Starting phenix.real_space_refine on Thu Jul 2 11:33:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mdu_23780/07_2026/7mdu_23780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdu_23780/07_2026/7mdu_23780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mdu_23780/07_2026/7mdu_23780.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mdu_23780/07_2026/7mdu_23780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mdu_23780/07_2026/7mdu_23780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdu_23780/07_2026/7mdu_23780.map" model { file = "/net/cci-nas-00/data/ceres_data/7mdu_23780/07_2026/7mdu_23780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdu_23780/07_2026/7mdu_23780.cif" } resolution = 3.3 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= 0.000 sd= 0.002 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 47 5.16 5 C 5206 2.51 5 N 1387 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8332 Number of models: 1 Model: "" Number of chains: 17 Chain: "H" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 863 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "A" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3501 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "E" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "F" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" 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 chiralities: 2 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 chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 3 Time building chain proxies: 1.45, per 1000 atoms: 0.17 Number of scatterers: 8332 At special positions: 0 Unit cell: (114.33, 69.01, 149.35, 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 47 16.00 O 1692 8.00 N 1387 7.00 C 5206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.07 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 137 " " NAG A 608 " - " ASN A 355 " " NAG A 609 " - " ASN A 398 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 618 " " NAG C 1 " - " ASN A 156 " " NAG D 1 " - " ASN A 197 " " NAG G 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 276 " " NAG K 1 " - " ASN A 295 " " NAG M 1 " - " ASN A 332 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 88 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 424.6 milliseconds 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1864 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 27 sheets defined 15.9% alpha, 77.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.056A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.971A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 571 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.768A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TRP H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.768A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TRP H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.400A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.849A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.945A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA8, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA9, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.603A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.768A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.549A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.768A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.957A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 271 through 274 removed outlier: 7.683A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.261A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.957A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.549A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.261A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 8 Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.070A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.103A