR C 118 PHE 0.014 0.001 PHE B 443 TRP 0.013 0.002 TRP A 349 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00309 (13359) covalent geometry : angle 0.59753 (18090) SS BOND : bond 0.00899 ( 24) SS BOND : angle 2.35951 ( 48) hydrogen bonds : bond 0.04298 ( 661) hydrogen bonds : angle 4.52018 ( 1911) Misc. bond : bond 0.00030 ( 3) link_BETA1-4 : bond 0.00610 ( 6) link_BETA1-4 : angle 1.31244 ( 18) link_NAG-ASN : bond 0.00256 ( 15) link_NAG-ASN : angle 2.27274 ( 45) *********************** 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 386 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 350 time to evaluate : 0.503 Fit side-chains REVERT: A 21 LYS cc_start: 0.8003 (mmtp) cc_final: 0.7741 (mttt) REVERT: A 29 MET cc_start: 0.7247 (mmm) cc_final: 0.7041 (mmm) REVERT: A 119 MET cc_start: 0.8661 (mmt) cc_final: 0.8259 (mmt) REVERT: A 271 GLU cc_start: 0.7721 (pt0) cc_final: 0.7500 (pt0) REVERT: A 273 TYR cc_start: 0.8491 (m-80) cc_final: 0.8265 (m-80) REVERT: A 293 ILE cc_start: 0.8340 (mm) cc_final: 0.8068 (mp) REVERT: A 302 ASP cc_start: 0.8115 (t0) cc_final: 0.7702 (t0) REVERT: A 353 ASP cc_start: 0.7596 (p0) cc_final: 0.7381 (p0) REVERT: A 409 SER cc_start: 0.8770 (m) cc_final: 0.8553 (p) REVERT: A 465 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7978 (mm-30) REVERT: B 21 LYS cc_start: 0.8357 (mttt) cc_final: 0.8129 (mttt) REVERT: B 121 LYS cc_start: 0.8313 (mtpp) cc_final: 0.8031 (tttm) REVERT: B 138 GLU cc_start: 0.7747 (mp0) cc_final: 0.7494 (mp0) REVERT: B 256 ARG cc_start: 0.8566 (tpt170) cc_final: 0.8346 (tpt170) REVERT: B 293 ILE cc_start: 0.8579 (mm) cc_final: 0.8336 (OUTLIER) REVERT: B 302 ASP cc_start: 0.7935 (t0) cc_final: 0.7517 (t0) REVERT: B 326 TYR cc_start: 0.8795 (m-80) cc_final: 0.8572 (m-80) REVERT: B 360 CYS cc_start: 0.7224 (m) cc_final: 0.7007 (m) REVERT: B 518 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7379 (mm-30) REVERT: C 203 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7487 (mm-30) REVERT: C 235 GLU cc_start: 0.8234 (pt0) cc_final: 0.7998 (pm20) REVERT: C 273 TYR cc_start: 0.8547 (m-80) cc_final: 0.8311 (m-80) REVERT: C 293 ILE cc_start: 0.8514 (mm) cc_final: 0.8231 (mt) REVERT: C 326 TYR cc_start: 0.8682 (m-80) cc_final: 0.8416 (m-80) REVERT: C 363 THR cc_start: 0.8743 (m) cc_final: 0.8473 (p) REVERT: C 399 CYS cc_start: 0.7391 (m) cc_final: 0.7183 (m) REVERT: C 468 MET cc_start: 0.8845 (mmm) cc_final: 0.8613 (mmm) REVERT: C 518 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7560 (mm-30) outliers start: 36 outliers final: 17 residues processed: 364 average time/residue: 0.6565 time to fit residues: 254.7311 Evaluate side-chains 357 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 341 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 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 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain C residue 67 VAL 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 490 GLU 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 153 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** B 475 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 HIS C 449 GLN C 475 ASN C 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.127264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.115561 restraints weight = 17458.572| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.71 r_work: 0.3469 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13407 Z= 0.126 Angle : 0.587 7.082 18201 Z= 0.298 Chirality : 0.043 0.166 1986 Planarity : 0.005 0.051 2325 Dihedral : 4.833 30.926 2172 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.06 % Allowed : 14.78 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.21), residues: 1569 helix: 1.76 (0.20), residues: 690 sheet: 1.21 (0.30), residues: 273 loop : 0.27 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 288 TYR 0.013 0.001 TYR C 118 PHE 0.023 0.001 PHE A 10 TRP 0.019 0.002 TRP C 349 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00292 (13359) covalent geometry : angle 0.56975 (18090) SS