Starting phenix.real_space_refine on Sat Jul 26 10:45:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mdu_23780/07_2025/7mdu_23780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdu_23780/07_2025/7mdu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mdu_23780/07_2025/7mdu_23780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdu_23780/07_2025/7mdu_23780.map" model { file = "/net/cci-nas-00/data/ceres_data/7mdu_23780/07_2025/7mdu_23780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdu_23780/07_2025/7mdu_23780.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.46, per 1000 atoms: 0.66 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: 2.41 Conformation dependent library (CDL) restraints added in 905.7 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: 1.44 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: 3.32 Time building geometry restraints manager: 2.80 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: 5.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.760 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (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 TRP 0.047 0.008 TRP H 47 HIS 0.017 0.002 HIS A 374 PHE 0.034 0.006 PHE L 98 TYR 0.043 0.008 TYR F 36 ARG 0.009 0.001 ARG E 71 Details of bonding type rmsd link_NAG-ASN : bond 0.07654 ( 21) link_NAG-ASN : angle 2.75243 ( 63) 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_ALPHA1-3 : bond 0.08079 ( 1) link_ALPHA1-3 : angle 4.37023 ( 3) hydrogen bonds : bond 0.15088 ( 295) hydrogen bonds : angle 7.74367 ( 1131) SS BOND : bond 0.01970 ( 15) SS BOND : angle 2.84185 ( 30) covalent geometry : bond 0.02346 ( 8501) covalent geometry : angle 1.75844 (11544) *********************** 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 : 0.903 Fit side-chains revert: symmetry clash REVERT: H 12 VAL cc_start: 0.6656 (t) cc_final: 0.6436 (t) REVERT: A 142 MET cc_start: 0.8235 (mmm) cc_final: 0.7944 (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: 0.8537 (m) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2555 time to fit residues: 79.5631 Evaluate side-chains 132 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 374 HIS F 17 GLN B 575 GLN B 577 GLN B 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.089396 restraints weight = 13752.505| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.45 r_work: 0.2832 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8549 Z= 0.175 Angle : 0.719 9.097 11673 Z= 0.379 Chirality : 0.046 0.241 1385 Planarity : 0.005 0.043 1433 Dihedral : 7.776 85.427 1775 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.16 % Allowed : 8.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 998 helix: 1.27 (0.45), residues: 140 sheet: 1.14 (0.29), residues: 319 loop : -0.04 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.008 0.001 HIS A 66 PHE 0.015 0.002 PHE A 383 TYR 0.026 0.002 TYR L 94 ARG 0.006 0.001 ARG A 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 21) link_NAG-ASN : angle 2.38730 ( 63) link_ALPHA1-6 : bond 0.00705 ( 1) link_ALPHA1-6 : angle 1.55137 ( 3) link_BETA1-4 : bond 0.00844 ( 10) link_BETA1-4 : angle 2.45669 ( 30) link_ALPHA1-3 : bond 0.01081 ( 1) link_ALPHA1-3 : angle 1.17459 ( 3) hydrogen bonds : bond 0.06112 ( 295) hydrogen bonds : angle 5.26073 ( 1131) SS BOND : bond 0.00410 ( 15) SS BOND : angle 1.51781 ( 30) covalent geometry : bond 0.00393 ( 8501) covalent geometry : angle 0.68507 (11544) *********************** 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 181 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.977 Fit side-chains REVERT: H 72 ASP cc_start: 0.7577 (t0) cc_final: 0.7356 (t0) REVERT: A 142 MET cc_start: 0.8127 (mmm) cc_final: 0.7824 (mmm) REVERT: A 373 THR cc_start: 0.8742 (m) cc_final: 0.8194 (p) REVERT: F 45 LYS cc_start: 0.8443 (tttt) cc_final: 0.8224 (ttpm) REVERT: L 42 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7964 (mmmt) REVERT: L 45 LYS cc_start: 0.8860 (tttt) cc_final: 0.8262 (tppt) REVERT: L 92 ASN cc_start: 0.8657 (t0) cc_final: 0.8435 (t0) outliers start: 19 outliers final: 15 residues processed: 175 average time/residue: 0.2142 time to fit residues: 51.3185 Evaluate side-chains 136 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 A residue 323 ILE 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 636 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 95 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 1 optimal weight: 0.0070 chunk 69 optimal weight: 4.