Starting phenix.real_space_refine on Tue Mar 3 20:19:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mdu_23780/03_2026/7mdu_23780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdu_23780/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mdu_23780/03_2026/7mdu_23780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdu_23780/03_2026/7mdu_23780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mdu_23780/03_2026/7mdu_23780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdu_23780/03_2026/7mdu_23780.map" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 27 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.93, per 1000 atoms: 0.23 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: 0.89 Conformation dependent library (CDL) restraints added in 292.3 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: 0.45 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: 1.60 Time building geometry restraints manager: 1.10 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 - 21.27: 5313 21.27 - 42.53: 122 42.53 - 63.80: 32 63.80 - 85.07: 14 85.07 - 106.33: 6 Dihedral angle restraints: 5487 sinusoidal: 2576 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 5484 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: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.610 Find NCS groups from input model: 0.060 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 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 : 10.793 106.332 3578 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 covalent geometry : bond 0.02346 ( 8501) covalent geometry : angle 1.75844 (11544) SS BOND : bond 0.01970 ( 15) SS BOND : angle 2.84185 ( 30) hydrogen bonds : bond 0.15088 ( 295) hydrogen bonds : angle 7.74367 ( 1131) link_ALPHA1-3 : bond 0.08079 ( 1) link_ALPHA1-3 : angle 4.37023 ( 3) link_ALPHA1-6 : bond 0.05600 ( 1) link_ALPHA1-6 : angle 3.80523 ( 3) link_BETA1-4 : bond 0.06981 ( 10) link_BETA1-4 : angle 4.74283 ( 30) link_NAG-ASN : bond 0.07654 ( 21) link_NAG-ASN : angle 2.75243 ( 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 : 0.293 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: 0.1119 time to fit residues: 35.1003 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 : 0.257 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 374 HIS 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 = 0.3448 r_free = 0.3448 target = 0.116579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090038 restraints weight = 13985.147| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.46 r_work: 0.2841 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2508 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= 0.162 Angle : 0.700 9.768 11673 Z= 0.368 Chirality : 0.046 0.226 1385 Planarity : 0.005 0.044 1433 Dihedral : 7.674 84.126 1775 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.82 % Allowed : 8.64 % Favored : 89.55 % 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: 0.76 (0.26), residues: 998 helix: 1.31 (0.45), residues: 140 sheet: 1.13 (0.29), residues: 319 loop : -0.04 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 308 TYR 0.022 0.001 TYR L 94 PHE 0.014 0.002 PHE H 78 TRP 0.017 0.002 TRP H 47 HIS 0.009 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8501) covalent geometry : angle 0.66861 (11544) SS BOND : bond 0.00394 ( 15) SS BOND : angle 1.26285 ( 30) hydrogen bonds : bond 0.05780 ( 295) hydrogen bonds : angle 5.16332 ( 1131) link_ALPHA1-3 : bond 0.01236 ( 1) link_ALPHA1-3 : angle 1.63384 ( 3) link_ALPHA1-6 : bond 0.00619 ( 1) link_ALPHA1-6 : angle 1.70340 ( 3) link_BETA1-4 : bond 0.00708 ( 10) link_BETA1-4 : angle 2.23366 ( 30) link_NAG-ASN : bond 0.00483 ( 21) link_NAG-ASN : angle 2.36205 ( 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 182 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.292 Fit side-chains REVERT: H 72 ASP cc_start: 0.7548 (t0) cc_final: 0.7343 (t0) REVERT: A 142 MET cc_start: 0.8180 (mmm) cc_final: 0.7871 (mmm) REVERT: F 45 LYS cc_start: 0.8445 (tttt) cc_final: 0.8228 (ttpm) REVERT: L 42 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7976 (mmmt) REVERT: L 45 LYS cc_start: 0.8862 (tttt) cc_final: 0.8237 (tppt) REVERT: L 92 ASN cc_start: 0.8650 (t0) cc_final: 0.8443 (t0) outliers start: 16 outliers final: 13 residues processed: 176 average time/residue: 0.0840 time to fit residues: 20.2116 Evaluate side-chains 133 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 0.0370 chunk 65 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 0.0030 chunk 47 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.3068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 293 GLN A 428 GLN E 3 GLN 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 = 0.3474 r_free = 0.3474 target = 0.118335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.092979 restraints weight = 13952.323| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.33 r_work: 0.2895 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8549 Z= 0.112 Angle : 0.571 9.137 11673 Z= 0.297 Chirality : 0.043 0.210 1385 Planarity : 0.004 0.033 1433 Dihedral : 6.722 74.022 1775 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.70 % Allowed : 11.14 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 998 helix: 1.22 (0.44), residues: 146 sheet: 0.90 (0.28), residues: 327 loop : -0.24 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 103 TYR 0.018 0.001 TYR A 318 PHE 0.012 0.001 PHE H 78 TRP 0.012 0.001 TRP H 47 HIS 0.005 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8501) covalent geometry : angle 0.54724 (11544) SS BOND : bond 0.00581 ( 15) SS BOND : angle 1.32256 ( 30) hydrogen bonds : bond 0.04389 ( 295) hydrogen bonds : angle 4.57167 ( 1131) link_ALPHA1-3 : bond 0.01309 ( 1) link_ALPHA1-3 : angle 1.06125 ( 3) link_ALPHA1-6 : bond 0.00888 ( 1) link_ALPHA1-6 : angle 1.70297 ( 3) link_BETA1-4 : bond 0.00584 ( 10) link_BETA1-4 : angle 1.68820 ( 30) link_NAG-ASN : bond 0.00408 ( 21) link_NAG-ASN : angle 1.78262 ( 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: 15 poor density : 147 time to evaluate : 0.299 Fit side-chains REVERT: H 102 PHE cc_start: 0.8683 (m-80) cc_final: 0.8340 (m-10) REVERT: A 111 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8405 (mp) REVERT: A 211 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7778 (mm-30) REVERT: F 45 LYS cc_start: 0.8328 (tttt) cc_final: 0.7998 (ttpp) REVERT: F 81 ASP cc_start: 0.7358 (t0) cc_final: 0.7099 (t0) REVERT: L 45 LYS cc_start: 0.8840 (tttt) cc_final: 0.8239 (tppt) outliers start: 15 outliers final: 9 residues processed: 156 average time/residue: 0.0894 time to fit residues: 19.4098 Evaluate side-chains 138 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 111 LEU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 60 ASP 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: 4.9990 chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN E 73 ASN L 6 GLN L 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.083727 restraints weight = 14346.876| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.52 r_work: 0.2724 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 8549 Z= 0.297 Angle : 0.719 10.802 11673 Z= 0.365 Chirality : 0.049 0.281 1385 Planarity : 0.005 0.041 1433 Dihedral : 6.889 63.642 1775 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.52 % Allowed : 10.68 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.05 (0.26), residues: 998 helix: 0.91 (0.45), residues: 142 sheet: 0.66 (0.29), residues: 305 loop : -0.53 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 617 TYR 0.019 0.002 TYR A 191 PHE 0.021 0.003 PHE H 78 TRP 0.017 0.002 TRP E 103 HIS 0.007 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00719 ( 8501) covalent geometry : angle 0.69376 (11544) SS BOND : bond 0.00588 ( 15) SS BOND : angle 1.41728 ( 30) hydrogen bonds : bond 0.05487 ( 295) hydrogen bonds : angle 4.83667 ( 1131) link_ALPHA1-3 : bond 0.00910 ( 1) link_ALPHA1-3 : angle 1.16843 ( 3) link_ALPHA1-6 : bond 0.01102 ( 1) link_ALPHA1-6 : angle 2.03596 ( 3) link_BETA1-4 : bond 0.00595 ( 10) link_BETA1-4 : angle 1.79491 ( 30) link_NAG-ASN : bond 0.00410 ( 21) link_NAG-ASN : angle 2.17437 ( 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 