Starting phenix.real_space_refine on Wed May 14 18:08:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2b_42904/05_2025/8v2b_42904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2b_42904/05_2025/8v2b_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v2b_42904/05_2025/8v2b_42904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2b_42904/05_2025/8v2b_42904.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2b_42904/05_2025/8v2b_42904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2b_42904/05_2025/8v2b_42904.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.81, per 1000 atoms: 0.65 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: 3.18 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.75 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: 4.20 Time building geometry restraints manager: 3.72 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.090 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.000 TRP C 438 HIS 0.001 0.000 HIS C 561 PHE 0.014 0.001 PHE A 120 TYR 0.004 0.000 TYR A 97 ARG 0.001 0.000 ARG A 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 18) link_NAG-ASN : angle 2.27338 ( 54) link_BETA1-4 : bond 0.00331 ( 11) link_BETA1-4 : angle 1.12576 ( 33) hydrogen bonds : bond 0.26039 ( 384) hydrogen bonds : angle 8.81572 ( 1092) SS BOND : bond 0.00174 ( 14) SS BOND : angle 0.79345 ( 28) covalent geometry : bond 0.00275 (12348) covalent geometry : angle 0.48260 (16822) *********************** 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 : 1.266 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: 0.2852 time to fit residues: 61.3739 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 : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 130 optimal weight: 20.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 112 GLN B 56 GLN B 57 HIS C 42 GLN C 46 GLN C 49 ASN C 171 GLN C 193 HIS C 300 GLN C 353 HIS C 376 HIS C 408 HIS C 466 ASN C 561 HIS C 565 GLN C 573 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.146200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.109183 restraints weight = 38574.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.109562 restraints weight = 23427.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.109511 restraints weight = 16678.874| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12391 Z= 0.277 Angle : 0.755 11.882 16937 Z= 0.357 Chirality : 0.051 0.363 1959 Planarity : 0.005 0.050 2107 Dihedral : 22.544 100.931 2180 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.36 % Allowed : 9.83 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.20), residues: 1447 helix: 2.37 (0.45), residues: 137 sheet: -0.94 (0.20), residues: 560 loop : -1.94 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 349 HIS 0.007 0.001 HIS C 408 PHE 0.023 0.002 PHE B 330 TYR 0.022 0.002 TYR A 183 ARG 0.004 0.001 ARG B 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 18) link_NAG-ASN : angle 3.48340 ( 54) link_BETA1-4 : bond 0.00481 ( 11) link_BETA1-4 : angle 1.95615 ( 33) hydrogen bonds : bond 0.07317 ( 384) hydrogen bonds : angle 6.59889 ( 1092) SS BOND : bond 0.00531 ( 14) SS BOND : angle 1.77940 ( 28) covalent geometry : bond 0.00638 (12348) covalent geometry : angle 0.72294 (16822) *********************** 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 111 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.333 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: 0.9408 (OUTLIER) cc_final: 0.9007 (mm) REVERT: A 108 ASP cc_start: 0.8661 (t0) cc_final: 0.8282 (t0) REVERT: B 30 TYR cc_start: 0.5199 (p90) cc_final: 0.4753 (p90) REVERT: B 322 ASP cc_start: 0.7148 (t0) cc_final: 0.6930 (t0) REVERT: B 343 ARG cc_start: 0.5560 (ptt180) cc_final: 0.3809 (ttm170) REVERT: B 350 LYS cc_start: 0.8557 (mttt) cc_final: 0.7813 (mttt) REVERT: B 415 PRO cc_start: 0.7210 (Cg_endo) cc_final: 0.6285 (Cg_exo) REVERT: B 594 THR cc_start: 0.6946 (OUTLIER) cc_final: 0.6423 (t) REVERT: C 174 TYR cc_start: 0.6588 (m-80) cc_final: 0.6374 (m-80) REVERT: C 418 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8557 (tttm) REVERT: C 540 PHE cc_start: 0.6999 (m-80) cc_final: 0.6270 (m-80) outliers start: 18 outliers final: 11 residues processed: 109 average time/residue: 0.2464 time to fit residues: 39.0987 Evaluate side-chains 93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 492 ILE 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 226 THR Chi-restraints excluded: chain C residue 319 ASN 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 125 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 181 GLN ** 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 = 0.4361 r_free = 0.4361 target = 0.146113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.104664 restraints weight = 39419.