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- 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 99 ASN A 293 GLN A 428 GLN E 3 GLN E 73 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN B 575 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.086420 restraints weight = 14127.396| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.42 r_work: 0.2784 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8549 Z= 0.220 Angle : 0.661 8.672 11673 Z= 0.342 Chirality : 0.047 0.256 1385 Planarity : 0.004 0.039 1433 Dihedral : 7.210 73.997 1775 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.18 % Allowed : 10.80 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 998 helix: 1.13 (0.45), residues: 145 sheet: 0.77 (0.29), residues: 320 loop : -0.35 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 103 HIS 0.004 0.001 HIS B 570 PHE 0.018 0.002 PHE H 78 TYR 0.020 0.002 TYR A 318 ARG 0.006 0.001 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 21) link_NAG-ASN : angle 2.02742 ( 63) link_ALPHA1-6 : bond 0.00926 ( 1) link_ALPHA1-6 : angle 1.70182 ( 3) link_BETA1-4 : bond 0.00501 ( 10) link_BETA1-4 : angle 1.74499 ( 30) link_ALPHA1-3 : bond 0.00982 ( 1) link_ALPHA1-3 : angle 1.15857 ( 3) hydrogen bonds : bond 0.05236 ( 295) hydrogen bonds : angle 4.85013 ( 1131) SS BOND : bond 0.00552 ( 15) SS BOND : angle 1.27964 ( 30) covalent geometry : bond 0.00522 ( 8501) covalent geometry : angle 0.63706 (11544) *********************** 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 168 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.824 Fit side-chains REVERT: H 72 ASP cc_start: 0.7560 (t0) cc_final: 0.7331 (t0) REVERT: H 102 PHE cc_start: 0.8761 (m-80) cc_final: 0.8399 (m-10) REVERT: A 269 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: F 45 LYS cc_start: 0.8479 (tttt) cc_final: 0.8220 (tttm) REVERT: L 45 LYS cc_start: 0.8899 (tttt) cc_final: 0.8303 (tppt) outliers start: 28 outliers final: 22 residues processed: 158 average time/residue: 0.2080 time to fit residues: 44.8251 Evaluate side-chains 143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 68 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 136 ASN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 371 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 68 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 VAL 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 30 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 428 GLN ** E 81 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 = 0.3383 r_free = 0.3383 target = 0.112195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.085939 restraints weight = 13999.784| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.42 r_work: 0.2778 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8549 Z= 0.184 Angle : 0.620 10.419 11673 Z= 0.317 Chirality : 0.045 0.259 1385 Planarity : 0.004 0.040 1433 Dihedral : 6.794 62.040 1775 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.27 % Allowed : 11.70 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 998 helix: 1.10 (0.46), residues: 142 sheet: 0.64 (0.29), residues: 315 loop : -0.53 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 571 HIS 0.004 0.001 HIS A 105 PHE 0.016 0.002 PHE H 78 TYR 0.011 0.001 TYR F 96 ARG 0.004 0.001 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 21) link_NAG-ASN : angle 1.93222 ( 63) link_ALPHA1-6 : bond 0.01036 ( 1) link_ALPHA1-6 : angle 1.98615 ( 3) link_BETA1-4 : bond 0.00518 ( 10) link_BETA1-4 : angle 1.56622 ( 30) link_ALPHA1-3 : bond 0.01162 ( 1) link_ALPHA1-3 : angle 1.19971 ( 3) hydrogen bonds : bond 0.04845 ( 295) hydrogen bonds : angle 4.69291 ( 1131) SS BOND : bond 