Starting phenix.real_space_refine on Sat Jan 18 10:00:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2b_42904/01_2025/8v2b_42904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2b_42904/01_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_42904/01_2025/8v2b_42904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2b_42904/01_2025/8v2b_42904.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2b_42904/01_2025/8v2b_42904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2b_42904/01_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-5571/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: 7.53, per 1000 atoms: 0.62 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: 2.83 Conformation dependent library (CDL) restraints added in 1.4 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: 1.77 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: 3.73 Time building geometry restraints manager: 3.33 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: 2.670 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: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.840 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- 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 12348 Z= 0.180 Angle : 0.483 6.192 16822 Z= 0.243 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 *********************** 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 : 1.252 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: 0.2994 time to fit residues: 64.2120 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 : 1.237 ------------------------------------------------------------------------------- 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 12348 Z= 0.414 Angle : 0.723 8.861 16822 Z= 0.349 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 *********************** 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 : 1.243 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: 0.2553 time to fit residues: 41.1232 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 : 1.317 ------------------------------------------------------------------------------- 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: 1.9990 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 12348 Z= 0.228 Angle : 0.657 9.115 16822 Z= 0.302 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 *********************** 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 : 1.308 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: 0.2390 time to fit residues: 35.0659 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 : 1.275 ------------------------------------------------------------------------------- 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: 6.9990 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: 0.0470 chunk 76 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 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 = 0.4369 r_free = 0.4369 target = 0.144647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.106602 restraints weight = 37916.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.105966 restraints weight = 22076.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.107333 restraints weight = 16447.186| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 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 = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12348 Z= 0.206 Angle : 0.641 9.206 16822 Z= 0.292 Chirality : 0.048 0.479 1959 Planarity : 0.004 0.041 2107 Dihedral : 14.953 96.809 2180 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.74 % Allowed : 13.69 % Favored : 84.57 % 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: -0.94 (0.21), residues: 1447 helix: 3.08 (0.46), residues: 137 sheet: -0.50 (0.21), residues: 588 loop : -1.47 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 349 HIS 0.005 0.001 HIS C 376 PHE 0.014 0.001 PHE B 330 TYR 0.016 0.001 TYR B 394 ARG 0.002 0.000 ARG C 265 *********************** 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 : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8252 (t0) cc_final: 0.8019 (t0) REVERT: A 100 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9016 (mm) REVERT: A 108 ASP cc_start: 0.8310 (t0) cc_final: 0.7970 (t0) REVERT: B 322 ASP cc_start: 0.7300 (t0) cc_final: 0.6892 (t0) REVERT: B 343 ARG cc_start: 0.5655 (ptt180) cc_final: 0.3922 (ttm170) REVERT: B 350 LYS cc_start: 0.8356 (mttt) cc_final: 0.7536 (ptpt) REVERT: B 365 GLU cc_start: 0.7328 (mp0) cc_final: 0.7127 (mp0) REVERT: B 438 TRP cc_start: 0.7576 (m100) cc_final: 0.7281 (m100) REVERT: B 450 LYS cc_start: 0.7594 (pttt) cc_final: 0.7186 (mptt) REVERT: B 468 TRP cc_start: 0.7144 (p-90) cc_final: 0.6538 (p-90) REVERT: B 469 GLN cc_start: 0.5777 (pt0) cc_final: 0.5565 (pt0) REVERT: C 64 MET cc_start: 0.6424 (mmm) cc_final: 0.6179 (mmm) REVERT: C 98 TRP cc_start: 0.8566 (t60) cc_final: 0.7806 (t60) REVERT: C 348 MET cc_start: 0.7714 (tpt) cc_final: 0.7448 (ttt) REVERT: C 418 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8353 (tttm) REVERT: C 509 MET cc_start: 0.8478 (mmt) cc_final: 0.7959 (mpp) REVERT: C 540 PHE cc_start: 0.6697 (m-80) cc_final: 0.6129 (m-80) outliers start: 23 outliers final: 17 residues processed: 100 average time/residue: 0.2121 time to fit residues: 33.0183 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 : 1.428 ------------------------------------------------------------------------------- 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: 0.8980 chunk 112 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 0.0870 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.146157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.109933 restraints weight = 38158.