BOND : bond 0.00435 ( 24) SS BOND : angle 1.77477 ( 48) hydrogen bonds : bond 0.03921 ( 661) hydrogen bonds : angle 4.26915 ( 1911) Misc. bond : bond 0.00028 ( 3) link_BETA1-4 : bond 0.00510 ( 6) link_BETA1-4 : angle 1.15258 ( 18) link_NAG-ASN : bond 0.00153 ( 15) link_NAG-ASN : angle 2.28135 ( 45) *********************** 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 387 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 344 time to evaluate : 0.315 Fit side-chains REVERT: A 29 MET cc_start: 0.7238 (mmm) cc_final: 0.7034 (mmm) REVERT: A 119 MET cc_start: 0.8719 (mmt) cc_final: 0.8288 (mmt) REVERT: A 271 GLU cc_start: 0.7676 (pt0) cc_final: 0.7445 (pt0) REVERT: A 293 ILE cc_start: 0.8360 (mm) cc_final: 0.8086 (mp) REVERT: A 302 ASP cc_start: 0.8130 (t0) cc_final: 0.7700 (t0) REVERT: A 465 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7960 (mm-30) REVERT: B 57 PHE cc_start: 0.8186 (m-80) cc_final: 0.7915 (m-80) REVERT: B 121 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8014 (tttm) REVERT: B 138 GLU cc_start: 0.7749 (mp0) cc_final: 0.7492 (mp0) REVERT: B 293 ILE cc_start: 0.8585 (mm) cc_final: 0.8335 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8002 (t0) cc_final: 0.7614 (t0) REVERT: B 326 TYR cc_start: 0.8744 (m-80) cc_final: 0.8493 (m-80) REVERT: B 360 CYS cc_start: 0.7287 (m) cc_final: 0.7060 (m) REVERT: B 393 THR cc_start: 0.8286 (p) cc_final: 0.8026 (m) REVERT: C 82 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8179 (mtm) REVERT: C 203 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7503 (mm-30) REVERT: C 235 GLU cc_start: 0.8215 (pt0) cc_final: 0.7948 (pm20) REVERT: C 273 TYR cc_start: 0.8572 (m-80) cc_final: 0.8312 (m-80) REVERT: C 293 ILE cc_start: 0.8450 (mm) cc_final: 0.8218 (mt) REVERT: C 326 TYR cc_start: 0.8644 (m-80) cc_final: 0.8376 (m-80) REVERT: C 363 THR cc_start: 0.8758 (m) cc_final: 0.8483 (p) REVERT: C 468 MET cc_start: 0.8845 (mmm) cc_final: 0.8591 (mmm) outliers start: 43 outliers final: 17 residues processed: 360 average time/residue: 0.6281 time to fit residues: 241.2997 Evaluate side-chains 354 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 337 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 120 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 B residue 143 ILE Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 526 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 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 475 ASN A 482 ASN B 106 ASN B 108 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS B 475 ASN B 482 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS C 475 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.127148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115305 restraints weight = 17543.795| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.73 r_work: 0.3462 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13407 Z= 0.137 Angle : 0.582 7.497 18201 Z= 0.295 Chirality : 0.043 0.172 1986 Planarity : 0.004 0.047 2325 Dihedral : 4.659 29.774 2172 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.27 % Allowed : 15.07 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.21), residues: 1569 helix: 1.80 (0.20), residues: 690 sheet: 1.25 (0.30), residues: 273 loop : 0.20 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 288 TYR 0.014 0.001 TYR C 118 PHE 0.013 0.001 PHE C 443 TRP 0.017 0.002 TRP C 349 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00320 (13359) covalent geometry : angle 0.56197 (18090) SS BOND : bond 0.00464 ( 24) SS BOND : angle 1.99324 ( 48) hydrogen bonds : bond 0.03963 ( 661) hydrogen bonds : angle 4.23636 ( 1911) Misc. bond : bond 0.00034 ( 3) link_BETA1-4 : bond 0.00516 ( 6) link_BETA1-4 : angle 1.09934 ( 18) link_NAG-ASN : bond 0.00097 ( 15) link_NAG-ASN : angle 2.27942 ( 45) *********************** 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 395 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 349 time to evaluate : 0.385 Fit side-chains REVERT: A 29 MET cc_start: 0.7280 (mmm) cc_final: 