pdb=" N PHE E 102 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AC5, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.506A pdb=" N TRP F 35 " --> pdb=" O MET F 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.506A pdb=" N TRP F 35 " --> pdb=" O MET F 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.579A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.314A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AC9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.692A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1131 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: 1.59 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 1706 1.32 - 1.46: 3056 1.46 - 1.60: 3665 1.60 - 1.75: 20 1.75 - 1.89: 54 Bond restraints: 8501 Sorted by residual: bond pdb=" CG GLN L 89 " pdb=" CD GLN L 89 " ideal model delta sigma weight residual 1.516 1.377 0.139 2.50e-02 1.60e+03 3.08e+01 bond pdb=" NE1 TRP B 623 " pdb=" CE2 TRP B 623 " ideal model delta sigma weight residual 1.370 1.311 0.059 1.10e-02 8.26e+03 2.93e+01 bond pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 1.512 1.400 0.112 2.20e-02 2.07e+03 2.58e+01 bond pdb=" CG GLU E 6 " pdb=" CD GLU E 6 " ideal model delta sigma weight residual 1.516 1.394 0.122 2.50e-02 1.60e+03 2.38e+01 bond pdb=" CB LEU A 125 " pdb=" CG LEU A 125 " ideal model delta sigma weight residual 1.530 1.433 0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 8496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 11170 4.25 - 8.50: 364 8.50 - 12.75: 8 12.75 - 17.00: 1 17.00 - 21.25: 1 Bond angle restraints: 11544 Sorted by residual: angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 112.47 91.22 21.25 2.06e+00 2.36e-01 1.06e+02 angle pdb=" N LEU B 544 " pdb=" CA LEU B 544 " pdb=" C LEU B 544 " ideal model delta sigma weight residual 110.48 97.30 13.18 1.48e+00 4.57e-01 7.93e+01 angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 120.31 128.55 -8.24 9.80e-01 1.04e+00 7.07e+01 angle pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" C TYR L 94 " ideal model delta sigma weight residual 112.35 123.39 -11.04 1.34e+00 5.57e-01 6.78e+01 angle pdb=" C CYS A 205 " pdb=" N PRO A 206 " pdb=" CA PRO A 206 " ideal model delta sigma weight residual 119.56 127.17 -7.61 1.02e+00 9.61e-01 5.57e+01 ... (remaining 11539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4617 17.81 - 35.63: 123 35.63 - 53.44: 43 53.44 - 71.25: 12 71.25 - 89.07: 5 Dihedral angle restraints: 4800 sinusoidal: 1889 harmonic: 2911 Sorted by residual: dihedral pdb=" C TYR L 94 " pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" CB TYR L 94 " ideal model delta harmonic sigma weight residual -122.60 -152.97 30.37 0 2.50e+00 1.60e-01 1.48e+02 dihedral pdb=" N TYR L 94 " pdb=" C TYR L 94 " pdb=" CA TYR L 94 " pdb=" CB TYR L 94 " ideal model delta harmonic sigma weight residual 122.80 150.96 -28.16 0 2.50e+00 1.60e-01 1.27e+02 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.34 -65.34 1 1.00e+01 1.00e-02 5.59e+01 ... (remaining 4797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.262: 1270 0.262 - 0.523: 114 0.523 - 0.785: 0 0.785 - 1.046: 0 1.046 - 1.307: 1 Chirality restraints: 1385 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 ... (remaining 1382 not shown) Planarity restraints: 1454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.251 2.00e-02 2.50e+03 2.10e-01 5.50e+02 pdb=" C7 NAG C 2 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.171 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.351 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.058 2.00e-02 2.50e+03 6.23e-02 4.85e+01 pdb=" CG ASN B 611 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 448 " -0.057 2.00e-02 2.50e+03 5.83e-02 4.25e+01 pdb=" CG ASN A 448 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 448 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 