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.110310 restraints weight = 25005.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.110356 restraints weight = 16386.090| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12348 Z= 0.150 Angle : 0.611 10.319 16822 Z= 0.274 Chirality : 0.046 0.338 1959 Planarity : 0.003 0.040 2107 Dihedral : 13.158 96.156 2180 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.29 % Allowed : 14.75 % Favored : 83.96 % 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: -0.66 (0.22), residues: 1447 helix: 3.25 (0.45), residues: 138 sheet: -0.31 (0.21), residues: 585 loop : -1.29 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 349 HIS 0.003 0.001 HIS C 374 PHE 0.011 0.001 PHE B 330 TYR 0.009 0.001 TYR C 616 ARG 0.004 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8245 (t0) cc_final: 0.7976 (t0) REVERT: A 100 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8849 (mm) REVERT: A 108 ASP cc_start: 0.8580 (t0) cc_final: 0.8264 (t0) REVERT: A 112 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7687 (tm130) REVERT: A 149 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7135 (mp0) REVERT: B 322 ASP cc_start: 0.7184 (t0) cc_final: 0.6776 (t0) REVERT: B 343 ARG cc_start: 0.5525 (ptt180) cc_final: 0.4011 (ttm170) REVERT: B 350 LYS cc_start: 0.8252 (mttt) cc_final: 0.7486 (ptpt) REVERT: B 450 LYS cc_start: 0.7535 (pttt) cc_final: 0.7202 (mptt) REVERT: B 468 TRP cc_start: 0.7124 (p-90) cc_final: 0.6718 (p-90) REVERT: B 593 TYR cc_start: 0.7661 (m-80) cc_final: 0.7432 (t80) REVERT: C 98 TRP cc_start: 0.8534 (t60) cc_final: 0.7719 (t60) REVERT: C 348 MET cc_start: 0.7558 (tpt) cc_final: 0.7344 (ttt) REVERT: C 418 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8540 (tttm) REVERT: C 509 MET cc_start: 0.8396 (mmt) cc_final: 0.7950 (mpp) REVERT: C 540 PHE cc_start: 0.6914 (m-80) cc_final: 0.6038 (m-80) outliers start: 17 outliers final: 10 residues processed: 97 average time/residue: 0.2262 time to fit residues: 33.5332 Evaluate side-chains 87 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 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 336 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 0.0670 chunk 47 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 58 optimal weight: 0.0170 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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** ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.147906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.107920 restraints weight = 39681.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.111694 restraints weight = 19798.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.111331 restraints weight = 11935.626| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12348 Z= 0.136 Angle : 0.583 8.374 16822 Z= 0.266 Chirality : 0.046 0.458 1959 Planarity : 0.003 0.040 2107 Dihedral : 11.531 95.733 2180 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.59 % Allowed : 15.13 % Favored : 83.28 % 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: -0.50 (0.22), residues: 1447 helix: 3.26 (0.46), residues: 139 sheet: -0.22 (0.21), residues: 592 loop : -1.14 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 96 HIS 0.002 0.000 HIS C 408 PHE 0.012 0.001 PHE B 330 TYR 0.012 0.001 TYR B 394 ARG 0.002 0.000 ARG B 519 *********************** 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 98 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8228 (t0) cc_final: 0.8020 (t0) REVERT: A 100 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9063 (mm) REVERT: A 108 ASP cc_start: 0.8174 (t0) cc_final: 0.7889 (t0) REVERT: A 112 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: B 322 ASP cc_start: 0.7276 (t0) cc_final: 0.6830 (t0) REVERT: B 343 ARG cc_start: 0.5453 (ptt180) cc_final: 0.4025 (ttm170) REVERT: B 350 LYS cc_start: 0.8311 (mttt) cc_final: 0.7731 (ptpt) REVERT: B 365 GLU cc_start: 0.7184 (mp0) cc_final: 0.6796 (mp0) REVERT: B 450 LYS cc_start: 0.7692 (pttt) cc_final: 0.7086 (mptt) REVERT: C 98 TRP cc_start: 0.8530 (t60) cc_final: 0.7861 (t60) REVERT: C 418 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8548 (tttm) REVERT: C 509 MET cc_start: 0.8248 (mmt) cc_final: 0.7797 (mpp) REVERT: C 540 PHE cc_start: 0.6706 (m-80) cc_final: 0.6013 (m-80) outliers start: 21 outliers final: 15 residues processed: 97 average time/residue: 0.2369 time to fit residues: 34.9022 Evaluate side-chains 90 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 534 VAL 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 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: 1.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.145147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.107373 restraints weight = 39165.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.106258 restraints weight = 24007.