164 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.305 Fit side-chains REVERT: H 102 PHE cc_start: 0.8877 (m-80) cc_final: 0.8526 (m-10) REVERT: A 269 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: A 318 TYR cc_start: 0.8904 (m-80) cc_final: 0.8682 (m-80) REVERT: F 45 LYS cc_start: 0.8488 (tttt) cc_final: 0.8197 (ttpm) REVERT: F 81 ASP cc_start: 0.7505 (t0) cc_final: 0.7232 (t0) outliers start: 31 outliers final: 23 residues processed: 156 average time/residue: 0.0970 time to fit residues: 20.3799 Evaluate side-chains 143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 136 ASN Chi-restraints excluded: chain A residue 269 GLU 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 F residue 11 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 106 VAL 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 15 VAL Chi-restraints excluded: chain L residue 22 THR 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: 0.8980 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 66 HIS A 103 GLN A 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.089818 restraints weight = 14110.837| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.42 r_work: 0.2861 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8549 Z= 0.115 Angle : 0.566 11.227 11673 Z= 0.288 Chirality : 0.043 0.218 1385 Planarity : 0.004 0.040 1433 Dihedral : 6.186 54.977 1775 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.27 % Allowed : 12.61 % Favored : 85.11 % 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: 0.20 (0.26), residues: 998 helix: 1.29 (0.45), residues: 145 sheet: 0.66 (0.29), residues: 329 loop : -0.52 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 24 TYR 0.011 0.001 TYR A 191 PHE 0.012 0.001 PHE H 78 TRP 0.008 0.001 TRP H 103 HIS 0.005 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8501) covalent geometry : angle 0.54666 (11544) SS BOND : bond 0.00262 ( 15) SS BOND : angle 0.83011 ( 30) hydrogen bonds : bond 0.04194 ( 295) hydrogen bonds : angle 4.42989 ( 1131) link_ALPHA1-3 : bond 0.01122 ( 1) link_ALPHA1-3 : angle 1.20371 ( 3) link_ALPHA1-6 : bond 0.01015 ( 1) link_ALPHA1-6 : angle 1.93948 ( 3) link_BETA1-4 : bond 0.00501 ( 10) link_BETA1-4 : angle 1.46059 ( 30) link_NAG-ASN : bond 0.00272 ( 21) link_NAG-ASN : angle 1.75607 ( 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 151 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.319 Fit side-chains REVERT: H 102 PHE cc_start: 0.8783 (m-80) cc_final: 0.8531 (m-10) REVERT: A 318 TYR cc_start: 0.8876 (m-80) cc_final: 0.8663 (m-80) REVERT: F 33 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8299 (m) REVERT: F 45 LYS cc_start: 0.8517 (tttt) cc_final: 0.8078 (ttpp) REVERT: F 81 ASP cc_start: 0.7641 (t0) cc_final: 0.7285 (t0) REVERT: B 624 ASP cc_start: 0.9040 (m-30) cc_final: 0.8828 (m-30) outliers start: 20 outliers final: 14 residues processed: 145 average time/residue: 0.0947 time to fit residues: 18.6598 Evaluate side-chains 140 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 412 ASP Chi-restraints excluded: chain A residue 426 MET 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 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain B residue 595 ILE 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: 0.3980 chunk 89 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 428 GLN E 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.085313 restraints weight = 14124.968| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.43 r_work: 0.2769 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3802 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= 0.177 Angle : 0.612 11.285 11673 Z= 0.309 Chirality : 0.044 0.152 1385 Planarity : 0.004 0.041 1433 Dihedral : 5.472 32.833 1775 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.73 % Allowed : 12.50 % Favored : 84.77 % 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: 0.17 (0.26), residues: 998 helix: 1.29 (0.45), residues: 145 sheet: 0.82 (0.30), residues: 301 loop : -0.60 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 24 TYR 0.022 0.002 TYR A 484 PHE 0.016 0.002 PHE