Starting phenix.real_space_refine on Fri May 16 11:42:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk1_38413/05_2025/8xk1_38413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk1_38413/05_2025/8xk1_38413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xk1_38413/05_2025/8xk1_38413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk1_38413/05_2025/8xk1_38413.map" model { file = "/net/cci-nas-00/data/ceres_data/8xk1_38413/05_2025/8xk1_38413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk1_38413/05_2025/8xk1_38413.cif" } resolution = 3.31 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= 0.006 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 124 5.16 5 C 9080 2.51 5 N 2451 2.21 5 O 2657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14312 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6413 Classifications: {'peptide': 794} Link IDs: {'PTRANS': 43, 'TRANS': 750} Chain breaks: 10 Chain: "B" Number of atoms: 6507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6507 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 43, 'TRANS': 761} Chain breaks: 6 Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 359 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain breaks: 1 Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 337 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain breaks: 1 Chain: "E" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 359 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain breaks: 1 Chain: "F" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 337 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain breaks: 1 Time building chain proxies: 10.25, per 1000 atoms: 0.72 Number of scatterers: 14312 At special positions: 0 Unit cell: (142.56, 100.98, 159.72, 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 124 16.00 O 2657 8.00 N 2451 7.00 C 9080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 215 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 328 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 887 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 822 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 215 " distance=2.03 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 228 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 243 " distance=2.03 Simple disulfide: pdb=" SG CYS B 239 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 674 " - pdb=" SG CYS B 887 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 822 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 18 " - pdb=" SG CYS E 61 " 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 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 32 sheets defined 19.7% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 43 through 50 removed outlier: 4.124A pdb=" N ARG A 46 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.749A pdb=" N PHE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.947A pdb=" N ARG A 162 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.664A pdb=" N GLU A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.740A pdb=" N CYS A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 462 through 470 removed outlier: 3.763A pdb=" N ILE A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 671 Processing helix chain 'A' and resid 716 through 741 removed outlier: 3.532A pdb=" N GLU A 722 " --> pdb=" O GLN A 718 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 733 " --> pdb=" O ARG A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 840 Processing helix chain 'A' and resid 890 through 896 Processing helix chain 'B' and resid 43 through 50 removed outlier: 3.714A pdb=" N ARG B 46 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 3.737A pdb=" N GLY B 227 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.599A pdb=" N CYS B 252 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.846A pdb=" N CYS B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.627A pdb=" N GLY B 344 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 356 Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 462 through 473 Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 665 through 671 removed outlier: 3.538A pdb=" N PHE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 724 removed outlier: 3.678A pdb=" N LEU B 723 " --> pdb=" O ILE B 719 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 741 Processing helix chain 'B' and resid 835 through 840 removed outlier: 3.947A pdb=" N ASP B 839 " --> pdb=" O GLU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 896 Processing helix chain 'C' and resid 8 through 19 removed outlier: 4.339A pdb=" N ASP C 12 " --> pdb=" O ALA C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 42 through 48 removed outlier: 3.970A pdb=" N GLU