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.107084 restraints weight = 17715.595| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12348 Z= 0.237 Angle : 0.619 10.076 16822 Z= 0.289 Chirality : 0.047 0.439 1959 Planarity : 0.004 0.041 2107 Dihedral : 10.710 95.277 2180 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % 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: -0.51 (0.22), residues: 1447 helix: 3.13 (0.46), residues: 139 sheet: -0.19 (0.21), residues: 590 loop : -1.15 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP C 96 HIS 0.003 0.001 HIS C 355 PHE 0.017 0.002 PHE B 330 TYR 0.013 0.001 TYR A 183 ARG 0.005 0.000 ARG C 265 *********************** 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 100 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8370 (t0) cc_final: 0.8095 (t0) REVERT: A 100 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.8946 (mm) REVERT: A 108 ASP cc_start: 0.8250 (t0) cc_final: 0.7867 (t0) REVERT: A 112 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7703 (tm130) REVERT: B 322 ASP cc_start: 0.7342 (t0) cc_final: 0.6891 (t0) REVERT: B 343 ARG cc_start: 0.5458 (ptt180) cc_final: 0.3970 (ttm170) REVERT: B 365 GLU cc_start: 0.7464 (mp0) cc_final: 0.7049 (mp0) REVERT: B 415 PRO cc_start: 0.7267 (Cg_endo) cc_final: 0.6170 (Cg_exo) REVERT: B 450 LYS cc_start: 0.7574 (pttt) cc_final: 0.7077 (mptt) REVERT: B 519 ARG cc_start: 0.7774 (ttp80) cc_final: 0.7428 (ttp80) REVERT: B 593 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6844 (t80) REVERT: C 348 MET cc_start: 0.7654 (tpt) cc_final: 0.7233 (ttt) REVERT: C 418 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8383 (tttm) REVERT: C 540 PHE cc_start: 0.6840 (m-80) cc_final: 0.6100 (m-80) outliers start: 24 outliers final: 15 residues processed: 98 average time/residue: 0.2205 time to fit residues: 33.2791 Evaluate side-chains 90 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 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 534 VAL Chi-restraints excluded: chain B residue 593 TYR 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 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: 0.8980 chunk 136 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** C 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.143602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.103732 restraints weight = 38384.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.107608 restraints weight = 18632.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.106316 restraints weight = 12436.083| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12348 Z= 0.228 Angle : 0.606 10.024 16822 Z= 0.286 Chirality : 0.046 0.440 1959 Planarity : 0.004 0.042 2107 Dihedral : 10.085 95.065 2180 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.82 % Allowed : 15.73 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.09 (0.45), residues: 139 sheet: -0.16 (0.21), residues: 592 loop : -1.10 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 96 HIS 0.003 0.001 HIS C 374 PHE 0.017 0.001 PHE B 330 TYR 0.024 0.001 TYR A 105 ARG 0.004 0.000 ARG C 265 *********************** 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 97 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8279 (t0) cc_final: 0.8029 (t0) REVERT: A 100 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9027 (mm) REVERT: A 108 ASP cc_start: 0.8261 (t0) cc_final: 0.7879 (t0) REVERT: A 112 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7751 (tm130) REVERT: B 322 ASP cc_start: 0.7431 (t0) cc_final: 0.6948 (t0) REVERT: B 343 ARG cc_start: 0.5291 (ptt180) cc_final: 0.3865 (ttm170) REVERT: B 365 GLU cc_start: 0.7393 (mp0) cc_final: 0.6934 (mp0) REVERT: B 415 PRO cc_start: 0.7186 (Cg_endo) cc_final: 0.6159 (Cg_exo) REVERT: B 450 LYS cc_start: 0.7648 (pttt) cc_final: 0.7165 (mptp) REVERT: B 519 ARG cc_start: 0.7523 (ttp80) cc_final: 0.7244 (ttp80) REVERT: B 593 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6848 (t80) REVERT: C 348 MET cc_start: 0.7429 (tpt) cc_final: 0.7157 (ttt) REVERT: C 418 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8675 (ttpp) REVERT: C 540 PHE cc_start: 0.6400 (m-80) cc_final: 0.6063 (m-80) outliers start: 24 outliers final: 20 residues processed: 94 average time/residue: 0.2185 time to fit residues: 32.0460 Evaluate side-chains 91 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 120 MET 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 B residue 593 TYR 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 226 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 446 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 105 optimal weight: 0.0070 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 chunk 118 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 overall best weight: 1.6400 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.143148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.105788 restraints weight = 38062.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.105148 restraints weight = 27467.