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.107583 restraints weight = 20752.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.107866 restraints weight = 11973.323| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12391 Z= 0.155 Angle : 0.697 16.535 16937 Z= 0.311 Chirality : 0.049 0.317 1959 Planarity : 0.004 0.045 2107 Dihedral : 17.786 97.499 2180 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.98 % Allowed : 12.71 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1447 helix: 2.88 (0.46), residues: 137 sheet: -0.64 (0.21), residues: 569 loop : -1.67 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 349 HIS 0.007 0.001 HIS C 59 PHE 0.013 0.001 PHE A 114 TYR 0.012 0.001 TYR A 105 ARG 0.002 0.000 ARG C 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 18) link_NAG-ASN : angle 3.82992 ( 54) link_BETA1-4 : bond 0.00392 ( 11) link_BETA1-4 : angle 2.11107 ( 33) hydrogen bonds : bond 0.05120 ( 384) hydrogen bonds : angle 5.76847 ( 1092) SS BOND : bond 0.00357 ( 14) SS BOND : angle 1.16253 ( 28) covalent geometry : bond 0.00350 (12348) covalent geometry : angle 0.65654 (16822) *********************** 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 100 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8952 (mm) REVERT: A 108 ASP cc_start: 0.8343 (t0) cc_final: 0.7983 (t0) REVERT: B 322 ASP cc_start: 0.7260 (t0) cc_final: 0.6901 (t0) REVERT: B 343 ARG cc_start: 0.5687 (ptt180) cc_final: 0.3945 (ttm170) REVERT: B 350 LYS cc_start: 0.8378 (mttt) cc_final: 0.7571 (ptpt) REVERT: B 365 GLU cc_start: 0.7351 (mp0) cc_final: 0.7003 (mp0) REVERT: B 450 LYS cc_start: 0.7645 (pttt) cc_final: 0.7182 (mptt) REVERT: B 451 TYR cc_start: 0.7641 (m-80) cc_final: 0.7437 (m-10) REVERT: B 468 TRP cc_start: 0.7001 (p-90) cc_final: 0.6123 (p-90) REVERT: B 469 GLN cc_start: 0.5704 (pt0) cc_final: 0.5392 (pt0) REVERT: C 98 TRP cc_start: 0.8621 (t60) cc_final: 0.7874 (t60) REVERT: C 348 MET cc_start: 0.7767 (tpt) cc_final: 0.7464 (ttt) REVERT: C 418 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8492 (tttm) REVERT: C 540 PHE cc_start: 0.6831 (m-80) cc_final: 0.5957 (m-80) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 0.2237 time to fit residues: 33.0055 Evaluate side-chains 85 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 336 VAL 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 19 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 7 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** 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 = 0.4339 r_free = 0.4339 target = 0.143503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.104385 restraints weight = 37959.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.103221 restraints weight = 24912.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.104859 restraints weight = 16481.846| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12391 Z= 0.150 Angle : 0.691 13.733 16937 Z= 0.308 Chirality : 0.049 0.493 1959 Planarity : 0.004 0.041 2107 Dihedral : 14.908 96.815 2180 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.74 % Allowed : 13.92 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1447 helix: 3.04 (0.46), residues: 137 sheet: -0.44 (0.21), residues: 568 loop : -1.46 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 349 HIS 0.006 0.001 HIS C 374 PHE 0.013 0.001 PHE B 330 TYR 0.016 0.001 TYR B 394 ARG 0.009 0.000 ARG B 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 18) link_NAG-ASN : angle 3.61411 ( 54) link_BETA1-4 : bond 0.00459 ( 11) link_BETA1-4 : angle 2.31020 ( 33) hydrogen bonds : bond 0.04685 ( 384) hydrogen bonds : angle 5.43009 ( 1092) SS BOND : bond 0.00290 ( 14) SS BOND : angle 1.61984 ( 28) covalent geometry : bond 0.00340 (12348) covalent geometry : angle 0.65083 (16822) *********************** 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: 23 poor density : 81 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8385 (t0) cc_final: 0.8163 (t0) REVERT: A 100 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9034 (mm) REVERT: A 108 ASP cc_start: 0.8240 (t0) cc_final: 0.7883 (t0) REVERT: B 322 ASP cc_start: 0.7346 (t0) cc_final: 0.6906 (t0) REVERT: B 343 ARG cc_start: 0.5669 (ptt180) cc_final: 0.3912 (ttm170) REVERT: B 350 LYS cc_start: 0.8376 (mttt) cc_final: 0.7516 (ptpt) REVERT: B 365 GLU cc_start: 0.7322 (mp0) cc_final: 0.7104 (mp0) REVERT: B 438 TRP cc_start: 0.7573 (m100) cc_final: 0.7305 (m100) REVERT: B 450 LYS cc_start: 0.7625 (pttt) cc_final: 0.7181 (mptt) REVERT: B 468 TRP cc_start: 0.7252 (p-90) cc_final: 0.6609 (p-90) REVERT: B 469 GLN cc_start: 0.5873 (pt0) cc_final: 0.5642 (pt0) REVERT: C 64 MET cc_start: 0.6544 (mmm) cc_final: 0.6295 (mmm) REVERT: C 348 MET cc_start: 0.7880 (tpt) cc_final: 0.7590 (ttt) REVERT: C 418 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8339 (tttm) REVERT: C 509 MET cc_start: 0.8458 (mmt) cc_final: 0.7924 (mpp) REVERT: C 540 PHE cc_start: 0.6655 (m-80) cc_final: 0.6102 (m-80) outliers start: 23 outliers final: 17 residues processed: 100 average time/residue: 0.1982 time to fit residues: 30.9242 Evaluate side-chains 93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 99 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 132 LEU 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 492 ILE 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 Chi-restraints excluded: chain C residue 337 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 3 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 27 optimal weight: 0.0010 chunk 47 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 85 optimal weight: 0.0770 chunk 30 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.144465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.106483 restraints weight = 38094.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.105735 restraints weight = 21967.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.107263 restraints weight = 16561.176| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12391 Z= 0.130 Angle : 0.673 13.890 16937 Z= 0.296 Chirality : 0.047 0.427 1959 Planarity : 0.004 0.042 2107 Dihedral : 12.519 95.903 2180 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.82 % Allowed : 15.36 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1447 helix: 3.10 (0.45), residues: 139 sheet: -0.23 (0.22), residues: 563 loop : -1.35 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 349 HIS 0.004 0.001 HIS C 374 PHE 0.013 0.001 PHE A 114 TYR 0.009 0.001 TYR C 303 ARG 0.003 0.000 ARG C 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 18) link_NAG-ASN : angle 3.75336 ( 54) link_BETA1-4 : bond 0.00610 ( 11) link_BETA1-4 : angle 2.56018 ( 33) hydrogen bonds : bond 0.04226 ( 384) hydrogen bonds : angle 5.13166 ( 1092) SS BOND : bond 0.00365 ( 14) SS BOND : angle 1.31387 ( 28) covalent geometry : bond 0.00294 (12348) covalent geometry : angle 0.62889 (16822) *********************** 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 103 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8316 (t0) cc_final: 0.7965 (t0) REVERT: A 100 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9032 (mm) REVERT: A 108 ASP cc_start: 0.8276 (t0) cc_final: 0.7911 (t0) REVERT: A 112 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7713 (tm130) REVERT: A 149 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7148 (mp0) REVERT: B 322 ASP cc_start: 0.7321 (t0) cc_final: 0.6893 (t0) REVERT: B 343 ARG cc_start: 0.5503 (ptt180) cc_final: 0.4042 (ttm170) REVERT: B 350 LYS cc_start: 0.8317 (mttt) cc_final: 0.7436 (ptpt) REVERT: B 365 GLU cc_start: 0.7323 (mp0) cc_final: 0.7065 (mp0) REVERT: B 438 TRP cc_start: 0.7607 (m100) cc_final: 0.7316 (m100) REVERT: B 450 LYS cc_start: 0.7570 (pttt) cc_final: 0.7184 (mptt) REVERT: B 468 TRP cc_start: 0.7354 (p-90) cc_final: 0.6707 (p-90) REVERT: B 469 GLN cc_start: 0.5855 (pt0) cc_final: 0.5630 (pt0) REVERT: B 593 TYR cc_start: 0.7645 (m-80) cc_final: 0.7440 (t80) REVERT: C 348 MET cc_start: 0.7639 (tpt) cc_final: 0.7424 (ttt) REVERT: C 418 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8433 (tttm) REVERT: C 509 MET cc_start: 0.8276 (mmt) cc_final: 0.7801 (mpp) REVERT: C 540 PHE cc_start: 0.6925 (m-80) cc_final: 0.6034 (m-80) outliers start: 24 outliers final: 17 residues processed: 100 average time/residue: 0.2000 time to fit residues: 31.2156 Evaluate side-chains 95 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 99 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 492 ILE Chi-restraints excluded: chain C residue 39 VAL 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 318 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 65 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 429 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 = 0.4355 r_free = 0.4355 target = 0.143708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.107741 restraints weight = 38481.