C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.557A pdb=" N MET C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR C 60 " --> pdb=" O ARG C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 removed outlier: 4.753A pdb=" N PHE D 16 " --> pdb=" O ASP D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'E' and resid 7 through 19 removed outlier: 3.685A pdb=" N VAL E 11 " --> pdb=" O GLY E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 53 through 60 removed outlier: 3.700A pdb=" N MET E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR E 60 " --> pdb=" O ARG E 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 18 removed outlier: 4.609A pdb=" N PHE F 16 " --> pdb=" O ASP F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 54 through 62 removed outlier: 4.165A pdb=" N MET F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR F 60 " --> pdb=" O ARG F 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.333A pdb=" N GLU A 33 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 55 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 37 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS A 59 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP A 39 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN A 61 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.333A pdb=" N GLU A 33 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 55 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 37 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS A 59 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP A 39 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN A 61 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR A 87 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY A 58 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N LEU A 89 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 60 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N PHE A 91 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE A 62 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL A 93 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 64 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 88 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE A 123 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 90 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 120 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N GLU A 147 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 122 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL A 144 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL A 173 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 146 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 243 removed outlier: 3.959A pdb=" N ALA A 254 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASN A 242 " --> pdb=" O CYS A 252 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS A 252 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA6, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA7, first strand: chain 'A' and resid 305 through 307 Processing sheet with id=AA8, first strand: chain 'A' and resid 338 through 339 removed outlier: 8.225A pdb=" N ILE A 363 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ILE A 391 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU A 418 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY A 393 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 348 removed outlier: 6.501A pdb=" N LEU A 367 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ARG A 398 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE A 369 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 395 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N LEU A 430 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 397 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 515 Processing sheet with id=AB2, first strand: chain 'A' and resid 557 through 561 removed outlier: 3.585A pdb=" N GLY A 529 " --> pdb=" O LEU A 596 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 626 through 634 removed outlier: 5.570A pdb=" N ASP A 627 " --> pdb=" O LYS A 643 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 633 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 786 through 790 removed outlier: 3.939A pdb=" N GLN A 815 " --> pdb=" O ARG A 821 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 821 " --> pdb=" O GLN A 815 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 786 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AB7, first strand: chain 'A' and resid 883 through 889 Processing sheet with id=AB8, first strand: chain 'B' and resid 33 through 40 removed outlier: 4.531A pdb=" N VAL B 34 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU B 57 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS B 59 " --> pdb=" O