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.105517 restraints weight = 18619.832| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12348 Z= 0.243 Angle : 0.611 9.752 16822 Z= 0.293 Chirality : 0.046 0.414 1959 Planarity : 0.004 0.043 2107 Dihedral : 9.845 94.812 2180 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.82 % Allowed : 16.57 % Favored : 81.62 % 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: -0.53 (0.22), residues: 1447 helix: 3.03 (0.45), residues: 139 sheet: -0.18 (0.21), residues: 596 loop : -1.17 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 468 HIS 0.003 0.001 HIS C 355 PHE 0.016 0.001 PHE B 330 TYR 0.013 0.001 TYR A 183 ARG 0.004 0.000 ARG C 265 *********************** 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: 24 poor density : 70 time to evaluate : 1.407 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: 0.9459 (OUTLIER) cc_final: 0.9154 (mm) REVERT: A 108 ASP cc_start: 0.8163 (t0) cc_final: 0.7806 (t0) REVERT: A 112 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7693 (tm130) REVERT: B 322 ASP cc_start: 0.7404 (t0) cc_final: 0.6954 (t0) REVERT: B 343 ARG cc_start: 0.5245 (ptt180) cc_final: 0.3828 (ttm170) REVERT: B 415 PRO cc_start: 0.7245 (Cg_endo) cc_final: 0.6351 (Cg_exo) REVERT: B 450 LYS cc_start: 0.7543 (pttt) cc_final: 0.7120 (mptt) REVERT: B 519 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7640 (ttp80) REVERT: B 593 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.6692 (t80) REVERT: C 337 THR cc_start: 0.7813 (t) cc_final: 0.7548 (t) REVERT: C 418 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8725 (ttpp) REVERT: C 540 PHE cc_start: 0.6675 (m-80) cc_final: 0.6120 (m-80) outliers start: 24 outliers final: 18 residues processed: 91 average time/residue: 0.2199 time to fit residues: 31.0746 Evaluate side-chains 90 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN 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 B residue 593 TYR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 0.0670 chunk 35 optimal weight: 4.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 605 HIS ** 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 = 0.4307 r_free = 0.4307 target = 0.141723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.103157 restraints weight = 38644.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.101894 restraints weight = 22712.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.102492 restraints weight = 16815.318| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12348 Z= 0.331 Angle : 0.676 12.917 16822 Z= 0.327 Chirality : 0.047 0.421 1959 Planarity : 0.004 0.045 2107 Dihedral : 9.868 96.507 2180 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.44 % Allowed : 17.32 % Favored : 81.24 % 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: -0.82 (0.22), residues: 1447 helix: 2.40 (0.45), residues: 145 sheet: -0.35 (0.21), residues: 595 loop : -1.32 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 96 HIS 0.004 0.001 HIS C 193 PHE 0.022 0.002 PHE B 330 TYR 0.017 0.002 TYR B 307 ARG 0.006 0.000 ARG C 265 ********************** 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 87 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 1.424 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: 0.8552 (t0) cc_final: 0.8326 (t0) REVERT: A 100 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8994 (mm) REVERT: B 322 ASP cc_start: 0.7548 (t0) cc_final: 0.7124 (t0) REVERT: B 343 ARG cc_start: 0.5318 (ptt180) cc_final: 0.3765 (ttm170) REVERT: B 450 LYS cc_start: 0.7642 (pttt) cc_final: 0.7147 (mptt) REVERT: B 519 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7424 (ttp80) REVERT: B 593 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.6922 (t80) REVERT: C 348 MET cc_start: 0.8113 (ttt) cc_final: 0.7847 (tpp) REVERT: C 418 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8704 (ttpp) REVERT: C 540 PHE cc_start: 0.6583 (m-80) cc_final: 0.6085 (m-80) outliers start: 19 outliers final: 15 residues processed: 85 average time/residue: 0.2398 time to fit residues: 31.1826 Evaluate side-chains 82 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 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 B residue 593 TYR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 226 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: 0.9980 chunk 42 optimal weight: 0.0980 chunk 115 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.145445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.106166 restraints weight = 38961.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.107790 restraints weight = 20941.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.108363 restraints weight = 13793.995| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12348 Z= 0.153 Angle : 0.577 8.775 16822 Z= 0.277 Chirality : 0.045 0.423 1959 Planarity : 0.003 0.043 2107 Dihedral : 9.262 94.427 2180 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.44 % Allowed : 17.47 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.53 (0.22), residues: 1447 helix: 2.80 (0.46), residues: 145 sheet: -0.17 (0.21), residues: 576 loop : -1.15 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 96 HIS 0.003 0.001 HIS C 408 PHE 0.010 0.001 PHE B 330 TYR 0.010 0.001 TYR C 616 ARG 0.003 0.000 ARG C 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5244.97 seconds wall clock time: 94 minutes 37.96 seconds (5677.96 seconds total)