448 " 0.090 2.00e-02 2.50e+03 pdb=" C1 NAG A 606 " -0.070 2.00e-02 2.50e+03 ... (remaining 1451 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2284 2.82 - 3.34: 7324 3.34 - 3.86: 13595 3.86 - 4.38: 16457 4.38 - 4.90: 26559 Nonbonded interactions: 66219 Sorted by model distance: nonbonded pdb=" N LEU B 544 " pdb=" O LEU B 544 " model vdw 2.302 2.496 nonbonded pdb=" O ILE L 2 " pdb=" OG1 THR L 97 " model vdw 2.354 3.040 nonbonded pdb=" N TYR L 50 " pdb=" O TYR L 50 " model vdw 2.375 2.496 nonbonded pdb=" N ASP E 84 " pdb=" OD1 ASP E 84 " model vdw 2.379 3.120 nonbonded pdb=" N ASP E 52A" pdb=" OD1 ASP E 52A" model vdw 2.397 3.120 ... (remaining 66214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.360 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.024 0.150 8549 Z= 1.252 Angle : 1.785 21.247 11673 Z= 1.160 Chirality : 0.141 1.307 1385 Planarity : 0.010 0.210 1433 Dihedral : 10.277 89.065 2891 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.21 % 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 are not related in a simple way. whole: 0.65 (0.25), residues: 998 helix: -0.48 (0.39), residues: 146 sheet: 1.14 (0.27), residues: 345 loop : 0.34 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 71 TYR 0.043 0.008 TYR F 36 PHE 0.034 0.006 PHE L 98 TRP 0.047 0.008 TRP H 47 HIS 0.017 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02346 / 1.23 ( 8501) covalent geometry : angle 1.75844 / 1.16 (11544) SS BOND : bond 0.01970 / 1.11 ( 15) SS BOND : angle 2.84185 / 1.79 ( 30) hydrogen bonds : bond 0.15088 / 10.01 ( 295) hydrogen bonds : angle 7.74367 / 5.44 ( 1131) link_ALPHA1-3 : bond 0.08079 / 4.25 ( 1) link_ALPHA1-3 : angle 4.37023 / 2.30 ( 3) link_ALPHA1-6 : bond 0.05600 / 2.95 ( 1) link_ALPHA1-6 : angle 3.80523 / 2.01 ( 3) link_BETA1-4 : bond 0.06981 / 3.70 ( 10) link_BETA1-4 : angle 4.74283 / 3.00 ( 30) link_NAG-ASN : bond 0.07654 / 4.84 ( 21) link_NAG-ASN : angle 2.75243 / 1.86 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: H 12 VAL cc_start: 0.6656 (t) cc_final: 0.6435 (t) REVERT: A 142 MET cc_start: 0.8235 (mmm) cc_final: 0.7947 (mmm) REVERT: L 45 LYS cc_start: 0.8840 (tttt) cc_final: 0.8538 (tppt) REVERT: L 72 THR cc_start: 0.8769 (t) cc_final: 0.8536 (m) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.0961 time to fit residues: 30.3216 Evaluate side-chains 131 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 374 HIS ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN B 575 GLN B 577 GLN B 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.090210 restraints weight = 13991.823| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.45 r_work: 0.2848 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8549 Z= 0.159 Angle : 0.691 9.430 11673 Z= 0.363 Chirality : 0.045 0.214 1385 Planarity : 0.005 0.042 1433 Dihedral : 5.254 27.658 1088 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.82 % Allowed : 8.41 % Favored : 89.77 % 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 are not related in a simple way. whole: 0.70 (0.26), residues: 998 helix: 1.12 (0.45), residues: 146 sheet: 1.06 (0.29), residues: 321 loop : -0.03 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 308 TYR 0.023 0.001 TYR L 94 PHE 0.014 0.002 PHE A 383 TRP 0.017 0.002 TRP H 47 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 8501) covalent geometry : angle 0.66087 / 0.36 (11544) SS BOND : bond 0.00583 / 0.30 ( 15) SS BOND : angle 1.32008 / 0.76 ( 30) hydrogen bonds : bond 0.05677 / 3.88 ( 295) hydrogen bonds : angle 5.13128 / 3.56 ( 1131) link_ALPHA1-3 : bond 0.00920 / 0.48 ( 1) link_ALPHA1-3 : angle 1.36226 / 0.76 ( 3) link_ALPHA1-6 : bond 0.00585 / 0.31 ( 1) link_ALPHA1-6 : angle 1.59759 / 0.89 ( 3) link_BETA1-4 : bond 0.00556 / 0.31 ( 10) link_BETA1-4 : angle 2.14854 / 1.43 ( 30) link_NAG-ASN : bond 0.00498 / 0.31 ( 21) link_NAG-ASN : angle 2.27491 / 1.54 