Starting phenix.real_space_refine on Wed Aug 5 22:30:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2b_42904/08_2026/8v2b_42904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2b_42904/08_2026/8v2b_42904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v2b_42904/08_2026/8v2b_42904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2b_42904/08_2026/8v2b_42904.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v2b_42904/08_2026/8v2b_42904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2b_42904/08_2026/8v2b_42904.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 49 5.16 5 C 7622 2.51 5 N 2005 2.21 5 O 2373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12049 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1343 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain breaks: 1 Chain: "B" Number of atoms: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4599 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 545} Chain: "C" Number of atoms: 5701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5701 Classifications: {'peptide': 703} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 666} 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: "E" 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: "F" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 NAG E 2 " occ=0.50 ... (12 atoms not shown) pdb=" O7 NAG E 2 " occ=0.50 Time building chain proxies: 2.78, per 1000 atoms: 0.23 Number of scatterers: 12049 At special positions: 0 Unit cell: (135.02, 154.8, 196.94, 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 49 16.00 O 2373 8.00 N 2005 7.00 C 7622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 456 " - pdb=" SG CYS B 464 " distance=2.03 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 252 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 282 " distance=2.03 Simple disulfide: pdb=" SG CYS C 363 " - pdb=" SG CYS C 403 " distance=2.03 Simple disulfide: pdb=" SG CYS C 559 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 668 " - pdb=" SG CYS C 684 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG B 701 " - " ASN B 225 " " NAG B 702 " - " ASN B 157 " " NAG B 703 " - " ASN B 388 " " NAG C 801 " - " ASN C 97 " " NAG C 802 " - " ASN C 130 " " NAG C 803 " - " ASN C 239 " " NAG C 804 " - " ASN C 377 " " NAG D 1 " - " ASN B 83 " " NAG E 1 " - " ASN B 551 " " NAG F 1 " - " ASN B 43 " " NAG G 1 " - " ASN B 131 " " NAG H 1 " - " ASN B 61 " " NAG I 1 " - " ASN C 74 " " NAG J 1 " - " ASN C 162 " " NAG K 1 " - " ASN C 271 " " NAG L 1 " - " ASN C 304 " " NAG M 1 " - " ASN C 323 " " NAG N 1 " - " ASN C 347 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 421.2 milliseconds 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 29 sheets defined 11.4% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.572A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 Processing helix chain 'A' and resid 169 through 201 Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.694A pdb=" N GLY B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.749A pdb=" N MET B 276 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 removed outlier: 4.179A pdb=" N ASN B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.571A pdb=" N ALA B 46 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 89 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B 48 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER B 87 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 38 removed outlier: 5.526A pdb=" N ASN B 114 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 105 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B 116 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 104 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 180 through 181 removed outlier: 3.564A pdb=" N CYS B 144 " --> pdb=" O CYS B 180 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP B 147 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN B 131 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N LYS B 219 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 136 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AA6, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.814A pdb=" N ASN B 225 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL B 243 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 268 through 269 Processing sheet with id=AA8, first strand: chain 'B' and resid 330 through 334 Processing sheet with id=AA9, first strand: chain 'B' and resid 376 through 380 removed outlier: 3.678A pdb=" N VAL B 366 " --> pdb=" O TYR B 378 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP B 363 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 365 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 396 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 426 through 433 removed outlier: 6.339A pdb=" N ASN B 427 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 442 " --> pdb=" O ASN B 427 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 472 removed outlier: 3.934A pdb=" N ASP B 467 " --> pdb=" O TRP B 455 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 450 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 490 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 510 " --> pdb=" O TYR B 490 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 494 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU B 506 " --> pdb=" O VAL B 494 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AB4, first strand: chain 'B' and resid 564 through 569 removed outlier: 4.309A pdb=" N ASN B 551 " --> pdb=" O TYR B 593 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR B 593 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR B 586 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 605 " --> pdb=" O TYR B 586 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 588 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU B 603 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N MET B 590 " --> pdb=" O GLY B 601 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 42 removed outlier: 7.345A pdb=" N GLU C 51 " --> pdb=" O HIS C 37 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL C 39 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN C 49 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE C 41 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU C 47 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP C 98 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 78 through 89 removed outlier: 6.468A pdb=" N THR C 78 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG C 72 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP C 80 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C 64 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 111 " --> pdb=" O LYS C 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB8, first strand: chain 'C' and resid 156 through 158 removed outlier: 3.533A pdb=" N THR C 226 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 177 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASN C 175 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 249 through 253 Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 274 removed outlier: 3.861A pdb=" N TYR C 303 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 322 " --> pdb=" O TYR C 303 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 334 through 340 removed outlier: 4.353A pdb=" N VAL C 336 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR C 349 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU C 338 " --> pdb=" O ASN C 347 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN C 347 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 372 through 375 Processing sheet with id=AC4, first strand: chain 'C' and resid 372 through 375 Processing sheet with id=AC5, first strand: chain 'C' and resid 433 through 440 removed outlier: 3.650A pdb=" N THR C 490 " --> pdb=" O LEU C 448 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 478 through 484 removed outlier: 3.695A pdb=" N MET C 517 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE C 503 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 530 through 534 removed outlier: 4.164A pdb=" N TYR C 616 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 607 " --> pdb=" O SER C 602 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER C 602 " --> pdb=" O ALA C 607 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 609 " --> pdb=" O GLU C 600 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU C 600 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 611 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 615 " --> pdb=" O TYR C 594 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG C 593 " --> pdb=" O HIS C 561 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 530 through 534 removed outlier: 4.164A pdb=" N TYR C 616 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 607 " --> pdb=" O SER C 602 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER C 602 " --> pdb=" O ALA C 607 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 609 " --> pdb=" O GLU C 600 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU C 600 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 611 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 615 " --> pdb=" O TYR C 594 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C 553 " --> pdb=" O ARG C 601 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 556 " --> pdb=" O LYS C 572 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 572 " --> pdb=" O VAL C 556 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP C 558 " --> pdb=" O GLN C 570 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 570 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 542 through 543 removed outlier: 4.138A pdb=" N ILE C 542 " --> pdb=" O THR C 581 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 581 " --> pdb=" O ILE C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 638 through 641 removed outlier: 3.920A pdb=" N PHE C 638 " --> pdb=" O VAL C 698 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 698 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 673 through 677 removed outlier: 4.082A pdb=" N LEU C 677 " --> pdb=" O SER C 681 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER C 681 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 682 " --> pdb=" O SER C 663 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 663 " --> pdb=" O VAL C 682 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS C 684 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 661 " --> pdb=" O CYS C 684 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY C 656 " --> pdb=" O TYR C 714 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR C 714 " --> pdb=" O GLY C 656 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 712 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER C 705 " --> pdb=" O THR C 730 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR C 730 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR C 707 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 728 " --> pdb=" O TYR C 707 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 709 " --> pdb=" O THR C 726 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1092 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: 2.21 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3818 1.34 - 1.46: 3022 1.46 - 1.58: 5440 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 12348 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.86e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 12343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 16248 1.24 - 2.48: 447 2.48 - 3.72: 115 3.72 - 4.95: 8 4.95 - 6.19: 4 Bond angle restraints: 16822 Sorted by residual: angle pdb=" N VAL B 560 " pdb=" CA VAL B 560 " pdb=" C VAL B 560 " ideal model delta sigma weight residual 113.20 110.49 2.71 9.60e-01 1.09e+00 7.97e+00 angle pdb=" C ARG C 72 " pdb=" N LEU C 73 " pdb=" CA LEU C 73 " ideal model delta sigma weight residual 121.54 125.16 -3.62 1.91e+00 2.74e-01 3.60e+00 angle pdb=" N THR A 117 " pdb=" CA THR A 117 " pdb=" C THR A 117 " ideal model delta sigma weight residual 109.81 113.80 -3.99 2.21e+00 2.05e-01 3.26e+00 angle pdb=" N ASN B 83 " pdb=" CA ASN B 83 " pdb=" C ASN B 83 " ideal model delta sigma weight residual 108.34 110.63 -2.29 1.31e+00 5.83e-01 3.05e+00 angle pdb=" N CYS C 282 " pdb=" CA CYS C 282 " pdb=" C CYS C 282 " ideal model delta sigma weight residual 108.46 111.01 -2.55 1.51e+00 4.39e-01 2.85e+00 ... (remaining 16817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 7180 22.77 - 45.54: 320 45.54 - 68.30: 135 68.30 - 91.07: 41 91.07 - 113.84: 120 Dihedral angle restraints: 7796 sinusoidal: 3509 harmonic: 4287 Sorted by residual: dihedral pdb=" CB CYS C 275 " pdb=" SG CYS C 275 " pdb=" SG CYS C 282 " pdb=" CB CYS C 282 " ideal model delta sinusoidal sigma weight residual -86.00 -35.63 -50.37 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS B 28 " pdb=" SG CYS B 28 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual 93.00 140.16 -47.16 1 1.00e+01 1.00e-02 3.07e+01 dihedral pdb=" CB CYS C 559 " pdb=" SG CYS C 559 " pdb=" SG CYS C 567 " pdb=" CB CYS C 567 " ideal model delta sinusoidal sigma weight residual 93.00 47.30 45.70 1 1.00e+01 1.00e-02 2.90e+01 ... (remaining 7793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1743 0.075 - 0.150: 211 0.150 - 0.225: 2 0.225 - 0.300: 1 0.300 - 0.375: 2 Chirality restraints: 1959 Sorted by residual: chirality pdb=" C1 NAG C 803 " pdb=" ND2 ASN C 239 " pdb=" C2 NAG C 803 " pdb=" O5 NAG C 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 74 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1956 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO C 55 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 183 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO C 184 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 184 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 184 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 64 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 65 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " -0.015 5.00e-02 4.00e+02 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1457 2.76 - 3.29: 10710 3.29 - 3.83: 18702 3.83 - 4.36: 20558 4.36 - 4.90: 36530 Nonbonded interactions: 87957 Sorted by model distance: nonbonded pdb=" OE2 GLU C 255 " pdb=" O3 NAG C 803 " model vdw 2.223 3.040 nonbonded pdb=" O LEU B 50 " pdb=" OG1 THR B 85 " model vdw 2.242 3.040 nonbonded pdb=" OE2 GLU C 283 " pdb=" OH TYR C 291 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR C 306 " pdb=" O6 NAG L 1 " model vdw 2.303 3.040 nonbonded pdb=" O SER B 581 " pdb=" OG1 THR B 584 " model vdw 2.307 3.040 ... (remaining 87952 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.220 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.003 0.063 12391 Z= 0.140 Angle : 0.501 9.586 16937 Z= 0.247 Chirality : 0.043 0.375 1959 Planarity : 0.003 0.031 2107 Dihedral : 21.988 113.841 4976 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.19), residues: 1447 helix: 1.78 (0.44), residues: 137 sheet: -1.36 (0.19), residues: 560 loop : -2.27 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 127 TYR 0.004 0.000 TYR A 97 PHE 0.014 0.001 PHE A 120 TRP 0.004 0.000 TRP C 438 HIS 0.001 0.000 HIS C 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (12348) covalent geometry : angle 0.48260 / 0.24 (16822) SS BOND : bond 0.00174 / 0.10 ( 14) SS BOND : angle 0.79345 / 0.46 ( 28) hydrogen bonds : bond 0.26039 / 17.59 ( 384) hydrogen bonds : angle 8.81572 / 6.21 ( 1092) link_BETA1-4 : bond 0.00331 / 0.17 ( 11) link_BETA1-4 : angle 1.12576 / 0.84 ( 33) link_NAG-ASN : bond 0.00509 / 0.27 ( 18) link_NAG-ASN : angle 2.27338 / 1.63 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8142 (t0) cc_final: 0.7835 (t0) REVERT: A 108 ASP cc_start: 0.7942 (t0) cc_final: 0.7654 (t0) REVERT: B 330 PHE cc_start: 0.6308 (t80) cc_final: 0.5385 (t80) REVERT: B 343 ARG cc_start: 0.5063 (ptt180) cc_final: 0.3505 (ttm170) REVERT: B 347 LEU cc_start: 0.8021 (mt) cc_final: 0.7443 (tp) REVERT: B 350 LYS cc_start: 0.8680 (mttt) cc_final: 0.7837 (mttt) REVERT: B 415 PRO cc_start: 0.7178 (Cg_endo) cc_final: 0.6023 (Cg_exo) REVERT: C 98 TRP cc_start: 0.8670 (t60) cc_final: 0.7989 (t60) REVERT: C 418 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8668 (tttm) REVERT: C 457 GLN cc_start: 0.7964 (mp10) cc_final: 0.7757 (mp10) REVERT: C 540 PHE cc_start: 0.6728 (m-80) cc_final: 0.6378 (m-80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1272 time to fit residues: 27.4831 Evaluate side-chains 90 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 112 GLN B 57 HIS C 42 GLN C 46 GLN C 49 ASN C 171 GLN C 193 HIS C 201 ASN C 300 GLN C 441 ASN C 466 ASN C 561 HIS C 565 GLN C 573 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.151218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.120477 restraints weight = 39591.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.118837 restraints weight = 27877.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.119287 restraints weight = 23144.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.119559 restraints weight = 18385.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.119796 restraints weight = 16765.217| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3944 r_free = 0.3944 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (13 function evaluations) r_final: 0.3920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12391 Z= 0.124 Angle : 0.635 9.946 16937 Z= 0.291 Chirality : 0.048 0.307 1959 Planarity : 0.004 0.044 2107 Dihedral : 22.095 99.392 2180 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.83 % Allowed : 8.85 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.21), residues: 1447 helix: 2.81 (0.45), residues: 137 sheet: -0.91 (0.20), residues: 593 loop : -1.72 (0.20), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 502 TYR 0.015 0.001 TYR A 105 PHE 0.012 0.001 PHE C 710 TRP 0.020 0.001 TRP B 349 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (12348) covalent geometry : angle 0.60691 / 0.28 (16822) SS BOND : bond 0.00285 / 0.16 ( 14) SS BOND : angle 1.08259 / 0.59 ( 28) hydrogen bonds : bond 0.04664 / 3.24 ( 384) hydrogen bonds : angle 6.09818 / 4.42 ( 1092) link_BETA1-4 : bond 0.00372 / 0.17 ( 11) link_BETA1-4 : angle 1.99352 / 1.39 ( 33) link_NAG-ASN : bond 0.00413 / 0.23 ( 18) link_NAG-ASN : angle 2.91914 / 2.09 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8231 (t0) cc_final: 0.7999 (t0) REVERT: A 100 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8769 (mm) REVERT: A 108 ASP cc_start: 0.8262 (t0) cc_final: 0.7907 (t0) REVERT: B 322 ASP cc_start: 0.6943 (t0) cc_final: 0.6635 (t0) REVERT: B 343 ARG cc_start: 0.5366 (ptt180) cc_final: 0.3738 (ttm170) REVERT: B 350 LYS cc_start: 0.8416 (mttt) cc_final: 0.7930 (pttp) REVERT: B 415 PRO cc_start: 0.7157 (Cg_endo) cc_final: 0.6434 (Cg_exo) REVERT: B 594 THR cc_start: 0.6779 (OUTLIER) cc_final: 0.6265 (t) REVERT: C 98 TRP cc_start: 0.8505 (t60) cc_final: 0.7842 (t60) REVERT: C 418 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8435 (tttm) REVERT: C 540 PHE cc_start: 0.6882 (m-80) cc_final: 0.6205 (m-80) outliers start: 11 outliers final: 5 residues processed: 107 average time/residue: 0.1138 time to fit residues: 17.9570 Evaluate side-chains 86 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 336 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 125 optimal weight: 0.0170 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 HIS C 376 HIS ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.149434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.114356 restraints weight = 39130.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.113876 restraints weight = 25541.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.113796 restraints weight = 19080.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.114441 restraints weight = 16863.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.114592 restraints weight = 14200.443| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12391 Z= 0.114 Angle : 0.641 11.774 16937 Z= 0.282 Chirality : 0.048 0.339 1959 Planarity : 0.003 0.038 2107 Dihedral : 18.588 121.532 2180 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.91 % Allowed : 11.12 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.21), residues: 1447 helix: 3.20 (0.46), residues: 137 sheet: -0.57 (0.20), residues: 593 loop : -1.46 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 519 TYR 0.012 0.001 TYR B 32 PHE 0.010 0.001 PHE B 44 TRP 0.022 0.001 TRP B 349 HIS 0.003 0.000 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (12348) covalent geometry : angle 0.60792 / 0.27 (16822) SS BOND : bond 0.00271 / 0.14 ( 14) SS BOND : angle 1.28941 / 0.69 ( 28) hydrogen bonds : bond 0.04071 / 2.84 ( 384) hydrogen bonds : angle 5.44449 / 3.94 ( 1092) link_BETA1-4 : bond 0.00401 / 0.18 ( 11) link_BETA1-4 : angle 2.05290 / 1.51 ( 33) link_NAG-ASN : bond 0.00563 / 0.30 ( 18) link_NAG-ASN : angle 3.20317 / 2.42 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8873 (mm) REVERT: A 108 ASP cc_start: 0.8243 (t0) cc_final: 0.7922 (t0) REVERT: B 322 ASP cc_start: 0.7137 (t0) cc_final: 0.6707 (t0) REVERT: B 343 ARG cc_start: 0.5565 (ptt180) cc_final: 0.4087 (ttm170) REVERT: B 350 LYS cc_start: 0.8226 (mttt) cc_final: 0.7973 (pttp) REVERT: B 415 PRO cc_start: 0.7088 (Cg_endo) cc_final: 0.6348 (Cg_exo) REVERT: B 594 THR cc_start: 0.6735 (OUTLIER) cc_final: 0.6206 (t) REVERT: C 418 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8585 (tttm) REVERT: C 540 PHE cc_start: 0.6772 (m-80) cc_final: 0.6061 (m-80) outliers start: 12 outliers final: 5 residues processed: 97 average time/residue: 0.1068 time to fit residues: 15.6432 Evaluate side-chains 84 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 337 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 24 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 0.0870 chunk 30 optimal weight: 4.