0.7061 (mmm) REVERT: A 119 MET cc_start: 0.8743 (mmt) cc_final: 0.8277 (mmt) REVERT: A 271 GLU cc_start: 0.7624 (pt0) cc_final: 0.7381 (pt0) REVERT: A 293 ILE cc_start: 0.8383 (mm) cc_final: 0.8177 (mt) REVERT: A 302 ASP cc_start: 0.8151 (t0) cc_final: 0.7728 (t0) REVERT: A 465 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7947 (mm-30) REVERT: A 518 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7553 (tp30) REVERT: B 21 LYS cc_start: 0.8230 (mttt) cc_final: 0.7969 (mttt) REVERT: B 53 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8045 (mp) REVERT: B 121 LYS cc_start: 0.8360 (mtpp) cc_final: 0.8029 (tttm) REVERT: B 138 GLU cc_start: 0.7768 (mp0) cc_final: 0.7490 (mp0) REVERT: B 293 ILE cc_start: 0.8566 (mm) cc_final: 0.8254 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8037 (t0) cc_final: 0.7644 (t0) REVERT: B 326 TYR cc_start: 0.8719 (m-80) cc_final: 0.8445 (m-80) REVERT: B 360 CYS cc_start: 0.7283 (m) cc_final: 0.7062 (m) REVERT: B 393 THR cc_start: 0.8311 (p) cc_final: 0.8087 (m) REVERT: C 203 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7514 (mm-30) REVERT: C 273 TYR cc_start: 0.8595 (m-80) cc_final: 0.8362 (m-80) REVERT: C 293 ILE cc_start: 0.8426 (mm) cc_final: 0.8211 (mt) REVERT: C 326 TYR cc_start: 0.8657 (m-80) cc_final: 0.8361 (m-80) REVERT: C 363 THR cc_start: 0.8795 (m) cc_final: 0.8535 (p) REVERT: C 468 MET cc_start: 0.8837 (mmm) cc_final: 0.8580 (mmm) outliers start: 46 outliers final: 18 residues processed: 365 average time/residue: 0.6213 time to fit residues: 242.0976 Evaluate side-chains 340 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 322 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 53 LEU 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 494 ARG Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 526 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 376 HIS A 475 ASN A 482 ASN B 108 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN C 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114122 restraints weight = 17311.972| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.71 r_work: 0.3447 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13407 Z= 0.188 Angle : 0.626 7.943 18201 Z= 0.316 Chirality : 0.044 0.182 1986 Planarity : 0.005 0.046 2325 Dihedral : 4.705 28.835 2172 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.91 % Allowed : 15.85 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.21), residues: 1569 helix: 1.72 (0.20), residues: 690 sheet: 1.18 (0.29), residues: 273 loop : 0.14 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 288 TYR 0.015 0.001 TYR C 118 PHE 0.024 0.002 PHE A 10 TRP 0.017 0.002 TRP C 349 HIS 0.004 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00453 (13359) covalent geometry : angle 0.60258 (18090) SS BOND : bond 0.00547 ( 24) SS BOND : angle 2.38293 ( 48) hydrogen bonds : bond 0.04297 ( 661) hydrogen bonds : angle 4.26792 ( 1911) Misc. bond : bond 0.00049 ( 3) link_BETA1-4 : bond 0.00523 ( 6) link_BETA1-4 : angle 1.10870 ( 18) link_NAG-ASN : bond 0.00173 ( 15) link_NAG-ASN : angle 2.43911 ( 45) *********************** 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 370 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 329 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.7890 (mmp) cc_final: 0.7567 (mmp) REVERT: A 29 MET cc_start: 0.7310 (mmm) cc_final: 0.7084 (mmm) REVERT: A 119 MET cc_start: 0.8752 (mmt) cc_final: 0.8356 (mmt) REVERT: A 271 GLU cc_start: 0.7648 (pt0) cc_final: 0.7417 (pt0) REVERT: A 293 ILE cc_start: 0.8371 (mm) cc_final: 0.8143 (mt) REVERT: A 302 ASP cc_start: 0.8178 (t0) cc_final: 0.7746 (t0) REVERT: A 373 MET cc_start: 0.8088 (mmm) cc_final: 0.7870 (mmp) REVERT: A 465 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7955 (mm-30) REVERT: B 131 ASN cc_start: 0.8458 (m-40) cc_final: 0.8251 (m-40) REVERT: B 138 GLU cc_start: 0.7783 (mp0) cc_final: 0.7579 (mp0) REVERT: B 293 ILE cc_start: 0.8550 (mm) cc_final: 0.8331 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8067 (t0) cc_final: 