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.319 Fit side-chains REVERT: H 72 ASP cc_start: 0.7468 (t0) cc_final: 0.7261 (t0) REVERT: A 142 MET cc_start: 0.8150 (mmm) cc_final: 0.7824 (mmm) REVERT: F 45 LYS cc_start: 0.8451 (tttt) cc_final: 0.8112 (ttpp) REVERT: L 42 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7964 (mmmt) REVERT: L 45 LYS cc_start: 0.8861 (tttt) cc_final: 0.8237 (tppt) REVERT: L 92 ASN cc_start: 0.8619 (t0) cc_final: 0.8402 (t0) outliers start: 16 outliers final: 13 residues processed: 177 average time/residue: 0.0810 time to fit residues: 19.8422 Evaluate side-chains 132 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 7.9990 chunk 5 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN E 3 GLN E 73 ASN E 81 GLN B 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088461 restraints weight = 13972.308| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.42 r_work: 0.2821 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8549 Z= 0.157 Angle : 0.604 8.797 11673 Z= 0.315 Chirality : 0.044 0.176 1385 Planarity : 0.004 0.035 1433 Dihedral : 4.894 23.312 1088 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.50 % Allowed : 11.02 % Favored : 86.48 % 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 are not related in a simple way. whole: 0.41 (0.26), residues: 998 helix: 1.22 (0.45), residues: 146 sheet: 0.80 (0.28), residues: 328 loop : -0.30 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 103 TYR 0.020 0.001 TYR A 318 PHE 0.016 0.002 PHE H 78 TRP 0.013 0.001 TRP H 47 HIS 0.005 0.001 HIS B 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 8501) covalent geometry : angle 0.58310 / 0.31 (11544) SS BOND : bond 0.00360 / 0.20 ( 15) SS BOND : angle 1.30643 / 0.75 ( 30) hydrogen bonds : bond 0.04764 / 3.22 ( 295) hydrogen bonds : angle 4.64304 / 3.19 ( 1131) link_ALPHA1-3 : bond 0.00711 / 0.37 ( 1) link_ALPHA1-3 : angle 1.66151 / 0.87 ( 3) link_ALPHA1-6 : bond 0.00480 / 0.25 ( 1) link_ALPHA1-6 : angle 1.44746 / 0.79 ( 3) link_BETA1-4 : bond 0.00553 / 0.28 ( 10) link_BETA1-4 : angle 1.53552 / 1.02 ( 30) link_NAG-ASN : bond 0.00334 / 0.21 ( 21) link_NAG-ASN : angle 1.77815 / 1.22 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.327 Fit side-chains REVERT: H 72 ASP cc_start: 0.7536 (t0) cc_final: 0.7318 (t0) REVERT: H 102 PHE cc_start: 0.8738 (m-80) cc_final: 0.8367 (m-10) REVERT: A 211 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7733 (mm-30) REVERT: F 45 LYS cc_start: 0.8407 (tttt) cc_final: 0.8058 (ttpp) REVERT: F 81 ASP cc_start: 0.7385 (t0) cc_final: 0.7166 (t0) REVERT: L 45 LYS cc_start: 0.8910 (tttt) cc_final: 0.8315 (tppt) outliers start: 22 outliers final: 13 residues processed: 153 average time/residue: 0.0889 time to fit residues: 18.8722 Evaluate side-chains 136 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 81 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 65 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN E 73 ASN L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.084899 restraints weight = 14279.264| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.51 r_work: 0.2742 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8549 Z= 0.216 Angle : 0.649 10.247 11673 Z= 0.332 Chirality : 0.045 0.175 1385 Planarity : 0.004 0.043 1433 Dihedral : 4.947 21.634 1088 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.95 % Allowed : 11.48 % Favored : 85.57 % 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 are not related in a simple way. whole: 0.10 (0.26), residues: 998 helix: 1.07 (0.46), residues: 142 sheet: 0.71 (0.29), residues: 317 loop : -0.59 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 617 TYR 0.019 0.002 TYR A 191 PHE 0.017 0.002 PHE H 78 TRP 0.014 0.002 TRP E 103 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 ( 8501) covalent geometry : angle 0.62960 / 0.33 (11544) SS BOND : bond 0.00477 / 0.24 ( 