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 408 HIS ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.146227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.109598 restraints weight = 38449.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.108890 restraints weight = 25212.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.109073 restraints weight = 18938.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.109609 restraints weight = 17762.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.109765 restraints weight = 14680.139| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12391 Z= 0.162 Angle : 0.692 10.182 16937 Z= 0.313 Chirality : 0.048 0.305 1959 Planarity : 0.004 0.042 2107 Dihedral : 14.959 109.001 2180 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.44 % Allowed : 12.93 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.21), residues: 1447 helix: 3.08 (0.45), residues: 138 sheet: -0.43 (0.20), residues: 598 loop : -1.38 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 281 TYR 0.016 0.001 TYR B 394 PHE 0.016 0.002 PHE B 330 TRP 0.027 0.001 TRP B 349 HIS 0.005 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (12348) covalent geometry : angle 0.66378 / 0.31 (16822) SS BOND : bond 0.00767 / 0.35 ( 14) SS BOND : angle 1.76226 / 0.94 ( 28) hydrogen bonds : bond 0.04781 / 3.32 ( 384) hydrogen bonds : angle 5.29845 / 3.82 ( 1092) link_BETA1-4 : bond 0.00494 / 0.23 ( 11) link_BETA1-4 : angle 2.30810 / 1.77 ( 33) link_NAG-ASN : bond 0.00513 / 0.33 ( 18) link_NAG-ASN : angle 2.83983 / 1.98 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9125 (mm) REVERT: A 108 ASP cc_start: 0.8259 (t0) cc_final: 0.7893 (t0) REVERT: B 322 ASP cc_start: 0.7264 (t0) cc_final: 0.6832 (t0) REVERT: B 343 ARG cc_start: 0.5647 (ptt180) cc_final: 0.3974 (ttm170) REVERT: B 350 LYS cc_start: 0.8379 (mttt) cc_final: 0.8166 (pttt) REVERT: B 365 GLU cc_start: 0.7474 (mp0) cc_final: 0.7164 (mp0) REVERT: B 450 LYS cc_start: 0.7584 (pttt) cc_final: 0.7198 (mptp) REVERT: B 594 THR cc_start: 0.6772 (OUTLIER) cc_final: 0.6198 (t) REVERT: C 418 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8497 (tttm) REVERT: C 540 PHE cc_start: 0.6715 (m-80) cc_final: 0.6176 (m-80) outliers start: 19 outliers final: 14 residues processed: 100 average time/residue: 0.1071 time to fit residues: 16.1316 Evaluate side-chains 92 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 336 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 100 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 0.0060 chunk 4 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 469 GLN C 181 GLN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.147924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.111014 restraints weight = 38898.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.111913 restraints weight = 23844.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.111649 restraints weight = 16557.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.111954 restraints weight = 15484.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.112147 restraints weight = 14405.084| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12391 Z= 0.101 Angle : 0.644 9.129 16937 Z= 0.283 Chirality : 0.046 0.341 1959 Planarity : 0.003 0.038 2107 Dihedral : 13.611 108.124 2180 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.13 % Allowed : 13.77 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1447 helix: 3.29 (0.46), residues: 138 sheet: -0.21 (0.21), residues: 582 loop : -1.28 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 76 TYR 0.009 0.001 TYR C 616 PHE 0.014 0.001 PHE B 330 TRP 0.031 0.001 TRP C 96 HIS 0.002 0.001 HIS C 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (12348) covalent geometry : angle 0.61203 / 0.28 (16822) SS BOND : bond 0.00302 / 0.14 ( 14) SS BOND : angle 1.23273 / 0.66 ( 28) hydrogen bonds : bond 0.03635 / 2.54 ( 384) hydrogen bonds : angle 4.95560 / 3.57 ( 1092) link_BETA1-4 : bond 0.00562 / 0.28 ( 11) link_BETA1-4 : angle 2.42411 / 1.89 ( 33) link_NAG-ASN : bond 0.00478 / 0.30 ( 18) link_NAG-ASN : angle 2.98761 / 2.20 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9071 (mm) REVERT: A 108 ASP cc_start: 0.8236 (t0) cc_final: 0.7887 (t0) REVERT: A 149 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7149 (mp0) REVERT: B 322 ASP cc_start: 0.7253 (t0) cc_final: 0.6809 (t0) REVERT: B 343 ARG cc_start: 0.5634 (ptt180) cc_final: 0.4037 (ttm170) REVERT: B 365 GLU cc_start: 0.7251 (mp0) cc_final: 0.6854 (mp0) REVERT: B 450 LYS cc_start: 0.7587 (pttt) cc_final: 0.7086 (mptt) REVERT: B 451 TYR cc_start: 0.7583 (m-80) cc_final: 0.7195 (m-10) REVERT: B 593 TYR cc_start: 0.7636 (m-80) cc_final: 0.7315 (t80) REVERT: B 594 THR cc_start: 0.6693 (OUTLIER) cc_final: 0.6018 (t) REVERT: C 64 MET cc_start: 0.6360 (mmm) cc_final: 0.6154 (mmm) REVERT: C 98 TRP cc_start: 0.8458 (t60) cc_final: 0.7832 (t60) REVERT: C 348 MET cc_start: 0.7547 (tpt) cc_final: 0.7227 (ttm) REVERT: C 418 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8513 (tttm) REVERT: C 540 PHE cc_start: 0.6871 (m-80) cc_final: 0.6119 (m-80) outliers start: 15 outliers final: 10 residues processed: 96 average time/residue: 0.0990 time to fit residues: 14.5740 Evaluate side-chains 90 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 336 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.143576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.101628 restraints weight = 38827.