PRO B 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 33 through 40 removed outlier: 4.531A pdb=" N VAL B 34 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU B 57 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS B 59 " --> pdb=" O PRO B 36 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N LEU B 89 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 60 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N PHE B 91 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE B 62 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL B 93 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU B 64 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 88 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE B 123 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 90 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 120 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLU B 147 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 122 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 144 " --> pdb=" O TYR B 171 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 198 through 201 Processing sheet with id=AC2, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AC3, first strand: chain 'B' and resid 273 through 275 Processing sheet with id=AC4, first strand: chain 'B' and resid 305 through 307 Processing sheet with id=AC5, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AC6, first strand: chain 'B' and resid 338 through 339 removed outlier: 3.682A pdb=" N ILE B 391 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AC8, first strand: chain 'B' and resid 498 through 500 Processing sheet with id=AC9, first strand: chain 'B' and resid 502 through 508 removed outlier: 6.983A pdb=" N ARG B 515 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE B 505 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU B 513 " --> pdb=" O ILE B 505 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR B 507 " --> pdb=" O LYS B 511 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LYS B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 557 through 561 removed outlier: 3.580A pdb=" N GLY B 529 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 626 through 632 removed outlier: 5.476A pdb=" N ASP B 627 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 643 " --> pdb=" O ASP B 627 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 786 through 790 Processing sheet with id=AD4, first strand: chain 'B' and resid 846 through 849 removed outlier: 3.680A pdb=" N CYS B 899 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 883 through 889 removed outlier: 3.509A pdb=" N LEU B 871 " --> pdb=" O THR B 916 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1011 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: 5.29 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2398 1.32 - 1.45: 4051 1.45 - 1.57: 8046 1.57 - 1.70: 0 1.70 - 1.83: 150 Bond restraints: 14645 Sorted by residual: bond pdb=" CA ARG A 110 " pdb=" C ARG A 110 " ideal model delta sigma weight residual 1.524 1.445 0.079 1.27e-02 6.20e+03 3.88e+01 bond pdb=" CA ARG B 110 " pdb=" C ARG B 110 " ideal model delta sigma weight residual 1.524 1.456 0.068 1.24e-02 6.50e+03 3.04e+01 bond pdb=" N LYS A 511 " pdb=" CA LYS A 511 " ideal model delta sigma weight residual 1.460 1.510 -0.050 1.02e-02 9.61e+03 2.36e+01 bond pdb=" CA THR B 140 " pdb=" C THR B 140 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.27e-02 6.20e+03 2.13e+01 bond pdb=" CA LYS A 511 " pdb=" C LYS A 511 " ideal model delta sigma weight residual 1.530 1.494 0.036 9.10e-03 1.21e+04 1.57e+01 ... (remaining 14640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 19560 2.33 - 4.67: 217 4.67 - 7.00: 34 7.00 - 9.34: 10 9.34 - 11.67: 5 Bond angle restraints: 19826 Sorted by residual: angle pdb=" N LYS A 511 " pdb=" CA LYS A 511 " pdb=" C LYS A 511 " ideal model delta sigma weight residual 108.49 117.59 -9.10 1.15e+00 7.56e-01 6.27e+01 angle pdb=" N ILE A 512 " pdb=" CA ILE A 512 " pdb=" C ILE A 512 " ideal model delta sigma weight residual 108.06 117.04 -8.98 1.28e+00 6.10e-01 4.93e+01 angle pdb=" C LYS A 511 " pdb=" CA LYS A 511 " pdb=" CB LYS A 511 " ideal model delta sigma weight residual 114.87 106.80 8.07 1.51e+00 4.39e-01 2.86e+01 angle pdb=" CA LYS A 511 " pdb=" C LYS A 511 " pdb=" N ILE A 512 " ideal model delta sigma weight residual 116.68 121.27 -4.59 8.80e-01 1.29e+00 2.72e+01 angle pdb=" N THR B 140 " pdb=" CA THR B 140 " pdb=" C THR B 140 " ideal model delta sigma weight residual 111.07 116.36 -5.29 1.07e+00 8.73e-01 2.45e+01 ... (remaining 19821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7772 17.80 - 35.60: 817 35.60 - 53.40: 212 53.40 - 71.20: 33 71.20 - 88.99: 25 Dihedral angle restraints: 8859 sinusoidal: 3682 harmonic: 