0.7692 (t0) REVERT: B 326 TYR cc_start: 0.8745 (m-80) cc_final: 0.8468 (m-80) REVERT: B 360 CYS cc_start: 0.7243 (m) cc_final: 0.7036 (m) REVERT: B 437 GLU cc_start: 0.7858 (tp30) cc_final: 0.7636 (tm-30) REVERT: B 448 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7525 (p) REVERT: C 273 TYR cc_start: 0.8607 (m-80) cc_final: 0.8347 (m-80) REVERT: C 326 TYR cc_start: 0.8692 (m-80) cc_final: 0.8348 (m-80) REVERT: C 359 GLU cc_start: 0.7777 (tp30) cc_final: 0.7213 (tp30) REVERT: C 363 THR cc_start: 0.8798 (m) cc_final: 0.8494 (p) REVERT: C 468 MET cc_start: 0.8850 (mmm) cc_final: 0.8625 (mmm) outliers start: 41 outliers final: 20 residues processed: 348 average time/residue: 0.6564 time to fit residues: 243.8853 Evaluate side-chains 343 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 323 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 142 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 359 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 465 GLU 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 47 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 319 GLN A 475 ASN A 482 ASN B 108 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114610 restraints weight = 17266.839| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.71 r_work: 0.3455 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13407 Z= 0.157 Angle : 0.627 10.972 18201 Z= 0.316 Chirality : 0.043 0.193 1986 Planarity : 0.005 0.045 2325 Dihedral : 4.664 28.573 2172 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.56 % Allowed : 17.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.21), residues: 1569 helix: 1.78 (0.20), residues: 690 sheet: 1.14 (0.29), residues: 273 loop : 0.16 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 494 TYR 0.014 0.001 TYR C 118 PHE 0.012 0.001 PHE B 188 TRP 0.016 0.002 TRP C 349 HIS 0.003 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00374 (13359) covalent geometry : angle 0.59844 (18090) SS BOND : bond 0.00589 ( 24) SS BOND : angle 2.93552 ( 48) hydrogen bonds : bond 0.04147 ( 661) hydrogen bonds : angle 4.30310 ( 1911) Misc. bond : bond 0.00038 ( 3) link_BETA1-4 : bond 0.00484 ( 6) link_BETA1-4 : angle 1.05211 ( 18) link_NAG-ASN : bond 0.00140 ( 15) link_NAG-ASN : angle 2.34926 ( 45) *********************** 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 371 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 335 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.7881 (mmp) cc_final: 0.7591 (mmp) REVERT: A 29 MET cc_start: 0.7283 (mmm) cc_final: 0.7060 (mmm) REVERT: A 82 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7022 (mmt) REVERT: A 119 MET cc_start: 0.8758 (mmt) cc_final: 0.8358 (mmt) REVERT: A 271 GLU cc_start: 0.7620 (pt0) cc_final: 0.7393 (pt0) REVERT: A 302 ASP cc_start: 0.8181 (t0) cc_final: 0.7768 (t0) REVERT: A 465 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7961 (mm-30) REVERT: A 518 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7817 (tp30) REVERT: B 57 PHE cc_start: 0.8265 (m-80) cc_final: 0.7983 (m-80) REVERT: B 131 ASN cc_start: 0.8430 (m-40) cc_final: 0.8230 (m-40) REVERT: B 138 GLU cc_start: 0.7756 (mp0) cc_final: 0.7554 (mp0) REVERT: B 293 ILE cc_start: 0.8562 (mm) cc_final: 0.8346 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8054 (t0) cc_final: 0.7679 (t0) REVERT: B 326 TYR cc_start: 0.8731 (m-80) cc_final: 0.8447 (m-80) REVERT: B 437 GLU cc_start: 0.7862 (tp30) cc_final: 0.7626 (tm-30) REVERT: B 448 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7523 (p) REVERT: C 273 TYR cc_start: 0.8608 (m-80) cc_final: 0.8308 (m-80) REVERT: C 326 TYR cc_start: 0.8670 (m-80) cc_final: 0.8326 (m-80) REVERT: C 359 GLU cc_start: 0.7766 (tp30) cc_final: 0.7306 (tp30) REVERT: C 363 THR cc_start: 0.8771 (m) cc_final: 0.8499 (p) REVERT: C 468 MET cc_start: 0.8836 (mmm) cc_final: 0.8589 (mmm) REVERT: C 470 ASP cc_start: 0.8040 (m-30) cc_final: 0.7823 (m-30) outliers start: 36 outliers final: 20 residues processed: 351 average time/residue: 0.6246 time to fit residues: 234.4588 