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.103438 restraints weight = 22530.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.103791 restraints weight = 14743.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.104286 restraints weight = 14054.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.104304 restraints weight = 12273.923| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12391 Z= 0.244 Angle : 0.749 12.007 16937 Z= 0.347 Chirality : 0.048 0.371 1959 Planarity : 0.004 0.039 2107 Dihedral : 12.484 105.902 2180 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.04 % Allowed : 14.90 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1447 helix: 2.77 (0.45), residues: 139 sheet: -0.33 (0.21), residues: 590 loop : -1.32 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 477 TYR 0.020 0.002 TYR B 307 PHE 0.022 0.002 PHE B 330 TRP 0.041 0.002 TRP C 96 HIS 0.006 0.001 HIS C 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 (12348) covalent geometry : angle 0.71697 / 0.34 (16822) SS BOND : bond 0.00483 / 0.27 ( 14) SS BOND : angle 1.61690 / 0.93 ( 28) hydrogen bonds : bond 0.05736 / 3.94 ( 384) hydrogen bonds : angle 5.42095 / 3.87 ( 1092) link_BETA1-4 : bond 0.00591 / 0.31 ( 11) link_BETA1-4 : angle 2.66796 / 2.10 ( 33) link_NAG-ASN : bond 0.00607 / 0.43 ( 18) link_NAG-ASN : angle 3.17821 / 2.16 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8376 (t0) cc_final: 0.8090 (t0) REVERT: A 100 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8952 (mm) REVERT: A 108 ASP cc_start: 0.8291 (t0) cc_final: 0.8084 (t70) REVERT: B 322 ASP cc_start: 0.7446 (t0) cc_final: 0.6966 (t0) REVERT: B 343 ARG cc_start: 0.5431 (ptt180) cc_final: 0.3773 (ttm170) REVERT: B 350 LYS cc_start: 0.8498 (pttt) cc_final: 0.8283 (pttp) REVERT: B 365 GLU cc_start: 0.7593 (mp0) cc_final: 0.7307 (mp0) REVERT: B 415 PRO cc_start: 0.7386 (Cg_endo) cc_final: 0.6397 (Cg_exo) REVERT: B 450 LYS cc_start: 0.7593 (pttt) cc_final: 0.7124 (mptt) REVERT: B 451 TYR cc_start: 0.7933 (m-80) cc_final: 0.7588 (m-10) REVERT: B 593 TYR cc_start: 0.7559 (m-80) cc_final: 0.7295 (t80) REVERT: B 594 THR cc_start: 0.6777 (OUTLIER) cc_final: 0.6457 (m) REVERT: C 64 MET cc_start: 0.6637 (mmm) cc_final: 0.6428 (mmm) REVERT: C 348 MET cc_start: 0.7879 (tpt) cc_final: 0.7571 (ttt) REVERT: C 418 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8496 (tttt) REVERT: C 502 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7570 (mmm-85) REVERT: C 540 PHE cc_start: 0.6802 (m-80) cc_final: 0.6110 (m-80) outliers start: 27 outliers final: 20 residues processed: 110 average time/residue: 0.0999 time to fit residues: 16.7947 Evaluate side-chains 101 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 446 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.145048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.108264 restraints weight = 37965.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.108409 restraints weight = 25257.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.107835 restraints weight = 17697.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.108525 restraints weight = 17334.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.108634 restraints weight = 14292.761| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12391 Z= 0.112 Angle : 0.630 10.117 16937 Z= 0.284 Chirality : 0.045 0.406 1959 Planarity : 0.003 0.042 2107 Dihedral : 11.469 105.206 2180 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.21 % Allowed : 16.34 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.22), residues: 1447 helix: 3.14 (0.46), residues: 139 sheet: -0.20 (0.21), residues: 592 loop : -1.17 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 519 TYR 0.010 0.001 TYR C 594 PHE 0.013 0.001 PHE B 330 TRP 0.037 0.001 TRP C 96 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (12348) covalent geometry : angle 0.59557 / 0.28 (16822) SS BOND : bond 0.00383 / 0.18 ( 14) SS BOND : angle 1.21597 / 0.67 ( 28) hydrogen bonds : bond 0.04001 / 2.77 ( 384) hydrogen bonds : angle 4.93651 / 3.52 ( 1092) link_BETA1-4 : bond 0.00630 / 0.31 ( 11) link_BETA1-4 : angle 2.61468 / 2.06 ( 33) link_NAG-ASN : bond 0.00406 / 0.23 ( 18) link_NAG-ASN : angle 3.02343 / 2.12 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8407 (t0) cc_final: 0.8048 (t0) REVERT: A 100 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8785 (mm) REVERT: A 108 ASP cc_start: 0.8393 (t0) cc_final: 0.8021 (t0) REVERT: B 322 ASP cc_start: 0.7300 (t0) cc_final: 0.6832 (t0) REVERT: B 343 ARG cc_start: 0.5418 (ptt180) cc_final: 0.3972 (ttm170) REVERT: B 350 LYS cc_start: 