15) SS BOND : angle 1.12698 / 0.67 ( 30) hydrogen bonds : bond 0.04975 / 3.35 ( 295) hydrogen bonds : angle 4.68002 / 3.21 ( 1131) link_ALPHA1-3 : bond 0.00526 / 0.28 ( 1) link_ALPHA1-3 : angle 1.54807 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00435 / 0.23 ( 1) link_ALPHA1-6 : angle 1.52230 / 0.83 ( 3) link_BETA1-4 : bond 0.00553 / 0.30 ( 10) link_BETA1-4 : angle 1.40420 / 0.96 ( 30) link_NAG-ASN : bond 0.00306 / 0.18 ( 21) link_NAG-ASN : angle 1.88907 / 1.31 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.279 Fit side-chains REVERT: H 72 ASP cc_start: 0.7657 (t0) cc_final: 0.7451 (t0) REVERT: H 102 PHE cc_start: 0.8839 (m-80) cc_final: 0.8531 (m-10) REVERT: A 318 TYR cc_start: 0.8884 (m-80) cc_final: 0.8654 (m-80) REVERT: F 33 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8234 (m) REVERT: F 45 LYS cc_start: 0.8503 (tttt) cc_final: 0.8128 (ttpp) REVERT: F 81 ASP cc_start: 0.7539 (t0) cc_final: 0.7227 (t0) outliers start: 26 outliers final: 22 residues processed: 144 average time/residue: 0.0869 time to fit residues: 17.0029 Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 103 GLN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.087904 restraints weight = 14185.151| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.37 r_work: 0.2825 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8549 Z= 0.180 Angle : 0.614 10.857 11673 Z= 0.312 Chirality : 0.044 0.156 1385 Planarity : 0.004 0.042 1433 Dihedral : 4.794 21.296 1088 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.18 % Allowed : 11.82 % Favored : 85.00 % 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 are not related in a simple way. whole: 0.06 (0.26), residues: 998 helix: 1.18 (0.45), residues: 145 sheet: 0.63 (0.29), residues: 313 loop : -0.62 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 617 TYR 0.011 0.001 TYR L 49 PHE 0.015 0.002 PHE H 78 TRP 0.011 0.001 TRP E 103 HIS 0.005 0.001 HIS B 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 8501) covalent geometry : angle 0.59584 / 0.31 (11544) SS BOND : bond 0.00390 / 0.20 ( 15) SS BOND : angle 1.09333 / 0.64 ( 30) hydrogen bonds : bond 0.04573 / 3.10 ( 295) hydrogen bonds : angle 4.55175 / 3.12 ( 1131) link_ALPHA1-3 : bond 0.00570 / 0.30 ( 1) link_ALPHA1-3 : angle 1.51687 / 0.79 ( 3) link_ALPHA1-6 : bond 0.00441 / 0.23 ( 1) link_ALPHA1-6 : angle 1.54583 / 0.85 ( 3) link_BETA1-4 : bond 0.00474 / 0.25 ( 10) link_BETA1-4 : angle 1.28267 / 0.87 ( 30) link_NAG-ASN : bond 0.00265 / 0.16 ( 21) link_NAG-ASN : angle 1.79069 / 1.24 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: H 72 ASP cc_start: 0.7775 (t0) cc_final: 0.7568 (t0) REVERT: A 318 TYR cc_start: 0.8934 (m-80) cc_final: 0.8712 (m-80) REVERT: E 75 LYS cc_start: 0.8803 (mtmm) cc_final: 0.8445 (mtmm) REVERT: F 33 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8347 (m) REVERT: F 45 LYS cc_start: 0.8596 (tttt) cc_final: 0.8146 (ttpp) REVERT: B 624 ASP cc_start: 0.9047 (m-30) cc_final: 0.8837 (m-30) outliers start: 28 outliers final: 23 residues processed: 150 average time/residue: 0.0955 time to fit residues: 19.6599 Evaluate side-chains 147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 61 optimal weight: 0.0000 chunk 19 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN B 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.090513 restraints weight = 14010.709| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.35 r_work: 0.2885 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8549 Z= 0.102 Angle : 0.543 10.519 11673 Z= 0.277 Chirality : 0.042 0.148 1385 Planarity : 0.004 0.039 1433 Dihedral : 4.467 19.626 1088 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.70 % Allowed : 13.86 % Favored : 84.43 % 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 are not related in a simple way. whole: 0.21 (0.27), residues: 998 helix: 1.45 (0.46), residues: 145 sheet: 0.68 (0.30), residues: 