Evaluate side-chains 342 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 321 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS 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 142 GLU 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 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 448 THR Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 490 GLU 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 7 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 475 ASN A 482 ASN B 108 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114642 restraints weight = 17181.455| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.71 r_work: 0.3457 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13407 Z= 0.167 Angle : 0.627 9.332 18201 Z= 0.316 Chirality : 0.043 0.198 1986 Planarity : 0.005 0.045 2325 Dihedral : 4.653 28.276 2172 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.70 % Allowed : 17.84 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.21), residues: 1569 helix: 1.82 (0.20), residues: 687 sheet: 1.09 (0.29), residues: 273 loop : 0.15 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 494 TYR 0.015 0.001 TYR C 118 PHE 0.028 0.001 PHE A 10 TRP 0.016 0.002 TRP C 349 HIS 0.003 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00399 (13359) covalent geometry : angle 0.60047 (18090) SS BOND : bond 0.00519 ( 24) SS BOND : angle 2.77336 ( 48) hydrogen bonds : bond 0.04181 ( 661) hydrogen bonds : angle 4.29984 ( 1911) Misc. bond : bond 0.00042 ( 3) link_BETA1-4 : bond 0.00475 ( 6) link_BETA1-4 : angle 1.01051 ( 18) link_NAG-ASN : bond 0.00145 ( 15) link_NAG-ASN : angle 2.35737 ( 45) *********************** 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 362 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 324 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.7921 (mmp) cc_final: 0.7707 (mmp) REVERT: A 29 MET cc_start: 0.7246 (mmm) cc_final: 0.7034 (mmm) REVERT: A 57 PHE cc_start: 0.8388 (m-80) cc_final: 0.8100 (m-80) REVERT: A 119 MET cc_start: 0.8747 (mmt) cc_final: 0.8336 (mmt) REVERT: A 302 ASP cc_start: 0.8186 (t0) cc_final: 0.7782 (t0) REVERT: A 465 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7976 (mm-30) REVERT: B 57 PHE cc_start: 0.8303 (m-80) cc_final: 0.8022 (m-80) REVERT: B 131 ASN cc_start: 0.8425 (m-40) cc_final: 0.8221 (m-40) REVERT: B 249 VAL cc_start: 0.8396 (m) cc_final: 0.8070 (p) REVERT: B 293 ILE cc_start: 0.8569 (mm) cc_final: 0.8364 (mt) REVERT: B 302 ASP cc_start: 0.8077 (t0) cc_final: 0.7708 (t0) REVERT: B 326 TYR cc_start: 0.8731 (m-80) cc_final: 0.8435 (m-80) REVERT: B 437 GLU cc_start: 0.7840 (tp30) cc_final: 0.7597 (tm-30) REVERT: B 448 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7512 (p) REVERT: C 273 TYR cc_start: 0.8552 (m-80) cc_final: 0.8239 (m-80) REVERT: C 326 TYR cc_start: 0.8676 (m-80) cc_final: 0.8333 (m-80) REVERT: C 359 GLU cc_start: 0.7813 (tp30) cc_final: 0.7241 (tp30) REVERT: C 363 THR cc_start: 0.8765 (m) cc_final: 0.8462 (p) REVERT: C 468 MET cc_start: 0.8829 (mmm) cc_final: 0.8594 (mmm) outliers start: 38 outliers final: 21 residues processed: 341 average time/residue: 0.6708 time to fit residues: 244.5053 Evaluate side-chains 343 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 321 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 142 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 359 GLU Chi-restraints excluded: chain A residue 526 LEU 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 448 THR Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 67 VAL 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 465 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 33 optimal weight: 0.0040 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 105 optimal weight: 0.0060 chunk 149 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN A 482 ASN B 108 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 475 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.128475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116594 