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.106259 restraints weight = 20866.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.106123 restraints weight = 18819.684| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12391 Z= 0.136 Angle : 0.658 13.606 16937 Z= 0.294 Chirality : 0.047 0.469 1959 Planarity : 0.004 0.041 2107 Dihedral : 11.130 95.507 2180 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.04 % Allowed : 15.73 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1447 helix: 3.11 (0.46), residues: 139 sheet: -0.29 (0.21), residues: 600 loop : -1.20 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 349 HIS 0.003 0.001 HIS C 374 PHE 0.015 0.001 PHE B 330 TYR 0.012 0.001 TYR B 394 ARG 0.004 0.000 ARG C 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 18) link_NAG-ASN : angle 3.72898 ( 54) link_BETA1-4 : bond 0.00630 ( 11) link_BETA1-4 : angle 2.66538 ( 33) hydrogen bonds : bond 0.04310 ( 384) hydrogen bonds : angle 5.09536 ( 1092) SS BOND : bond 0.00299 ( 14) SS BOND : angle 1.31260 ( 28) covalent geometry : bond 0.00310 (12348) covalent geometry : angle 0.61141 (16822) *********************** 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 107 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 1.317 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: 0.8325 (t0) cc_final: 0.8040 (t0) REVERT: A 100 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9025 (mm) REVERT: A 108 ASP cc_start: 0.8317 (t0) cc_final: 0.7949 (t0) REVERT: A 112 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7738 (tm130) REVERT: B 99 VAL cc_start: 0.7547 (OUTLIER) cc_final: 0.7144 (t) REVERT: B 322 ASP cc_start: 0.7337 (t0) cc_final: 0.6879 (t0) REVERT: B 343 ARG cc_start: 0.5405 (ptt180) cc_final: 0.3984 (ttm170) REVERT: B 350 LYS cc_start: 0.8307 (mttt) cc_final: 0.7860 (mttt) REVERT: B 365 GLU cc_start: 0.7418 (mp0) cc_final: 0.7156 (mp0) REVERT: B 415 PRO cc_start: 0.7239 (Cg_endo) cc_final: 0.6242 (Cg_exo) REVERT: B 450 LYS cc_start: 0.7559 (pttt) cc_final: 0.7159 (mptt) REVERT: B 519 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7532 (ttp80) REVERT: B 593 TYR cc_start: 0.7731 (m-80) cc_final: 0.7474 (t80) REVERT: C 348 MET cc_start: 0.7673 (tpt) cc_final: 0.7472 (ttt) REVERT: C 418 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8405 (tttm) REVERT: C 509 MET cc_start: 0.8353 (mmt) cc_final: 0.7866 (mpp) REVERT: C 540 PHE cc_start: 0.6829 (m-80) cc_final: 0.6155 (m-80) outliers start: 27 outliers final: 19 residues processed: 105 average time/residue: 0.2123 time to fit residues: 34.4107 Evaluate side-chains 96 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 112 GLN 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 99 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 132 LEU 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 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 318 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 93 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 ASN ** 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 = 0.4384 r_free = 0.4384 target = 0.145274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.109504 restraints weight = 38335.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.109032 restraints weight = 24569.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.109160 restraints weight = 16682.724| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12391 Z= 0.104 Angle : 0.620 12.812 16937 Z= 0.278 Chirality : 0.046 0.435 1959 Planarity : 0.003 0.041 2107 Dihedral : 10.331 94.991 2180 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.82 % Allowed : 16.