313 loop : -0.52 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.020 0.001 TYR A 484 PHE 0.012 0.001 PHE H 78 TRP 0.008 0.001 TRP A 96 HIS 0.003 0.001 HIS B 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 8501) covalent geometry : angle 0.52691 / 0.27 (11544) SS BOND : bond 0.00266 / 0.15 ( 15) SS BOND : angle 0.83128 / 0.49 ( 30) hydrogen bonds : bond 0.03822 / 2.61 ( 295) hydrogen bonds : angle 4.26979 / 2.93 ( 1131) link_ALPHA1-3 : bond 0.00705 / 0.37 ( 1) link_ALPHA1-3 : angle 1.35712 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00508 / 0.27 ( 1) link_ALPHA1-6 : angle 1.51076 / 0.82 ( 3) link_BETA1-4 : bond 0.00404 / 0.21 ( 10) link_BETA1-4 : angle 1.20980 / 0.84 ( 30) link_NAG-ASN : bond 0.00240 / 0.15 ( 21) link_NAG-ASN : angle 1.56101 / 1.09 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7529 (tt0) cc_final: 0.7316 (mt-10) REVERT: A 318 TYR cc_start: 0.8881 (m-80) cc_final: 0.8639 (m-80) REVERT: A 411 ASN cc_start: 0.7914 (m-40) cc_final: 0.6946 (p0) REVERT: E 75 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8551 (mtmm) REVERT: F 33 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8219 (m) REVERT: F 45 LYS cc_start: 0.8567 (tttt) cc_final: 0.8325 (ptmt) REVERT: B 624 ASP cc_start: 0.8963 (m-30) cc_final: 0.8759 (m-30) outliers start: 15 outliers final: 10 residues processed: 141 average time/residue: 0.0800 time to fit residues: 15.4577 Evaluate side-chains 133 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 0.0870 chunk 24 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 38 optimal weight: 0.0670 chunk 66 optimal weight: 7.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.092750 restraints weight = 14083.440| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.33 r_work: 0.2911 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8549 Z= 0.094 Angle : 0.518 10.203 11673 Z= 0.264 Chirality : 0.042 0.150 1385 Planarity : 0.004 0.038 1433 Dihedral : 4.215 18.503 1088 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.39 % Allowed : 13.52 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.27), residues: 998 helix: 1.63 (0.46), residues: 145 sheet: 0.78 (0.31), residues: 293 loop : -0.44 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.011 0.001 TYR F 49 PHE 0.014 0.001 PHE H 78 TRP 0.009 0.001 TRP H 34 HIS 0.003 0.001 HIS B 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 ( 8501) covalent geometry : angle 0.50359 / 0.26 (11544) SS BOND : bond 0.00244 / 0.14 ( 15) SS BOND : angle 0.76396 / 0.46 ( 30) hydrogen bonds : bond 0.03538 / 2.43 ( 295) hydrogen bonds : angle 4.05811 / 2.79 ( 1131) link_ALPHA1-3 : bond 0.00677 / 0.36 ( 1) link_ALPHA1-3 : angle 1.37663 / 0.73 ( 3) link_ALPHA1-6 : bond 0.00540 / 0.28 ( 1) link_ALPHA1-6 : angle 1.45982 / 0.79 ( 3) link_BETA1-4 : bond 0.00416 / 0.22 ( 10) link_BETA1-4 : angle 1.15634 / 0.80 ( 30) link_NAG-ASN : bond 0.00232 / 0.14 ( 21) link_NAG-ASN : angle 1.43587 / 1.00 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.311 Fit side-chains REVERT: A 111 LEU cc_start: 0.8914 (tp) cc_final: 0.8706 (mt) REVERT: A 211 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8006 (mm-30) REVERT: A 318 TYR cc_start: 0.8855 (m-80) cc_final: 0.8649 (m-80) REVERT: A 411 ASN cc_start: 0.7844 (m-40) cc_final: 0.6928 (p0) REVERT: E 75 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8609 (mtmm) REVERT: F 33 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8223 (m) REVERT: B 624 ASP cc_start: 0.8847 (m-30) cc_final: 0.8647 (m-30) outliers start: 21 outliers final: 15 residues processed: 157 average time/residue: 0.0880 time to fit residues: 19.1018 Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 0.0670 chunk 87 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 188 ASN F 17 GLN L 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.089518 restraints weight = 14151.456| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.37 