restraints weight = 17432.629| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.73 r_work: 0.3488 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13407 Z= 0.118 Angle : 0.610 9.703 18201 Z= 0.306 Chirality : 0.042 0.184 1986 Planarity : 0.004 0.045 2325 Dihedral : 4.557 28.316 2172 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.99 % Allowed : 19.19 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.21), residues: 1569 helix: 1.95 (0.20), residues: 687 sheet: 1.06 (0.30), residues: 273 loop : 0.17 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 187 TYR 0.013 0.001 TYR C 414 PHE 0.011 0.001 PHE C 443 TRP 0.015 0.002 TRP C 349 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00266 (13359) covalent geometry : angle 0.58598 (18090) SS BOND : bond 0.00707 ( 24) SS BOND : angle 2.62746 ( 48) hydrogen bonds : bond 0.03732 ( 661) hydrogen bonds : angle 4.26370 ( 1911) Misc. bond : bond 0.00016 ( 3) link_BETA1-4 : bond 0.00496 ( 6) link_BETA1-4 : angle 1.01041 ( 18) link_NAG-ASN : bond 0.00173 ( 15) link_NAG-ASN : angle 2.11378 ( 45) *********************** 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 357 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 329 time to evaluate : 0.364 Fit side-chains REVERT: A 7 MET cc_start: 0.7903 (mmp) cc_final: 0.7697 (mmp) REVERT: A 29 MET cc_start: 0.7250 (mmm) cc_final: 0.7037 (mmm) REVERT: A 57 PHE cc_start: 0.8374 (m-80) cc_final: 0.8072 (m-80) REVERT: A 119 MET cc_start: 0.8731 (mmt) cc_final: 0.8269 (mmt) REVERT: A 271 GLU cc_start: 0.7637 (pt0) cc_final: 0.7393 (pt0) REVERT: A 302 ASP cc_start: 0.8146 (t0) cc_final: 0.7720 (t0) REVERT: A 353 ASP cc_start: 0.7439 (p0) cc_final: 0.6994 (p0) REVERT: A 375 LEU cc_start: 0.8202 (tp) cc_final: 0.7957 (tt) REVERT: A 465 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 141 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8039 (mm110) REVERT: B 249 VAL cc_start: 0.8377 (m) cc_final: 0.8068 (p) REVERT: B 293 ILE cc_start: 0.8562 (mm) cc_final: 0.8327 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8046 (t0) cc_final: 0.7661 (t0) REVERT: B 326 TYR cc_start: 0.8691 (m-80) cc_final: 0.8436 (m-80) REVERT: B 437 GLU cc_start: 0.7797 (tp30) cc_final: 0.7485 (tm-30) REVERT: B 448 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7478 (p) REVERT: C 273 TYR cc_start: 0.8479 (m-80) cc_final: 0.8143 (m-80) REVERT: C 326 TYR cc_start: 0.8632 (m-80) cc_final: 0.8317 (m-80) REVERT: C 359 GLU cc_start: 0.7828 (tp30) cc_final: 0.7348 (tp30) REVERT: C 363 THR cc_start: 0.8756 (m) cc_final: 0.8492 (p) REVERT: C 468 MET cc_start: 0.8843 (mmm) cc_final: 0.8594 (mmm) outliers start: 28 outliers final: 20 residues processed: 342 average time/residue: 0.6310 time to fit residues: 230.7249 Evaluate side-chains 346 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 326 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 142 GLU Chi-restraints excluded: chain A residue 215 ILE 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 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 67 VAL 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 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 60 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 105 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 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 475 ASN A 482 ASN B 108 ASN B 131 ASN B 133 GLN B 319 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 475 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.115491 restraints weight = 17464.308| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.74 r_work: 0.3472 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13407 Z= 0.143 Angle : 0.619 10.931 18201 Z= 0.312 Chirality : 0.043 0.192 1986 Planarity : 0.005 0.045 2325 Dihedral : 4.523 27.773 2172 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.71 % Allowed : 19.69 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.21), residues: 1569 helix: 1.95 (0.20), residues: 687 sheet: 1.07 (0.29), residues: 273 loop : 0.14 