H 78 TRP 0.010 0.001 TRP H 34 HIS 0.004 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8501) covalent geometry : angle 0.59218 (11544) SS BOND : bond 0.00395 ( 15) SS BOND : angle 0.96080 ( 30) hydrogen bonds : bond 0.04519 ( 295) hydrogen bonds : angle 4.47032 ( 1131) link_ALPHA1-3 : bond 0.00933 ( 1) link_ALPHA1-3 : angle 1.09044 ( 3) link_ALPHA1-6 : bond 0.00884 ( 1) link_ALPHA1-6 : angle 1.43403 ( 3) link_BETA1-4 : bond 0.00579 ( 10) link_BETA1-4 : angle 1.55949 ( 30) link_NAG-ASN : bond 0.00293 ( 21) link_NAG-ASN : angle 1.81736 ( 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 152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.305 Fit side-chains REVERT: H 102 PHE cc_start: 0.8786 (m-80) cc_final: 0.8531 (m-10) REVERT: A 318 TYR cc_start: 0.8844 (m-80) cc_final: 0.8640 (m-80) REVERT: F 33 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8216 (m) REVERT: F 45 LYS cc_start: 0.8487 (tttt) cc_final: 0.8037 (ttpp) outliers start: 24 outliers final: 22 residues processed: 143 average time/residue: 0.0927 time to fit residues: 18.1534 Evaluate side-chains 147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU 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 47 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 125 LEU 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 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 4 MET Chi-restraints excluded: chain L residue 9 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 5.9990 chunk 24 optimal weight: 0.0670 chunk 91 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 425 ASN A 428 GLN B 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089043 restraints weight = 14106.431| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.41 r_work: 0.2850 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3953 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= 0.136 Angle : 0.564 11.080 11673 Z= 0.287 Chirality : 0.043 0.147 1385 Planarity : 0.004 0.039 1433 Dihedral : 5.058 32.376 1775 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.73 % Allowed : 13.18 % 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: 0.23 (0.27), residues: 998 helix: 1.43 (0.46), residues: 145 sheet: 0.84 (0.30), residues: 301 loop : -0.59 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.012 0.001 TYR A 191 PHE 0.013 0.001 PHE H 78 TRP 0.008 0.001 TRP H 34 HIS 0.003 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8501) covalent geometry : angle 0.54521 (11544) SS BOND : bond 0.00332 ( 15) SS BOND : angle 0.82133 ( 30) hydrogen bonds : bond 0.04142 ( 295) hydrogen bonds : angle 4.33589 ( 1131) link_ALPHA1-3 : bond 0.00896 ( 1) link_ALPHA1-3 : angle 1.16385 ( 3) link_ALPHA1-6 : bond 0.00394 ( 1) link_ALPHA1-6 : angle 1.44168 ( 3) link_BETA1-4 : bond 0.00479 ( 10) link_BETA1-4 : angle 1.44472 ( 30) link_NAG-ASN : bond 0.00259 ( 21) link_NAG-ASN : angle 1.73233 ( 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 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: H 102 PHE cc_start: 0.8772 (m-80) cc_final: 0.8536 (m-10) REVERT: A 411 ASN cc_start: 0.7931 (m-40) cc_final: 0.6991 (p0) REVERT: F 33 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8289 (m) REVERT: B 624 ASP cc_start: 0.8999 (m-30) cc_final: 0.8793 (m-30) outliers start: 24 outliers final: 22 residues processed: 140 average time/residue: 0.0934 time to fit residues: 17.8384 Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU 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 47 ASP Chi-restraints excluded: chain A residue 110 SER 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 60 ASP Chi-restraints excluded: chain L residue 9 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 0.0050 chunk 87 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.087383 restraints weight = 14192.672| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.39 r_work: 0.2832 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8549 Z= 0.172 Angle : 0.597 11.280 11673 Z= 0.302 Chirality : 0.044 0.148 1385 Planarity : 0.004 0.039 1433 Dihedral : 5.275 32.937 1775 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.41 % Allowed : 13.18 % 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: 0.14 (0.27), residues: 998 helix: 1.37 (0.45), residues: 145 sheet: 0.80 (0.30), residues: 301 loop : -0.67 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 617 TYR 0.022 0.002 TYR A 484 PHE 0.016 0.002 PHE H 78 TRP 0.011 0.001 TRP H 34 HIS 0.003 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8501) covalent geometry : angle 0.57756 (11544) SS BOND : bond 0.00384 ( 15) SS BOND : angle 0.92815 ( 30) hydrogen bonds : bond 0.04451 ( 295) hydrogen bonds : angle 4.39195 ( 1131) link_ALPHA1-3 : bond 0.00683 ( 1) link_ALPHA1-3 : angle 1.27296 ( 3) link_ALPHA1-6 : bond 0.00527 ( 1) link_ALPHA1-6 : angle 1.53763 ( 3) link_BETA1-4 : bond 0.00472 ( 10) link_BETA1-4 : angle 1.45792 ( 30) link_NAG-ASN : bond 0.00294 ( 21) link_NAG-ASN : angle 1.82671 ( 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 152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.323 Fit side-chains REVERT: H 102 PHE cc_start: 0.8809 (m-80) cc_final: 0.8458 (m-10) REVERT: A 411 ASN cc_start: 0.7833 (m-40) cc_final: 0.6922 (p0) REVERT: F 33 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8324 (m) REVERT: F 45 LYS cc_start: 0.8594 (tttt) cc_final: 0.8129 (ttpp) REVERT: L 105 GLU cc_start: 0.2094 (OUTLIER) cc_final: 0.1073 (tp30) outliers start: 30 outliers final: 23 residues processed: 141 average time/residue: 0.0910 time to fit residues: 17.6344 Evaluate side-chains 144 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU 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 47 ASP Chi-restraints excluded: chain A residue 110 SER 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 L residue 11 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain B residue 636 SER 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: 2.9990 chunk 75 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN F 17 GLN L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.087365 restraints weight = 14177.477| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.35 r_work: 0.2822 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8549 Z= 0.181 Angle : 0.599 11.243 11673 Z= 0.304 Chirality : 0.044 0.148 1385 Planarity : 0.004 0.039 1433 Dihedral : 5.387 36.084 1775 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.41 % Allowed : 12.84 % Favored : 83.75 % 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: 1.33 (0.45), residues: 145 sheet: 0.73 (0.30), residues: 301 loop : -0.70 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 617 TYR 0.020 0.001 TYR A 484 PHE 0.015 0.002 PHE H 78 TRP 0.010 0.001 TRP H 34 HIS 0.003 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8501) covalent geometry : angle 0.57917 (11544) SS BOND : bond 0.00394 ( 15) SS BOND : angle 0.96377 ( 30) hydrogen bonds : bond 0.04462 ( 295) hydrogen bonds : angle 4.42011 ( 1131) link_ALPHA1-3 : bond 0.00644 ( 1) link_ALPHA1-3 : angle 1.39860 ( 3) link_ALPHA1-6 : bond 0.00432 ( 1) link_ALPHA1-6 : angle 1.44285 ( 3) link_BETA1-4 : bond 0.00467 ( 10) link_BETA1-4 : angle 1.47069 ( 30) link_NAG-ASN : bond 0.00296 ( 21) link_NAG-ASN : angle 1.82952 ( 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 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.243 Fit side-chains REVERT: H 102 PHE cc_start: 0.8797 (m-80) cc_final: 0.8492 (m-10) REVERT: A 318 TYR cc_start: 0.8941 (m-80) cc_final: 0.8702 (m-80) REVERT: A 411 ASN cc_start: 0.7843 (m-40) cc_final: 0.6949 (p0) REVERT: F 33 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8329 (m) REVERT: B 624 ASP cc_start: 0.8980 (m-30) cc_final: 0.8778 (m-30) outliers start: 30 outliers final: 26 residues processed: 144 average time/residue: 0.0959 time to fit residues: 18.8137 Evaluate side-chains 149 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU 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 47 ASP Chi-restraints excluded: chain A residue 110 SER 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 A residue 505 VAL 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 L residue 4 MET Chi-restraints excluded: chain L residue 