0.8413 (pttt) cc_final: 0.8020 (pttp) REVERT: B 365 GLU cc_start: 0.7353 (mp0) cc_final: 0.7089 (mp0) REVERT: B 450 LYS cc_start: 0.7567 (pttt) cc_final: 0.7270 (mptt) REVERT: B 519 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7457 (ttp80) REVERT: B 593 TYR cc_start: 0.7729 (m-80) cc_final: 0.7396 (t80) REVERT: B 594 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6484 (m) REVERT: C 348 MET cc_start: 0.7525 (tpt) cc_final: 0.7300 (ttt) REVERT: C 418 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8508 (tttp) REVERT: C 502 ARG cc_start: 0.8009 (mmt180) cc_final: 0.7436 (mmm-85) REVERT: C 540 PHE cc_start: 0.6742 (m-80) cc_final: 0.6150 (m-80) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 0.1106 time to fit residues: 15.1084 Evaluate side-chains 86 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 336 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 126 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.142236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.102779 restraints weight = 38411.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.101294 restraints weight = 24588.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.102008 restraints weight = 17188.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.102491 restraints weight = 14920.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.102627 restraints weight = 12911.961| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12391 Z= 0.248 Angle : 0.742 12.346 16937 Z= 0.347 Chirality : 0.048 0.414 1959 Planarity : 0.004 0.039 2107 Dihedral : 11.288 104.732 2180 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.74 % Allowed : 16.26 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.22), residues: 1447 helix: 2.72 (0.45), residues: 139 sheet: -0.35 (0.21), residues: 590 loop : -1.31 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 26 TYR 0.023 0.002 TYR A 105 PHE 0.026 0.002 PHE B 330 TRP 0.030 0.002 TRP C 96 HIS 0.006 0.001 HIS C 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 (12348) covalent geometry : angle 0.70720 / 0.34 (16822) SS BOND : bond 0.00531 / 0.30 ( 14) SS BOND : angle 1.64427 / 0.95 ( 28) hydrogen bonds : bond 0.05774 / 3.97 ( 384) hydrogen bonds : angle 5.46105 / 3.87 ( 1092) link_BETA1-4 : bond 0.00616 / 0.30 ( 11) link_BETA1-4 : angle 2.76302 / 2.19 ( 33) link_NAG-ASN : bond 0.00564 / 0.39 ( 18) link_NAG-ASN : angle 3.28934 / 2.26 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8412 (t0) cc_final: 0.8210 (t0) REVERT: A 100 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8936 (mm) REVERT: A 108 ASP cc_start: 0.8285 (t0) cc_final: 0.8080 (t70) REVERT: B 322 ASP cc_start: 0.7509 (t0) cc_final: 0.7070 (t0) REVERT: B 343 ARG cc_start: 0.5295 (ptt180) cc_final: 0.3674 (ttm170) REVERT: B 365 GLU cc_start: 0.7612 (mp0) cc_final: 0.7321 (mp0) REVERT: B 415 PRO cc_start: 0.7232 (Cg_endo) cc_final: 0.6246 (Cg_exo) REVERT: B 593 TYR cc_start: 0.7719 (m-80) cc_final: 0.7326 (t80) REVERT: B 594 THR cc_start: 0.6760 (OUTLIER) cc_final: 0.6524 (m) REVERT: C 418 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8660 (ttpp) REVERT: C 540 PHE cc_start: 0.6773 (m-80) cc_final: 0.6097 (m-80) outliers start: 23 outliers final: 19 residues processed: 96 average time/residue: 0.0813 time to fit residues: 12.0460 Evaluate side-chains 94 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 446 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 48 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.1649 > 50:) chunk 112 optimal weight: 0.9980 chunk 91 optimal weight: 0.0040 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.143891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.106006 restraints weight = 38131.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.106993 restraints weight = 21661.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.106720 restraints weight = 15851.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.107415 restraints weight = 15399.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.107394 restraints weight = 12956.794| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12391 Z= 0.118 Angle : 0.633 10.897 16937 Z= 0.290 Chirality : 0.045 0.424 1959 Planarity : 0.003 0.043 2107 Dihedral : 10.727 105.066 2180 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.29 % Allowed : 17.17 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1447 helix: 3.14 (0.45), residues: 139 sheet: -0.11 (0.22), residues: 571 loop : -1.17 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 519 TYR 0.017 0.001 TYR A 105 PHE 0.013 0.001 PHE B 330 TRP 0.029 0.001 TRP C 96 HIS 0.003 0.001 HIS C 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (12348) covalent geometry : angle 0.59724 / 0.28 (16822) SS BOND : bond 0.00335 / 0.18 ( 14) SS BOND : angle 1.12721 / 0.65 ( 28) hydrogen bonds : bond 0.04081 / 2.83 ( 384) hydrogen bonds : angle 5.01190 / 3.56 ( 1092) link_BETA1-4 : bond 0.00663 / 0.32 ( 11) link_BETA1-4 : angle 2.63867 / 2.08 ( 33) link_NAG-ASN : bond 0.00409 / 0.23 ( 18) link_NAG-ASN : angle 3.08580 / 2.15 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8315 (t0) cc_final: 0.7990 (t0) REVERT: A 100 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9059 (mm) REVERT: A 108 ASP cc_start: 0.8212 (t0) cc_final: 0.7817 (t0) REVERT: B 322 ASP cc_start: 0.7372 (t0) cc_final: 0.6929 (t0) REVERT: B 343 ARG cc_start: 0.5271 (ptt180) cc_final: 0.3945 (ttm170) REVERT: B 350 LYS cc_start: 0.8555 (pttt) cc_final: 0.7634 (ptmt) REVERT: B 365 GLU cc_start: 0.7281 (mp0) cc_final: 0.6946 (mp0) REVERT: B 450 LYS cc_start: 0.7582 (pttt) cc_final: 0.7160 (mptt) REVERT: B 469 GLN cc_start: 0.6636 (pt0) cc_final: 0.6279 (tt0) REVERT: B 519 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7777 (ttp80) REVERT: B 593 TYR cc_start: 0.7674 (m-80) cc_final: 0.7387 (t80) REVERT: B 594 THR cc_start: 0.6664 (OUTLIER) cc_final: 0.6438 (m) REVERT: C 418 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8730 (ttpp) REVERT: C 540 PHE cc_start: 0.6692 (m-80) cc_final: 0.6109 (m-80) outliers start: 17 outliers final: 14 residues processed: 83 average time/residue: 0.0735 time to fit residues: 9.3837 Evaluate side-chains 81 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 0.0270 chunk 130 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 85 optimal weight: 0.0020 chunk 96 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.145378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.109305 restraints weight = 38065.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.109186 restraints weight = 24565.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.109466 restraints weight = 15758.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.109939 restraints weight = 15344.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.109953 restraints weight = 13671.100| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12391 Z= 0.101 Angle : 0.597 10.689 16937 Z= 0.275 Chirality : 0.044 0.426 1959 Planarity : 0.003 0.041 2107 Dihedral : 10.079 101.732 2180 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.51 % Allowed : 17.02 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.22), residues: 1447 helix: 3.02 (0.46), residues: 145 sheet: -0.00 (0.22), residues: 571 loop : -1.03 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 519 TYR 0.009 0.001 TYR C 616 PHE 0.011 0.001 PHE B 330 TRP 0.028 0.001 TRP C 96 HIS 0.005 0.001 HIS C 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (12348) covalent geometry : angle 0.56208 / 0.27 (16822) SS BOND : bond 0.00282 / 0.14 ( 14) SS BOND : angle 0.98135 / 0.57 ( 28) hydrogen bonds : bond 0.03543 / 2.46 ( 384) hydrogen bonds : angle 4.69725 / 3.34 ( 1092) link_BETA1-4 : bond 0.00694 / 0.34 ( 11) link_BETA1-4 : angle 2.48897 / 1.97 ( 33) link_NAG-ASN : bond 0.00415 / 0.24 ( 18) link_NAG-ASN : angle 2.99028 / 2.11 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8335 (t0) cc_final: 0.8004 (t0) REVERT: A 100 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8764 (mm) REVERT: A 108 ASP cc_start: 0.8260 (t0) cc_final: 0.7915 (t0) REVERT: B 322 ASP cc_start: 0.7365 (t0) cc_final: 0.6888 (t0) REVERT: B 343 ARG cc_start: 0.5462 (ptt180) cc_final: 0.4045 (ttm170) REVERT: B 350 LYS cc_start: 0.8502 (pttt) cc_final: 0.7610 (ptmt) REVERT: B 365 GLU cc_start: 0.7350 (mp0) cc_final: 0.7088 (mp0) REVERT: B 519 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7897 (ttp80) REVERT: B 593 TYR cc_start: 0.7737 (m-80) cc_final: 0.7391 (t80) REVERT: C 348 MET cc_start: 0.7554 (tpt) cc_final: 0.7266 (ttt) REVERT: C 418 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8777 (ttpp) REVERT: C 540 PHE cc_start: 0.6767 (m-80) cc_final: 0.6188 (m-80) outliers start: 20 outliers final: 15 residues processed: 88 average time/residue: 0.0915 time to fit residues: 12.5244 Evaluate side-chains 84 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 0.8980 chunk 132 optimal weight: 30.0000 chunk 117 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 118 optimal weight: 20.0000 chunk 19 optimal weight: 0.0470 chunk 91 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.143953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.106717 restraints weight = 37962.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.106462 restraints weight = 21727.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.107510 restraints weight = 15026.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.108008 restraints weight = 13405.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.107670 restraints weight = 11192.620| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12391 Z= 0.134 Angle : 0.617 10.666 16937 Z= 0.289 Chirality : 0.045 0.420 1959 Planarity : 0.004 0.040 2107 Dihedral : 9.929 100.907 2180 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.59 % Allowed : 17.32 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.22), residues: 1447 helix: 2.91 (0.45), residues: 145 sheet: -0.11 (0.21), residues: 593 loop : -1.05 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 519 TYR 0.011 0.001 TYR C 303 PHE 0.015 0.001 PHE B 330 TRP 0.024 0.001 TRP B 331 HIS 0.003 0.001 HIS C 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (12348) covalent geometry : angle 0.58400 / 0.28 (16822) SS BOND : bond 0.00320 / 0.18 ( 14) SS BOND : angle 1.23664 / 0.70 ( 28) hydrogen bonds : bond 0.04226 / 2.92 ( 384) hydrogen bonds : angle 4.84081 / 3.43 ( 1092) link_BETA1-4 : bond 0.00607 / 0.30 ( 11) link_BETA1-4 : angle 2.42606 / 1.91 ( 33) link_NAG-ASN : bond 0.00407 / 0.24 ( 18) link_NAG-ASN : angle 2.97881 / 2.08 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.90 seconds wall clock time: 47 minutes 27.42 seconds (2847.42 seconds total)