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.014 0.001 TYR A 118 PHE 0.028 0.001 PHE A 10 TRP 0.015 0.002 TRP C 349 HIS 0.004 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00337 (13359) covalent geometry : angle 0.59393 (18090) SS BOND : bond 0.00516 ( 24) SS BOND : angle 2.72517 ( 48) hydrogen bonds : bond 0.03896 ( 661) hydrogen bonds : angle 4.26928 ( 1911) Misc. bond : bond 0.00032 ( 3) link_BETA1-4 : bond 0.00466 ( 6) link_BETA1-4 : angle 0.96325 ( 18) link_NAG-ASN : bond 0.00100 ( 15) link_NAG-ASN : angle 2.21757 ( 45) ********************** 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 349 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 325 time to evaluate : 0.343 Fit side-chains REVERT: A 7 MET cc_start: 0.7949 (mmp) cc_final: 0.7732 (mmp) REVERT: A 57 PHE cc_start: 0.8407 (m-80) cc_final: 0.8100 (m-80) REVERT: A 119 MET cc_start: 0.8739 (mmt) cc_final: 0.8338 (mmt) REVERT: A 271 GLU cc_start: 0.7641 (pt0) cc_final: 0.7429 (pt0) REVERT: A 302 ASP cc_start: 0.8147 (t0) cc_final: 0.7727 (t0) REVERT: A 353 ASP cc_start: 0.7396 (p0) cc_final: 0.7167 (p0) REVERT: A 465 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7979 (mm-30) REVERT: B 141 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8105 (mm110) REVERT: B 249 VAL cc_start: 0.8387 (m) cc_final: 0.8085 (p) REVERT: B 293 ILE cc_start: 0.8553 (mm) cc_final: 0.8327 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8029 (t0) cc_final: 0.7658 (t0) REVERT: B 326 TYR cc_start: 0.8715 (m-80) cc_final: 0.8380 (m-80) REVERT: B 381 CYS cc_start: 0.6592 (OUTLIER) cc_final: 0.6237 (t) REVERT: B 437 GLU cc_start: 0.7803 (tp30) cc_final: 0.7486 (tm-30) REVERT: B 448 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7463 (p) REVERT: C 273 TYR cc_start: 0.8527 (m-80) cc_final: 0.8181 (m-80) REVERT: C 326 TYR cc_start: 0.8667 (m-80) cc_final: 0.8309 (m-80) REVERT: C 359 GLU cc_start: 0.7922 (tp30) cc_final: 0.7383 (tp30) REVERT: C 363 THR cc_start: 0.8759 (m) cc_final: 0.8462 (p) REVERT: C 468 MET cc_start: 0.8829 (mmm) cc_final: 0.8573 (mmm) outliers start: 24 outliers final: 19 residues processed: 339 average time/residue: 0.6455 time to fit residues: 234.0923 Evaluate side-chains 347 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 327 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 215 ILE 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 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 336 VAL 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 68 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 chunk 135 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 482 ASN B 108 ASN B 131 ASN B 133 GLN B 319 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 475 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.127661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115720 restraints weight = 17425.795| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.73 r_work: 0.3477 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13407 Z= 0.135 Angle : 0.629 10.441 18201 Z= 0.315 Chirality : 0.043 0.192 1986 Planarity : 0.004 0.044 2325 Dihedral : 4.483 27.474 2172 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.71 % Allowed : 19.97 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.21), residues: 1569 helix: 1.95 (0.20), residues: 687 sheet: 1.06 (0.30), residues: 273 loop : 0.12 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 187 TYR 0.014 0.001 TYR A 118 PHE 0.011 0.001 PHE A 114 TRP 0.016 0.002 TRP C 219 HIS 0.003 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00316 (13359) covalent geometry : angle 0.60593 (18090) SS BOND : bond 0.00496 ( 24) SS BOND : angle 2.69269 ( 48) hydrogen bonds : bond 0.03816 ( 661) hydrogen bonds : angle 4.27460 ( 1911) Misc. bond : bond 0.00028 ( 3) link_BETA1-4 : bond 0.00481 ( 6) link_BETA1-4 : angle 0.93190 ( 18) link_NAG-ASN : bond 0.00092 ( 15) link_NAG-ASN : angle 2.13346 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5168.24 seconds wall clock time: 88 minutes 24.68 seconds (5304.68 seconds total)