0.00487 ( 15) SS BOND : angle 1.19231 ( 30) covalent geometry : bond 0.00437 ( 8501) covalent geometry : angle 0.59689 (11544) *********************** 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 152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.013 Fit side-chains REVERT: H 72 ASP cc_start: 0.7590 (t0) cc_final: 0.7375 (t0) REVERT: A 269 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: A 318 TYR cc_start: 0.8841 (m-80) cc_final: 0.8615 (m-80) REVERT: F 45 LYS cc_start: 0.8488 (tttt) cc_final: 0.7994 (ttpp) REVERT: L 45 LYS cc_start: 0.8934 (tttt) cc_final: 0.8329 (tppt) outliers start: 20 outliers final: 17 residues processed: 146 average time/residue: 0.2867 time to fit residues: 56.1523 Evaluate side-chains 137 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.850 ------------------------------------------------------------------------------- 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 269 GLU 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 E residue 68 THR Chi-restraints excluded: chain F residue 20 THR 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 15 VAL 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 69 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.089539 restraints weight = 13992.995| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.34 r_work: 0.2871 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8549 Z= 0.117 Angle : 0.579 13.111 11673 Z= 0.293 Chirality : 0.043 0.222 1385 Planarity : 0.004 0.039 1433 Dihedral : 6.245 56.377 1775 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.93 % Allowed : 12.61 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 998 helix: 1.30 (0.46), residues: 142 sheet: 0.65 (0.29), residues: 329 loop : -0.59 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.004 0.001 HIS B 570 PHE 0.013 0.001 PHE H 78 TYR 0.020 0.001 TYR A 191 ARG 0.003 0.000 ARG A 419 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 21) link_NAG-ASN : angle 1.74289 ( 63) link_ALPHA1-6 : bond 0.01020 ( 1) link_ALPHA1-6 : angle 1.95607 ( 3) link_BETA1-4 : bond 0.00504 ( 10) link_BETA1-4 : angle 1.45281 ( 30) link_ALPHA1-3 : bond 0.01162 ( 1) link_ALPHA1-3 : angle 1.23455 ( 3) hydrogen bonds : bond 0.04193 ( 295) hydrogen bonds : angle 4.44507 ( 1131) SS BOND : bond 0.00280 ( 15) SS BOND : angle 0.81925 ( 30) covalent geometry : bond 0.00262 ( 8501) covalent geometry : angle 0.56028 (11544) *********************** 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 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.798 Fit side-chains REVERT: H 45 LEU cc_start: 0.8534 (mt) cc_final: 0.8206 (mt) REVERT: A 211 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7970 (mm-30) REVERT: A 318 TYR cc_start: 0.8886 (m-80) cc_final: 0.8679 (m-80) REVERT: A 373 THR cc_start: 0.8827 (m) cc_final: 0.8284 (p) REVERT: E 75 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8562 (mtmm) REVERT: F 33 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8311 (m) REVERT: F 45 LYS cc_start: 0.8525 (tttt) cc_final: 0.8279 (ptmt) REVERT: L 45 LYS cc_start: 0.8945 (tttt) cc_final: 0.8451 (tppt) outliers start: 17 outliers final: 12 residues processed: 138 average time/residue: 0.3496 time to fit residues: 66.1174 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 : 2.317 ------------------------------------------------------------------------------- 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 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 31 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 114 GLN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.085965 restraints weight = 14112.159| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.36 r_work: 0.2759 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8549 Z= 0.240 Angle : 0.673 13.333 11673 Z= 0.338 Chirality : 0.046 0.153 1385 Planarity : 0.004 0.042 1433 Dihedral : 5.848 34.175 1775 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.95 % Allowed : 12.39 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 998 helix: 1.34 (0.47), residues: 136 sheet: 0.64 (0.29), residues: 318 loop : -0.78 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 103 HIS 0.005 0.001 HIS A 330 PHE 0.020 0.002 PHE H 78 TYR 0.021 0.002 TYR A 484 ARG 0.004 0.001 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 21) link_NAG-ASN : angle 1.99313 ( 63) link_ALPHA1-6 : bond 0.00847 ( 1) link_ALPHA1-6 : angle 2.14180 ( 3) link_BETA1-4 : bond 0.00589 ( 10) link_BETA1-4 : angle 1.65032 ( 30) link_ALPHA1-3 : bond 0.00852 ( 1) link_ALPHA1-3 : angle 1.14160 ( 3) hydrogen bonds : bond 0.05075 ( 295) hydrogen bonds : angle 4.70638 ( 1131) SS BOND : bond 0.00480 ( 15) SS BOND : angle 1.15555 ( 30) covalent geometry : bond 0.00579 ( 8501) covalent geometry : angle 0.65162 (11544) *********************** 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 149 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.718 Fit side-chains REVERT: A 269 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: A 318 TYR cc_start: 0.8952 (m-80) cc_final: 0.8732 (m-80) REVERT: F 33 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8319 (m) REVERT: F 45 LYS cc_start: 0.8619 (tttt) cc_final: 0.8327 (tttm) REVERT: L 105 GLU cc_start: 0.1824 (OUTLIER) cc_final: 0.0773 (tp30) outliers start: 26 outliers final: 20 residues processed: 140 average time/residue: 0.3073 time to fit residues: 57.5038 Evaluate side-chains 140 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 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 125 LEU Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain F residue 11 VAL 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 L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 105 GLU 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 94 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 425 ASN L 92 ASN B 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089060 restraints weight = 14007.577| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.35 r_work: 0.2851 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8549 Z= 0.122 Angle : 0.566 13.014 11673 Z= 0.287 Chirality : 0.043 0.149 1385 Planarity : 0.004 0.038 1433 Dihedral : 5.343 34.469 1775 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.27 % Allowed : 13.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 998 helix: 1.61 (0.47), residues: 136 sheet: 0.53 (0.30), residues: 319 loop : -0.66 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 34 HIS 0.004 0.001 HIS B 570 PHE 0.013 0.001 PHE H 78 TYR 0.021 0.001 TYR A 484 ARG 0.002 0.000 ARG A 419 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 21) link_NAG-ASN : angle 1.76658 ( 63) link_ALPHA1-6 : bond 0.00469 ( 1) link_ALPHA1-6 : angle 1.47479 ( 3) link_BETA1-4 : bond 0.00493 ( 10) link_BETA1-4 : angle 1.44286 ( 30) link_ALPHA1-3 : bond 0.00866 ( 1) link_ALPHA1-3 : angle 1.20034 ( 3) hydrogen bonds : bond 0.04199 ( 295) hydrogen bonds : angle 4.43574 ( 1131) SS BOND : bond 0.00312 ( 15) SS BOND : angle 0.82049 ( 30) covalent geometry : bond 0.00279 ( 8501) covalent geometry : angle 0.54710 (11544) *********************** 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: 20 poor density : 128 time to evaluate : 1.003 Fit side-chains REVERT: H 101 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: A 318 TYR cc_start: 0.8919 (m-80) cc_final: 0.8703 (m-80) REVERT: A 411 ASN cc_start: 0.7846 (m-40) cc_final: 0.6913 (p0) REVERT: F 33 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8301 (m) REVERT: F 45 LYS cc_start: 0.8593 (tttt) cc_final: 0.8133 (ttpp) outliers start: 20 outliers final: 13 residues processed: 140 average time/residue: 0.2809 time to fit residues: 53.8739 Evaluate side-chains 139 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 61 optimal weight: 0.0470 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.089644 restraints weight = 14121.474| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.34 r_work: 0.2859 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8549 Z= 0.115 Angle : 0.550 12.366 11673 Z= 0.279 Chirality : 0.042 0.149 1385 Planarity : 0.004 0.038 1433 Dihedral : 5.089 34.479 1775 