9 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 61 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 81 optimal weight: 0.0670 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 103 GLN A 188 ASN F 17 GLN L 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.088451 restraints weight = 14102.964| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.35 r_work: 0.2839 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8549 Z= 0.135 Angle : 0.560 11.028 11673 Z= 0.285 Chirality : 0.043 0.146 1385 Planarity : 0.004 0.037 1433 Dihedral : 5.200 37.139 1775 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.64 % Allowed : 12.84 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.13 (0.27), residues: 998 helix: 1.46 (0.46), residues: 145 sheet: 0.71 (0.30), residues: 301 loop : -0.64 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 24 TYR 0.021 0.001 TYR A 484 PHE 0.013 0.001 PHE H 78 TRP 0.010 0.001 TRP H 34 HIS 0.003 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8501) covalent geometry : angle 0.54105 (11544) SS BOND : bond 0.00347 ( 15) SS BOND : angle 0.83381 ( 30) hydrogen bonds : bond 0.04117 ( 295) hydrogen bonds : angle 4.29245 ( 1131) link_ALPHA1-3 : bond 0.00650 ( 1) link_ALPHA1-3 : angle 1.34433 ( 3) link_ALPHA1-6 : bond 0.00466 ( 1) link_ALPHA1-6 : angle 1.41662 ( 3) link_BETA1-4 : bond 0.00442 ( 10) link_BETA1-4 : angle 1.41301 ( 30) link_NAG-ASN : bond 0.00263 ( 21) link_NAG-ASN : angle 1.72361 ( 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 163 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.305 Fit side-chains REVERT: H 102 PHE cc_start: 0.8760 (m-80) cc_final: 0.8453 (m-10) REVERT: A 318 TYR cc_start: 0.8920 (m-80) cc_final: 0.8680 (m-80) REVERT: A 411 ASN cc_start: 0.7935 (m-40) cc_final: 0.7011 (p0) REVERT: F 33 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8303 (m) REVERT: L 4 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7270 (ptm) REVERT: B 624 ASP cc_start: 0.8936 (m-30) cc_final: 0.8720 (m-30) outliers start: 32 outliers final: 26 residues processed: 152 average time/residue: 0.0940 time to fit residues: 19.5064 Evaluate side-chains 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU 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 47 ASP Chi-restraints excluded: chain A residue 110 SER 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 A residue 505 VAL 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 75 LYS 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 L residue 4 MET Chi-restraints excluded: chain L residue 9 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 85 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.0040 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 188 ASN F 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.090178 restraints weight = 14178.422| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.40 r_work: 0.2872 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8549 Z= 0.105 Angle : 0.534 9.950 11673 Z= 0.273 Chirality : 0.042 0.143 1385 Planarity : 0.004 0.035 1433 Dihedral : 4.833 36.539 1775 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.73 % Allowed : 13.75 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.19 (0.27), residues: 998 helix: 1.61 (0.46), residues: 145 sheet: 0.70 (0.30), residues: 305 loop : -0.60 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 94 TYR 0.012 0.001 TYR A 191 PHE 0.010 0.001 PHE H 78 TRP 0.014 0.001 TRP H 36 HIS 0.003 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8501) covalent geometry : angle 0.51717 (11544) SS BOND : bond 0.00302 ( 15) SS BOND : angle 0.79581 ( 30) hydrogen bonds : bond 0.03718 ( 295) hydrogen bonds : angle 4.13135 ( 1131) link_ALPHA1-3 : bond 0.00684 ( 1) link_ALPHA1-3 : angle 1.29293 ( 3) link_ALPHA1-6 : bond 0.00444 ( 1) link_ALPHA1-6 : angle 1.38832 ( 3) link_BETA1-4 : bond 0.00429 ( 10) link_BETA1-4 : angle 1.36195 ( 30) link_NAG-ASN : bond 0.00248 ( 21) link_NAG-ASN : angle 1.59029 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2068.26 seconds wall clock time: 36 minutes 5.59 seconds (2165.59 seconds total)