5177 Sorted by residual: dihedral pdb=" CB CYS A 293 " pdb=" SG CYS A 293 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -174.50 88.50 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 328 " pdb=" CB CYS A 328 " ideal model delta sinusoidal sigma weight residual -86.00 -170.82 84.82 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS B 315 " pdb=" SG CYS B 315 " pdb=" SG CYS B 328 " pdb=" CB CYS B 328 " ideal model delta sinusoidal sigma weight residual 93.00 171.38 -78.38 1 1.00e+01 1.00e-02 7.67e+01 ... (remaining 8856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1463 0.035 - 0.069: 427 0.069 - 0.103: 180 0.103 - 0.138: 71 0.138 - 0.172: 11 Chirality restraints: 2152 Sorted by residual: chirality pdb=" CB ILE B 391 " pdb=" CA ILE B 391 " pdb=" CG1 ILE B 391 " pdb=" CG2 ILE B 391 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA ARG A 110 " pdb=" N ARG A 110 " pdb=" C ARG A 110 " pdb=" CB ARG A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA ARG B 110 " pdb=" N ARG B 110 " pdb=" C ARG B 110 " pdb=" CB ARG B 110 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 2149 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 506 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ARG A 506 " -0.057 2.00e-02 2.50e+03 pdb=" O ARG A 506 " 0.021 2.00e-02 2.50e+03 pdb=" N THR A 507 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 275 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C PHE A 275 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE A 275 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN A 276 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 139 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C ILE A 139 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE A 139 " -0.012 2.00e-02 2.50e+03 pdb=" N THR A 140 " -0.011 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2015 2.76 - 3.29: 14246 3.29 - 3.83: 24284 3.83 - 4.36: 27834 4.36 - 4.90: 47694 Nonbonded interactions: 116073 Sorted by model distance: nonbonded pdb=" NH2 ARG A 41 " pdb=" O VAL B 740 " model vdw 2.220 3.120 nonbonded pdb=" O VAL A 740 " pdb=" NH2 ARG B 41 " model vdw 2.224 3.120 nonbonded pdb=" NH1 ARG F 21 " pdb=" OH TYR F 24 " model vdw 2.229 3.120 nonbonded pdb=" O ARG B 801 " pdb=" OG1 THR B 832 " model vdw 2.245 3.040 nonbonded pdb=" O PHE B 509 " pdb=" OG1 THR B 617 " model vdw 2.251 3.040 ... (remaining 116068 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 'A' and (resid 30 through 85 or resid 87 through 934)) selection = (chain 'B' and (resid 30 through 132 or resid 134 through 187 or resid 196 throu \ gh 470 or resid 473 through 478 or resid 484 through 600 or resid 605 through 80 \ 1 or resid 803 through 842 or resid 844 through 934)) } ncs_group { reference = (chain 'C' and (resid 6 through 26 or resid 42 through 63)) selection = chain 'D' selection = (chain 'E' and (resid 6 through 26 or resid 42 through 63)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.140 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: 0.680 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.300 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.010 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 0.079 14679 Z= 0.188 Angle : 0.642 11.673 19894 Z= 0.340 Chirality : 0.043 0.172 2152 Planarity : 0.004 0.033 2562 Dihedral : 15.792 88.995 5409 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.97 % Favored : 93.86 % Rotamer: Outliers : 0.68 % Allowed : 19.09 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.21), residues: 1725 helix: -1.01 (0.31), residues: 275 sheet: 0.07 (0.27), residues: 359 loop : -0.78 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 659 HIS 0.003 0.001 HIS B 456 PHE 0.016 0.001 PHE A 658 TYR 0.014 0.001 TYR B 154 ARG 0.006 0.000 ARG E 55 Details of bonding type rmsd hydrogen bonds : bond 0.23992 ( 376) hydrogen bonds : angle 9.32658 ( 1011) SS BOND : bond 0.00156 ( 34) SS BOND : angle 0.67128 ( 68) covalent geometry : bond 0.00316 (14645) covalent geometry : angle 0.64229 (19826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 91 average time/residue: 0.3203 time to fit residues: 43.0718 Evaluate side-chains 81 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain F residue 53 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 50.0000 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 70 optimal weight: 40.0000 chunk 137 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 307 HIS A 450 GLN A 568 ASN A 574 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 621 ASN B 856 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.096982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.061854 restraints weight = 57421.548| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 7.16 r_work: 0.3161 rms_B_bonded: 