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.16 % Allowed : 14.20 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.27), residues: 998 helix: 1.78 (0.47), residues: 136 sheet: 0.56 (0.30), residues: 319 loop : -0.63 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 34 HIS 0.004 0.001 HIS B 570 PHE 0.013 0.001 PHE H 78 TYR 0.011 0.001 TYR A 191 ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 21) link_NAG-ASN : angle 1.70558 ( 63) link_ALPHA1-6 : bond 0.00521 ( 1) link_ALPHA1-6 : angle 1.48311 ( 3) link_BETA1-4 : bond 0.00473 ( 10) link_BETA1-4 : angle 1.41051 ( 30) link_ALPHA1-3 : bond 0.00829 ( 1) link_ALPHA1-3 : angle 1.22491 ( 3) hydrogen bonds : bond 0.03983 ( 295) hydrogen bonds : angle 4.29890 ( 1131) SS BOND : bond 0.00290 ( 15) SS BOND : angle 0.75936 ( 30) covalent geometry : bond 0.00263 ( 8501) covalent geometry : angle 0.53088 (11544) *********************** 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 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.884 Fit side-chains revert: symmetry clash REVERT: H 101 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: A 211 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8021 (mm-30) REVERT: A 318 TYR cc_start: 0.8890 (m-80) cc_final: 0.8677 (m-80) REVERT: A 411 ASN cc_start: 0.7824 (m-40) cc_final: 0.6889 (p0) REVERT: F 33 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8243 (m) REVERT: B 624 ASP cc_start: 0.8942 (m-30) cc_final: 0.8742 (m-30) outliers start: 19 outliers final: 13 residues processed: 139 average time/residue: 0.4453 time to fit residues: 87.1401 Evaluate side-chains 139 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 3.018 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain B residue 595 ILE 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 1 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 72 optimal weight: 0.0870 chunk 7 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN F 17 GLN L 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.090243 restraints weight = 14201.951| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.35 r_work: 0.2875 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8549 Z= 0.118 Angle : 0.548 12.228 11673 Z= 0.278 Chirality : 0.042 0.145 1385 Planarity : 0.004 0.037 1433 Dihedral : 4.949 34.801 1775 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.16 % Allowed : 14.55 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.27), residues: 998 helix: 2.01 (0.48), residues: 131 sheet: 0.49 (0.30), residues: 303 loop : -0.63 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 34 HIS 0.003 0.001 HIS B 570 PHE 0.013 0.001 PHE H 78 TYR 0.022 0.001 TYR A 484 ARG 0.003 0.000 ARG F 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 21) link_NAG-ASN : angle 1.62773 ( 63) link_ALPHA1-6 : bond 0.00448 ( 1) link_ALPHA1-6 : angle 1.41968 ( 3) link_BETA1-4 : bond 0.00458 ( 10) link_BETA1-4 : angle 1.39767 ( 30) link_ALPHA1-3 : bond 0.00747 ( 1) link_ALPHA1-3 : angle 1.25972 ( 3) hydrogen bonds : bond 0.03940 ( 295) hydrogen bonds : angle 4.24760 ( 1131) SS BOND : bond 0.00305 ( 15) SS BOND : angle 0.77779 ( 30) covalent geometry : bond 0.00275 ( 8501) covalent geometry : angle 0.53032 (11544) *********************** 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 147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 2.189 Fit side-chains REVERT: H 101 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7260 (m-30) REVERT: A 211 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8015 (mm-30) REVERT: A 268 GLU cc_start: 0.8127 (pm20) cc_final: 0.7808 (tt0) REVERT: A 318 TYR cc_start: 0.8912 (m-80) cc_final: 0.8706 (m-80) REVERT: A 411 ASN cc_start: 0.7944 (m-40) cc_final: 0.7016 (p0) REVERT: F 33 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8253 (m) REVERT: F 45 LYS cc_start: 0.8554 (tttt) cc_final: 0.8307 (ptmt) REVERT: L 4 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7273 (ptm) outliers start: 19 outliers final: 15 residues processed: 142 average time/residue: 0.5955 time to fit residues: 125.9126 Evaluate side-chains 