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1447 helix: 3.28 (0.46), residues: 139 sheet: -0.18 (0.21), residues: 598 loop : -1.11 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 468 HIS 0.003 0.001 HIS C 408 PHE 0.013 0.001 PHE B 330 TYR 0.020 0.001 TYR A 105 ARG 0.003 0.000 ARG B 519 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 18) link_NAG-ASN : angle 3.50344 ( 54) link_BETA1-4 : bond 0.00693 ( 11) link_BETA1-4 : angle 2.62237 ( 33) hydrogen bonds : bond 0.03731 ( 384) hydrogen bonds : angle 4.84923 ( 1092) SS BOND : bond 0.00270 ( 14) SS BOND : angle 1.06991 ( 28) covalent geometry : bond 0.00232 (12348) covalent geometry : angle 0.57663 (16822) *********************** 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 101 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8300 (t0) cc_final: 0.7984 (t0) REVERT: A 100 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8782 (mm) REVERT: A 108 ASP cc_start: 0.8410 (t0) cc_final: 0.8104 (t0) REVERT: A 112 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7769 (tm130) REVERT: B 322 ASP cc_start: 0.7242 (t0) cc_final: 0.6816 (t0) REVERT: B 343 ARG cc_start: 0.5448 (ptt180) cc_final: 0.3983 (ttm170) REVERT: B 350 LYS cc_start: 0.8151 (mttt) cc_final: 0.7918 (ptpt) REVERT: B 365 GLU cc_start: 0.7329 (mp0) cc_final: 0.7071 (mp0) REVERT: B 415 PRO cc_start: 0.7096 (Cg_endo) cc_final: 0.6211 (Cg_exo) REVERT: B 450 LYS cc_start: 0.7585 (pttt) cc_final: 0.7210 (mptt) REVERT: B 519 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7500 (ttp80) REVERT: B 593 TYR cc_start: 0.7770 (m-80) cc_final: 0.7550 (t80) REVERT: C 98 TRP cc_start: 0.8483 (t60) cc_final: 0.7847 (t60) REVERT: C 418 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8687 (ttpp) REVERT: C 540 PHE cc_start: 0.6738 (m-80) cc_final: 0.6140 (m-80) outliers start: 24 outliers final: 15 residues processed: 100 average time/residue: 0.1981 time to fit residues: 30.9167 Evaluate side-chains 91 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 112 GLN 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 82 ILE 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 534 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 86 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 3.9990 chunk 20 optimal weight: 0.0020 chunk 136 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.143921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.106314 restraints weight = 38457.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.106379 restraints weight = 23892.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.106783 restraints weight = 15744.205| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12391 Z= 0.137 Angle : 0.645 15.863 16937 Z= 0.293 Chirality : 0.045 0.407 1959 Planarity : 0.004 0.044 2107 Dihedral : 9.898 96.259 2180 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.59 % Allowed : 17.25 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1447 helix: 3.21 (0.46), residues: 139 sheet: -0.19 (0.21), residues: 591 loop : -1.10 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 484 HIS 0.003 0.001 HIS C 408 PHE 0.015 0.001 PHE B 330 TYR 0.011 0.001 TYR C 303 ARG 0.004 0.000 ARG C 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 18) link_NAG-ASN : angle 4.11118 ( 54) link_BETA1-4 : bond 0.00671 ( 11) link_BETA1-4 : angle 2.62783 ( 33) hydrogen bonds : bond 0.04288 ( 384) hydrogen bonds : angle 4.98023 ( 1092) SS BOND : bond 0.00354 ( 14) SS BOND : angle 1.18536 ( 28) covalent geometry : bond 0.00317 (12348) covalent geometry : angle 0.59096 (16822) *********************** 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 95 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 1.189 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: 0.8328 (t0) cc_final: 0.8077 (t0) REVERT: A 100 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9041 (mm) REVERT: A 108 ASP cc_start: 0.8110 (t0) cc_final: 0.7763 (t0) REVERT: A 112 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7773 (tm130) REVERT: B 322 ASP cc_start: 0.7416 (t0) cc_final: 0.6939 (t0) REVERT: B 343 ARG cc_start: 0.5429 (ptt180) cc_final: 0.4033 (ttm170) REVERT: B 350 LYS cc_start: 0.8342 (mttt) cc_final: 0.8063 (pttp) REVERT: B 365 GLU cc_start: 0.7406 (mp0) cc_final: 0.7095 (mp0) REVERT: B 415 PRO cc_start: 0.7205 (Cg_endo) cc_final: 0.6236 (Cg_exo) REVERT: B 450 LYS cc_start: 0.7665 (pttt) cc_final: 0.7237 (mptp) REVERT: B 519 