6.85 restraints_weight: 2.0000 r_work: 0.3287 rms_B_bonded: 5.41 restraints_weight: 4.0000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 14679 Z= 0.250 Angle : 0.664 10.319 19894 Z= 0.344 Chirality : 0.045 0.238 2152 Planarity : 0.004 0.035 2562 Dihedral : 5.297 54.162 1940 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.61 % Allowed : 17.79 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1725 helix: -0.80 (0.31), residues: 283 sheet: -0.07 (0.27), residues: 347 loop : -0.87 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 556 HIS 0.006 0.001 HIS A 127 PHE 0.018 0.002 PHE B 91 TYR 0.018 0.002 TYR B 428 ARG 0.006 0.001 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 376) hydrogen bonds : angle 6.96989 ( 1011) SS BOND : bond 0.00283 ( 34) SS BOND : angle 0.85085 ( 68) covalent geometry : bond 0.00564 (14645) covalent geometry : angle 0.66369 (19826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 82 time to evaluate : 1.613 Fit side-chains REVERT: B 83 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8585 (ttt) REVERT: B 575 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7034 (m90) REVERT: D 46 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7741 (tm-30) REVERT: D 56 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7724 (tpp-160) outliers start: 58 outliers final: 32 residues processed: 129 average time/residue: 0.2249 time to fit residues: 45.6878 Evaluate side-chains 109 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 11 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 30.0000 chunk 153 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.096737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.061610 restraints weight = 58092.840| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 7.32 r_work: 0.3145 rms_B_bonded: 6.89 restraints_weight: 2.0000 r_work: 0.3277 rms_B_bonded: 5.37 restraints_weight: 4.0000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 14679 Z= 0.243 Angle : 0.670 11.575 19894 Z= 0.343 Chirality : 0.045 0.226 2152 Planarity : 0.004 0.037 2562 Dihedral : 5.347 50.088 1938 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.48 % Allowed : 17.97 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1725 helix: -0.72 (0.31), residues: 284 sheet: -0.31 (0.27), residues: 347 loop : -0.93 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 659 HIS 0.012 0.001 HIS B 575 PHE 0.019 0.002 PHE B 91 TYR 0.017 0.001 TYR A 394 ARG 0.004 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 376) hydrogen bonds : angle 6.67092 ( 1011) SS BOND : bond 0.00530 ( 34) SS BOND : angle 1.49578 ( 68) covalent geometry : bond 0.00551 (14645) covalent geometry : angle 0.66549 (19826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 78 time to evaluate : 1.700 Fit side-chains REVERT: B 83 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8216 (ttt) REVERT: D 12 ASP cc_start: 0.9737 (m-30) cc_final: 0.9347 (p0) REVERT: D 52 CYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7617 (m) REVERT: D 56 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7817 (tpp-160) outliers start: 72 outliers final: 45 residues processed: 142 average time/residue: 0.2242 time to fit residues: 51.1409 Evaluate side-chains 121 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 74 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 61 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 135 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 141 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 HIS ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.097729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.062911 restraints weight = 57359.676| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 7.27 r_work: 0.3188 rms_B_bonded: 6.86 restraints_weight: 2.0000 r_work: 0.3317 rms_B_bonded: 5.42 restraints_weight: 4.0000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14679 Z= 0.138 Angle : 0.612 11.154 19894 Z= 0.306 Chirality : 0.043 0.173 2152 Planarity : 0.004 0.035 2562 Dihedral : 5.077 45.386 1938 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.92 % Allowed : 18.66 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.21), residues: 1725 helix: -0.60 (0.32), residues: 289 sheet: -0.11 (0.27), residues: 345 loop : -0.87 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 439 HIS 0.005 0.001 HIS A 444 PHE 0.015 0.001 PHE B 91 TYR 0.013 0.001 TYR B 534 ARG 0.002 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 376) hydrogen bonds : angle 6.29656 ( 1011) SS BOND : bond 0.00196 ( 34) SS BOND : angle 0.84559 ( 68) covalent geometry : bond 0.00311 (14645) covalent geometry : angle 0.61099 (19826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 83 time to evaluate : 1.648 Fit side-chains revert: symmetry clash REVERT: A 513 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8001 (mm) REVERT: B 321 MET cc_start: 0.8367 (tpt) cc_final: 0.8159 (tpt) REVERT: D 12 ASP cc_start: 0.9744 (m-30) cc_final: 0.9368 (p0) REVERT: D 52 CYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7458 (m) REVERT: D 56 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7832 (tpp-160) outliers start: 63 outliers final: 43 residues processed: 134 average time/residue: 0.2472 time to fit residues: 51.1373 Evaluate side-chains 125 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 61 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 90 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** B 135 ASN ** 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 = 0.4084 r_free = 0.4084 target = 0.095718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.060371 restraints weight = 57359.605| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 7.30 r_work: 0.3118 rms_B_bonded: 6.94 restraints_weight: 2.0000 r_work: 0.3246 rms_B_bonded: 5.37 restraints_weight: 4.0000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 14679 Z= 0.306 Angle : 0.717 11.560 19894 Z= 0.363 Chirality : 0.046 0.256 2152 Planarity : 0.004 0.038 2562 Dihedral : 5.481 47.764 1938 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.29 % Allowed : 17.97 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1725 helix: -0.63 (0.32), residues: 278 sheet: -0.36 (0.27), residues: 345 loop : -1.04 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 278 HIS 0.011 0.001 HIS A 444 PHE 0.020 0.002 PHE B 91 TYR 0.022 0.002 TYR B 428 ARG 0.004 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 376) hydrogen bonds : angle 6.36496 ( 1011) SS BOND : bond 0.00320 ( 34) SS BOND : angle 0.95337 ( 68) covalent geometry : bond 0.00697 (14645) covalent geometry : angle 0.71627 (19826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 73 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8343 (ttt) REVERT: D 52 CYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7504 (m) REVERT: D 56 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7924 (tpp-160) outliers start: 85 outliers final: 60 residues processed: 147 average time/residue: 0.2560 time to fit residues: 58.0131 Evaluate side-chains 135 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 73 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 61 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** 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 = 0.4119 r_free = 0.4119 target = 0.097566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.063694 restraints weight = 57631.682| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 5.90 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14679 Z= 0.130 Angle : 0.617 10.976 19894 Z= 0.308 Chirality : 0.044 0.171 2152 Planarity : 0.004 0.034 2562 Dihedral : 5.106 43.378 1938 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.92 % Allowed : 19.34 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.21), residues: 1725 helix: -0.58 (0.32), residues: 289 sheet: -0.17 (0.28), residues: 345 loop : -0.92 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 439 HIS 0.004 0.001 HIS A 444 PHE 0.016 0.001 PHE B 91 TYR 0.015 0.001 TYR A 259 ARG 0.003 0.000 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 376) hydrogen bonds : angle 6.07344 ( 1011) SS BOND : bond 0.00168 ( 34) SS BOND : angle 0.65199 ( 68) covalent geometry : bond 0.00294 (14645) covalent geometry : angle 0.61683 (19826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 80 time to evaluate : 1.684 Fit side-chains revert: symmetry clash REVERT: B 321 MET cc_start: 0.8230 (tpt) cc_final: 0.7805 (tpp) REVERT: B 575 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7538 (m170) REVERT: D 52 CYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7241 (m) outliers start: 63 outliers final: 47 residues processed: 134 average time/residue: 0.2382 time to fit residues: 49.6140 Evaluate side-chains 126 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 77 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 61 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 46 optimal weight: 0.0970 chunk 43 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 74 optimal weight: 0.0470 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** 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 = 0.4138 r_free = 0.4138 target = 0.098580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.070154 restraints weight = 57245.256| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 6.15 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14679 Z= 0.102 Angle : 0.607 10.862 19894 Z= 0.300 Chirality : 0.043 0.149 2152 Planarity : 0.003 0.034 2562 Dihedral : 4.837 37.105 1938 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.30 % Allowed : 19.59 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.00 (0.21), residues: 1725 helix: -0.56 (0.32), residues: 284 sheet: 0.01 (0.28), residues: 345 loop : -0.92 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 439 HIS 0.002 0.000 HIS A 892 PHE 0.016 0.001 PHE F 16 TYR 0.015 0.001 TYR A 259 ARG 0.003 0.000 ARG E 55 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 376) hydrogen bonds : angle 5.83554 ( 1011) SS BOND : bond 0.00147 ( 34) SS BOND : angle 0.64643 ( 68) covalent geometry : bond 0.00225 (14645) covalent geometry : angle 0.60648 (19826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 85 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7927 (ttt) cc_final: 0.7608 (ttt) REVERT: A 513 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7772 (mm) REVERT: B 83 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7826 (ttt) REVERT: B 321 MET cc_start: 0.8257 (tpt) cc_final: 0.7844 (tpp) REVERT: B 724 GLU cc_start: 0.7432 (mp0) cc_final: 0.7176 (pm20) REVERT: B 725 GLU cc_start: 0.7902 (pm20) cc_final: 0.7045 (tm-30) REVERT: D 12 ASP cc_start: 0.9725 (m-30) cc_final: 0.9374 (p0) REVERT: D 52 CYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7188 (m) REVERT: F 12 ASP cc_start: 0.9607 (OUTLIER) cc_final: 0.9237 (p0) outliers start: 53 outliers final: 41 residues processed: 128 average time/residue: 0.2689 time to fit residues: 54.9396 Evaluate side-chains 122 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 77 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 61 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 171 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 152 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 HIS ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.098545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.063474 restraints weight = 57426.597| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 7.06 r_work: 0.3212 rms_B_bonded: 6.69 restraints_weight: 2.0000 r_work: 0.3335 rms_B_bonded: 5.20 restraints_weight: 4.0000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14679 Z= 0.113 Angle : 0.614 10.793 19894 Z= 0.302 Chirality : 0.043 0.150 2152 Planarity : 0.004 0.046 2562 Dihedral : 4.792 32.953 1938 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.73 % Allowed : 19.47 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.99 (0.21), residues: 1725 helix: -0.67 (0.31), residues: 296 sheet: -0.01 (0.28), residues: 352 loop : -0.87 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 439 HIS 0.002 0.000 HIS A 444 PHE 0.013 0.001 PHE B 91 TYR 0.013 0.001 TYR B 806 ARG 0.013 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 376) hydrogen bonds : angle 5.78302 ( 1011) SS BOND : bond 0.00140 ( 34) SS BOND : angle 0.60096 ( 68) covalent geometry : bond 0.00255 (14645) covalent geometry : angle 0.61389 (19826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 80 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.8464 (ttt) cc_final: 0.8127 (ttt) REVERT: B 321 MET cc_start: 0.8401 (tpt) cc_final: 0.8153 (tpp) REVERT: B 575 HIS cc_start: 0.7566 (OUTLIER) cc_final: 0.6990 (m90) REVERT: B 725 GLU cc_start: 0.8148 (pm20) cc_final: 0.7873 (pm20) REVERT: D 12 ASP cc_start: 0.9740 (m-30) cc_final: 0.9395 (p0) REVERT: D 52 CYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7434 (m) REVERT: D 56 ARG cc_start: 0.8241 (tpp-160) cc_final: 0.7987 (tpp80) REVERT: F 53 ASP cc_start: 0.8053 (m-30) cc_final: 0.7832 (m-30) outliers start: 60 outliers final: 49 residues processed: 131 average time/residue: 0.2212 time to fit residues: 45.8233 Evaluate side-chains 126 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 75 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 24 TYR Chi-restraints excluded: chain F residue 61 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 134 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 159 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 154 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 115 optimal weight: 0.0980 chunk 12 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** 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 = 0.4137 r_free = 0.4137 target = 0.098531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.063219 restraints weight = 56821.246| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 7.42 r_work: 0.3215 rms_B_bonded: 6.60 restraints_weight: 2.0000 r_work: 0.3338 rms_B_bonded: 5.31 restraints_weight: 4.0000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14679 Z= 0.117 Angle : 0.648 12.261 19894 Z= 0.315 Chirality : 0.043 0.149 2152 Planarity : 0.004 0.055 2562 Dihedral : 4.791 29.979 1938 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.17 % Allowed : 19.96 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1725 