r_work: 0.2861 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8549 Z= 0.144 Angle : 0.568 10.778 11673 Z= 0.287 Chirality : 0.043 0.152 1385 Planarity : 0.004 0.036 1433 Dihedral : 4.281 18.111 1088 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.95 % Allowed : 13.41 % Favored : 83.64 % 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 are not related in a simple way. whole: 0.31 (0.27), residues: 998 helix: 1.61 (0.46), residues: 145 sheet: 0.84 (0.30), residues: 305 loop : -0.55 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.014 0.001 TYR E 91 PHE 0.015 0.001 PHE H 78 TRP 0.010 0.001 TRP H 34 HIS 0.002 0.001 HIS B 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 8501) covalent geometry : angle 0.55310 / 0.28 (11544) SS BOND : bond 0.00335 / 0.17 ( 15) SS BOND : angle 0.92767 / 0.58 ( 30) hydrogen bonds : bond 0.04048 / 2.76 ( 295) hydrogen bonds : angle 4.17627 / 2.88 ( 1131) link_ALPHA1-3 : bond 0.00563 / 0.30 ( 1) link_ALPHA1-3 : angle 1.43785 / 0.76 ( 3) link_ALPHA1-6 : bond 0.00549 / 0.29 ( 1) link_ALPHA1-6 : angle 1.46518 / 0.80 ( 3) link_BETA1-4 : bond 0.00428 / 0.23 ( 10) link_BETA1-4 : angle 1.19264 / 0.81 ( 30) link_NAG-ASN : bond 0.00215 / 0.14 ( 21) link_NAG-ASN : angle 1.56514 / 1.10 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.265 Fit side-chains REVERT: A 318 TYR cc_start: 0.8902 (m-80) cc_final: 0.8661 (m-80) REVERT: A 411 ASN cc_start: 0.7882 (m-40) cc_final: 0.6963 (p0) REVERT: E 75 LYS cc_start: 0.8879 (mtmm) cc_final: 0.8664 (mtmm) REVERT: L 105 GLU cc_start: 0.1951 (OUTLIER) cc_final: 0.0952 (tp30) REVERT: B 624 ASP cc_start: 0.8916 (m-30) cc_final: 0.8706 (m-30) outliers start: 26 outliers final: 17 residues processed: 145 average time/residue: 0.0845 time to fit residues: 16.9146 Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 0.0060 chunk 83 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.0040 chunk 32 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN F 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.090185 restraints weight = 14173.662| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.29 r_work: 0.2881 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8549 Z= 0.112 Angle : 0.544 10.931 11673 Z= 0.274 Chirality : 0.042 0.152 1385 Planarity : 0.004 0.036 1433 Dihedral : 4.229 17.417 1088 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.61 % Allowed : 13.75 % Favored : 83.64 % 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 are not related in a simple way. whole: 0.32 (0.27), residues: 998 helix: 1.65 (0.46), residues: 145 sheet: 0.80 (0.30), residues: 302 loop : -0.50 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.021 0.001 TYR A 484 PHE 0.012 0.001 PHE H 78 TRP 0.010 0.001 TRP H 36 HIS 0.003 0.001 HIS B 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 8501) covalent geometry : angle 0.52936 / 0.27 (11544) SS BOND : bond 0.00296 / 0.16 ( 15) SS BOND : angle 0.95166 / 0.57 ( 30) hydrogen bonds : bond 0.03795 / 2.60 ( 295) hydrogen bonds : angle 4.11217 / 2.83 ( 1131) link_ALPHA1-3 : bond 0.00631 / 0.33 ( 1) link_ALPHA1-3 : angle 1.35683 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00515 / 0.27 ( 1) link_ALPHA1-6 : angle 1.47145 / 0.80 ( 3) link_BETA1-4 : bond 0.00390 / 0.20 ( 10) link_BETA1-4 : angle 1.17579 / 0.81 ( 30) link_NAG-ASN : bond 0.00213 / 0.14 ( 21) link_NAG-ASN : angle 1.49803 / 1.05 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.331 Fit side-chains REVERT: A 318 TYR cc_start: 0.8886 (m-80) cc_final: 0.8648 (m-80) REVERT: A 411 ASN cc_start: 0.7870 (m-40) cc_final: 0.6955 (p0) REVERT: E 75 LYS cc_start: 0.8876 (mtmm) cc_final: 0.8604 (mtmm) REVERT: L 4 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7326 (ptm) REVERT: L 105 GLU cc_start: 0.1944 (OUTLIER) cc_final: 0.0967 (tp30) REVERT: B 624 ASP cc_start: 0.8846 (m-30) cc_final: 0.8636 (m-30) outliers