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7433 (ttp80) REVERT: B 593 TYR cc_start: 0.7706 (m-80) cc_final: 0.7505 (t80) REVERT: C 418 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8654 (ttpp) REVERT: C 509 MET cc_start: 0.8306 (mmt) cc_final: 0.7988 (mpp) REVERT: C 540 PHE cc_start: 0.6738 (m-80) cc_final: 0.6098 (m-80) outliers start: 21 outliers final: 17 residues processed: 95 average time/residue: 0.2108 time to fit residues: 30.9862 Evaluate side-chains 91 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 82 ILE 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 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 ASN 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 140 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 105 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 118 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 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 = 0.4373 r_free = 0.4373 target = 0.144642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.105202 restraints weight = 38161.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.108406 restraints weight = 20164.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.107996 restraints weight = 11528.206| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12391 Z= 0.109 Angle : 0.615 14.540 16937 Z= 0.279 Chirality : 0.045 0.412 1959 Planarity : 0.003 0.044 2107 Dihedral : 9.478 94.687 2180 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.66 % Allowed : 17.70 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1447 helix: 3.29 (0.46), residues: 139 sheet: -0.18 (0.21), residues: 596 loop : -1.01 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 468 HIS 0.003 0.001 HIS C 408 PHE 0.011 0.001 PHE B 330 TYR 0.018 0.001 TYR A 105 ARG 0.003 0.000 ARG C 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 18) link_NAG-ASN : angle 3.84451 ( 54) link_BETA1-4 : bond 0.00687 ( 11) link_BETA1-4 : angle 2.55660 ( 33) hydrogen bonds : bond 0.03752 ( 384) hydrogen bonds : angle 4.77911 ( 1092) SS BOND : bond 0.00333 ( 14) SS BOND : angle 1.04113 ( 28) covalent geometry : bond 0.00247 (12348) covalent geometry : angle 0.56489 (16822) *********************** 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 94 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 1.193 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: 0.8308 (t0) cc_final: 0.8060 (t0) REVERT: A 100 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8985 (mm) REVERT: A 108 ASP cc_start: 0.8171 (t0) cc_final: 0.7867 (t0) REVERT: A 112 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7755 (tm130) REVERT: B 322 ASP cc_start: 0.7448 (t0) cc_final: 0.6962 (t0) REVERT: B 343 ARG cc_start: 0.5515 (ptt180) cc_final: 0.4111 (ttm170) REVERT: B 350 LYS cc_start: 0.8156 (mttt) cc_final: 0.7859 (pmtt) REVERT: B 365 GLU cc_start: 0.7282 (mp0) cc_final: 0.6954 (mp0) REVERT: B 415 PRO cc_start: 0.7114 (Cg_endo) cc_final: 0.6092 (Cg_exo) REVERT: B 450 LYS cc_start: 0.7628 (pttt) cc_final: 0.7183 (mptp) REVERT: B 471 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6860 (mm-30) REVERT: B 519 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7415 (ttp80) REVERT: B 593 TYR cc_start: 0.7713 (m-80) cc_final: 0.7512 (t80) REVERT: C 348 MET cc_start: 0.7953 (tpp) cc_final: 0.7708 (ttm) REVERT: C 418 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8734 (ttpp) REVERT: C 509 MET cc_start: 0.8265 (mmt) cc_final: 0.8007 (mpp) REVERT: C 540 PHE cc_start: 0.6696 (m-80) cc_final: 0.6106 (m-80) outliers start: 22 outliers final: 18 residues processed: 92 average time/residue: 0.2083 time to fit residues: 29.8777 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 : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 82 ILE 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 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 ASN 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 43 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 141 optimal weight: 0.0370 chunk 87 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 429 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 = 0.4363 r_free = 0.4363 target = 0.146068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.107257 restraints weight = 39045.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.108560 restraints weight = 21731.