helix: -0.69 (0.31), residues: 297 sheet: 0.02 (0.29), residues: 343 loop : -0.83 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 439 HIS 0.015 0.001 HIS B 575 PHE 0.013 0.001 PHE B 91 TYR 0.016 0.001 TYR B 806 ARG 0.012 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 376) hydrogen bonds : angle 5.76991 ( 1011) SS BOND : bond 0.00155 ( 34) SS BOND : angle 1.43055 ( 68) covalent geometry : bond 0.00271 (14645) covalent geometry : angle 0.64374 (19826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 75 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.8445 (ttt) cc_final: 0.8104 (ttt) REVERT: B 321 MET cc_start: 0.8413 (tpt) cc_final: 0.7839 (tpp) REVERT: D 12 ASP cc_start: 0.9741 (m-30) cc_final: 0.9395 (p0) REVERT: D 52 CYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7410 (m) REVERT: F 12 ASP cc_start: 0.9652 (m-30) cc_final: 0.9332 (p0) REVERT: F 53 ASP cc_start: 0.8059 (m-30) cc_final: 0.7839 (m-30) outliers start: 51 outliers final: 49 residues processed: 117 average time/residue: 0.2212 time to fit residues: 41.2274 Evaluate side-chains 123 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 73 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 24 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 43 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 158 optimal weight: 0.4980 chunk 134 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.098587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063274 restraints weight = 56826.471| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 7.31 r_work: 0.3214 rms_B_bonded: 6.83 restraints_weight: 2.0000 r_work: 0.3343 rms_B_bonded: 5.30 restraints_weight: 4.0000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14679 Z= 0.115 Angle : 0.650 12.644 19894 Z= 0.315 Chirality : 0.043 0.160 2152 Planarity : 0.004 0.053 2562 Dihedral : 4.725 24.872 1938 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.30 % Allowed : 20.02 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1725 helix: -0.65 (0.32), residues: 297 sheet: 0.05 (0.28), residues: 343 loop : -0.81 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 439 HIS 0.004 0.001 HIS A 444 PHE 0.013 0.001 PHE B 91 TYR 0.013 0.001 TYR A 259 ARG 0.012 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.02956 ( 376) hydrogen bonds : angle 5.70023 ( 1011) SS BOND : bond 0.00137 ( 34) SS BOND : angle 0.89587 ( 68) covalent geometry : bond 0.00264 (14645) covalent geometry : angle 0.64915 (19826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 78 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.8427 (ttt) cc_final: 0.8069 (ttt) REVERT: A 321 MET cc_start: 0.8095 (tpp) cc_final: 0.7431 (tpp) REVERT: B 321 MET cc_start: 0.8434 (tpt) cc_final: 0.7922 (tpp) REVERT: B 575 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.7013 (m90) REVERT: D 12 ASP cc_start: 0.9739 (m-30) cc_final: 0.9397 (p0) REVERT: F 12 ASP cc_start: 0.9652 (m-30) cc_final: 0.9319 (p0) REVERT: F 53 ASP cc_start: 0.8087 (m-30) cc_final: 0.7853 (m-30) outliers start: 53 outliers final: 50 residues processed: 122 average time/residue: 0.2534 time to fit residues: 49.0939 Evaluate side-chains 126 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 75 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 24 TYR Chi-restraints excluded: chain F residue 61 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 34 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 159 optimal weight: 0.1980 chunk 50 optimal weight: 0.2980 chunk 15 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.097535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062215 restraints weight = 57158.191| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 7.15 r_work: 0.3170 rms_B_bonded: 6.89 restraints_weight: 2.0000 r_work: 0.3300 rms_B_bonded: 5.29 restraints_weight: 4.0000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14679 Z= 0.176 Angle : 0.666 11.208 19894 Z= 0.326 Chirality : 0.044 0.208 2152 Planarity : 0.004 0.062 2562 Dihedral : 4.840 21.510 1937 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.48 % Allowed : 19.59 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1725 helix: -0.64 (0.32), residues: 297 sheet: -0.10 (0.28), residues: 348 loop : -0.83 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 439 HIS 0.013 0.001 HIS B 575 PHE 0.014 0.001 PHE B 91 TYR 0.012 0.001 TYR B 806 ARG 0.012 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 376) hydrogen bonds : angle 5.74044 ( 1011) SS BOND : bond 0.00194 ( 34) SS BOND : angle 1.13478 ( 68) covalent geometry : bond 0.00404 (14645) covalent geometry : angle 0.66351 (19826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13170.85 seconds wall clock time: 228 minutes 0.83 seconds (13680.83 seconds total)