143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 GLN L 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090940 restraints weight = 14143.688| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.36 r_work: 0.2879 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8549 Z= 0.112 Angle : 0.542 12.113 11673 Z= 0.275 Chirality : 0.042 0.145 1385 Planarity : 0.004 0.035 1433 Dihedral : 4.796 35.038 1775 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.50 % Allowed : 14.66 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.27), residues: 998 helix: 2.03 (0.48), residues: 131 sheet: 0.44 (0.30), residues: 315 loop : -0.58 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 34 HIS 0.003 0.001 HIS B 570 PHE 0.012 0.001 PHE H 78 TYR 0.013 0.001 TYR A 191 ARG 0.006 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 21) link_NAG-ASN : angle 1.59846 ( 63) link_ALPHA1-6 : bond 0.00441 ( 1) link_ALPHA1-6 : angle 1.41409 ( 3) link_BETA1-4 : bond 0.00429 ( 10) link_BETA1-4 : angle 1.36992 ( 30) link_ALPHA1-3 : bond 0.00719 ( 1) link_ALPHA1-3 : angle 1.27710 ( 3) hydrogen bonds : bond 0.03844 ( 295) hydrogen bonds : angle 4.19213 ( 1131) SS BOND : bond 0.00329 ( 15) SS BOND : angle 0.80201 ( 30) covalent geometry : bond 0.00258 ( 8501) covalent geometry : angle 0.52499 (11544) ********************** 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 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.231 Fit side-chains REVERT: H 76 ASN cc_start: 0.8453 (m-40) cc_final: 0.8210 (m110) REVERT: H 101 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7219 (m-30) REVERT: A 211 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8002 (mm-30) REVERT: A 318 TYR cc_start: 0.8884 (m-80) cc_final: 0.8681 (m-80) REVERT: A 411 ASN cc_start: 0.7935 (m-40) cc_final: 0.7007 (p0) REVERT: F 33 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8266 (m) REVERT: F 45 LYS cc_start: 0.8552 (tttt) cc_final: 0.8330 (ptmt) REVERT: L 4 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7244 (ptm) REVERT: B 624 ASP cc_start: 0.8949 (m-30) cc_final: 0.8742 (m-30) outliers start: 22 outliers final: 15 residues processed: 146 average time/residue: 0.2398 time to fit residues: 47.8735 Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU 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 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 7 THR 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 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 54 LEU Chi-restraints excluded: chain B residue 595 ILE 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 38 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 66 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN F 17 GLN L 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.089888 restraints weight = 14252.411| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.38 r_work: 0.2866 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8549 Z= 0.123 Angle : 0.545 11.841 11673 Z= 0.276 Chirality : 0.042 0.145 1385 Planarity : 0.004 0.036 1433 Dihedral : 4.802 35.198 1775 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.16 % Allowed : 15.00 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 998 helix: 2.05 (0.47), residues: 131 sheet: 0.46 (0.29), residues: 326 loop : -0.58 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.003 0.001 HIS B 570 PHE 0.012 0.001 PHE H 78 TYR 0.013 0.001 TYR A 191 ARG 0.003 0.000 ARG F 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 21) link_NAG-ASN : angle 1.60590 ( 63) link_ALPHA1-6 : bond 0.00471 ( 1) link_ALPHA1-6 : angle 1.42374 ( 3) link_BETA1-4 : bond 0.00432 ( 10) link_BETA1-4 : angle 1.38238 ( 30) link_ALPHA1-3 : bond 0.00648 ( 1) link_ALPHA1-3 : angle 1.35484 ( 3) hydrogen bonds : bond 0.03949 ( 295) hydrogen bonds : angle 4.18510 ( 1131) SS BOND : bond 0.00335 ( 15) SS BOND : angle 0.92309 ( 30) covalent geometry : bond 0.00287 ( 8501) covalent geometry : angle 0.52685 (11544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5678.31 seconds wall clock time: 106 minutes 38.42 seconds (6398.42 seconds total)