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.108369 restraints weight = 13383.449| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4008 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= 0.113 Angle : 0.610 13.865 16937 Z= 0.279 Chirality : 0.045 0.415 1959 Planarity : 0.003 0.043 2107 Dihedral : 9.147 95.486 2180 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.51 % Allowed : 17.93 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1447 helix: 2.90 (0.46), residues: 145 sheet: -0.15 (0.21), residues: 597 loop : -1.01 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 468 HIS 0.003 0.001 HIS C 408 PHE 0.011 0.001 PHE B 330 TYR 0.010 0.001 TYR B 394 ARG 0.002 0.000 ARG C 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 18) link_NAG-ASN : angle 3.65340 ( 54) link_BETA1-4 : bond 0.00662 ( 11) link_BETA1-4 : angle 2.47189 ( 33) hydrogen bonds : bond 0.03822 ( 384) hydrogen bonds : angle 4.73805 ( 1092) SS BOND : bond 0.00340 ( 14) SS BOND : angle 1.00076 ( 28) covalent geometry : bond 0.00258 (12348) covalent geometry : angle 0.56450 (16822) ********************** 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 : 1.297 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: 0.8301 (t0) cc_final: 0.8082 (t0) REVERT: A 100 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8872 (mm) REVERT: A 108 ASP cc_start: 0.8288 (t0) cc_final: 0.7952 (t0) REVERT: A 112 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7753 (tm130) REVERT: B 322 ASP cc_start: 0.7410 (t0) cc_final: 0.6930 (t0) REVERT: B 343 ARG cc_start: 0.5493 (ptt180) cc_final: 0.4005 (ttm170) REVERT: B 365 GLU cc_start: 0.7355 (mp0) cc_final: 0.7050 (mp0) REVERT: B 450 LYS cc_start: 0.7601 (pttt) cc_final: 0.7091 (mptt) REVERT: B 453 LEU cc_start: 0.7896 (mt) cc_final: 0.7612 (mm) REVERT: B 519 ARG cc_start: 0.7820 (ttp80) cc_final: 0.7527 (ttp80) REVERT: B 593 TYR cc_start: 0.7699 (m-80) cc_final: 0.7488 (t80) REVERT: C 348 MET cc_start: 0.8023 (tpp) cc_final: 0.7786 (ttm) REVERT: C 418 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8736 (ttpp) REVERT: C 509 MET cc_start: 0.8253 (mmt) cc_final: 0.8049 (mpp) REVERT: C 540 PHE cc_start: 0.6659 (m-80) cc_final: 0.6101 (m-80) outliers start: 20 outliers final: 16 residues processed: 87 average time/residue: 0.2210 time to fit residues: 29.7723 Evaluate side-chains 87 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 82 ILE 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 369 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 319 ASN 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 3 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 124 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 118 optimal weight: 20.0000 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 429 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 = 0.4383 r_free = 0.4383 target = 0.145283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.104892 restraints weight = 38147.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.107509 restraints weight = 17481.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.109048 restraints weight = 10758.270| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 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 = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12391 Z= 0.097 Angle : 0.585 13.063 16937 Z= 0.269 Chirality : 0.045 0.415 1959 Planarity : 0.003 0.043 2107 Dihedral : 8.841 95.422 2180 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.59 % Allowed : 17.85 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.22), residues: 1447 helix: 3.01 (0.47), residues: 145 sheet: -0.06 (0.21), residues: 595 loop : -0.95 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 468 HIS 0.002 0.000 HIS C 408 PHE 0.010 0.001 PHE B 330 TYR 0.010 0.001 TYR C 616 ARG 0.002 0.000 ARG C 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 18) link_NAG-ASN : angle 3.49833 ( 54) link_BETA1-4 : bond 0.00672 ( 11) link_BETA1-4 : angle 2.37783 ( 33) hydrogen bonds : bond 0.03396 ( 384) hydrogen bonds : angle 4.62140 ( 1092) SS BOND : bond 0.00289 ( 14) SS BOND : angle 0.85687 ( 28) covalent geometry : bond 0.00217 (12348) covalent geometry : angle 0.54122 (16822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5341.01 seconds wall clock time: 93 minutes 49.13 seconds (5629.13 seconds total)