start: 23 outliers final: 18 residues processed: 143 average time/residue: 0.0909 time to fit residues: 17.6667 Evaluate side-chains 151 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 188 ASN A 348 GLN F 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.088637 restraints weight = 14133.203| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.35 r_work: 0.2847 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8549 Z= 0.169 Angle : 0.595 10.823 11673 Z= 0.299 Chirality : 0.044 0.152 1385 Planarity : 0.004 0.037 1433 Dihedral : 4.380 17.278 1088 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.50 % Allowed : 14.20 % Favored : 83.30 % 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 are not related in a simple way. whole: 0.21 (0.27), residues: 998 helix: 1.49 (0.45), residues: 146 sheet: 0.81 (0.30), residues: 300 loop : -0.61 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 617 TYR 0.013 0.001 TYR E 91 PHE 0.014 0.002 PHE H 78 TRP 0.010 0.001 TRP H 34 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 8501) covalent geometry : angle 0.57860 / 0.30 (11544) SS BOND : bond 0.00388 / 0.20 ( 15) SS BOND : angle 1.09659 / 0.65 ( 30) hydrogen bonds : bond 0.04298 / 2.92 ( 295) hydrogen bonds : angle 4.25560 / 2.93 ( 1131) link_ALPHA1-3 : bond 0.00494 / 0.26 ( 1) link_ALPHA1-3 : angle 1.47429 / 0.77 ( 3) link_ALPHA1-6 : bond 0.00526 / 0.28 ( 1) link_ALPHA1-6 : angle 1.44762 / 0.80 ( 3) link_BETA1-4 : bond 0.00428 / 0.23 ( 10) link_BETA1-4 : angle 1.20498 / 0.81 ( 30) link_NAG-ASN : bond 0.00244 / 0.16 ( 21) link_NAG-ASN : angle 1.66301 / 1.17 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.334 Fit side-chains REVERT: A 318 TYR cc_start: 0.8915 (m-80) cc_final: 0.8703 (m-80) REVERT: A 411 ASN cc_start: 0.7904 (m-40) cc_final: 0.7015 (p0) REVERT: E 75 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8608 (mtmm) REVERT: L 105 GLU cc_start: 0.2134 (OUTLIER) cc_final: 0.1011 (tp30) REVERT: B 624 ASP cc_start: 0.8901 (m-30) cc_final: 0.8668 (m-30) outliers start: 22 outliers final: 18 residues processed: 138 average time/residue: 0.0995 time to fit residues: 18.7048 Evaluate side-chains 147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 85 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 76 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN F 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.089196 restraints weight = 14193.554| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.36 r_work: 0.2860 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8549 Z= 0.134 Angle : 0.564 10.823 11673 Z= 0.284 Chirality : 0.043 0.152 1385 Planarity : 0.004 0.036 1433 Dihedral : 4.319 17.668 1088 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.50 % Allowed : 14.09 % Favored : 83.41 % 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 are not related in a simple way. whole: 0.23 (0.27), residues: 998 helix: 1.58 (0.45), residues: 146 sheet: 0.74 (0.30), residues: 312 loop : -0.59 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 103 TYR 0.020 0.001 TYR A 484 PHE 0.012 0.001 PHE H 78 TRP 0.009 0.001 TRP H 34 HIS 0.003 0.001 HIS B 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 8501) covalent geometry : angle 0.54807 / 0.28 (11544) SS BOND : bond 0.00328 / 0.18 ( 15) SS BOND : angle 0.96416 / 0.58 ( 30) hydrogen bonds : bond 0.04022 / 2.75 ( 295) hydrogen bonds : angle 4.20642 / 2.89 ( 1131) link_ALPHA1-3 : bond 0.00575 / 0.30 ( 1) link_ALPHA1-3 : angle 1.36279 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00481 / 0.25 ( 1) link_ALPHA1-6 : angle 1.43206 / 0.79 ( 3) link_BETA1-4 : bond 0.00394 / 0.21 ( 10) link_BETA1-4 : angle 1.20709 / 0.82 ( 30) link_NAG-ASN : bond 0.00231 / 0.15 ( 21) link_NAG-ASN : angle 1.59318 / 1.12 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2107.70 seconds wall clock time: 36 minutes 51.60 seconds (2211.60 seconds total)