Starting phenix.real_space_refine on Thu Jun 12 22:30:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk1_38413/06_2025/8xk1_38413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk1_38413/06_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_38413/06_2025/8xk1_38413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk1_38413/06_2025/8xk1_38413.map" model { file = "/net/cci-nas-00/data/ceres_data/8xk1_38413/06_2025/8xk1_38413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk1_38413/06_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-5710/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: 11.19, per 1000 atoms: 0.78 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: 3.47 Conformation dependent library (CDL) restraints added in 1.9 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: 1.89 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: 8.93 Time building geometry restraints manager: 4.19 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: 66.850 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: 0.770 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 43.480 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.400 ------------------------------------------------------------------------------- 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 : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 91 average time/residue: 0.3200 time to fit residues: 42.7626 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 : 1.490 ------------------------------------------------------------------------------- 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 = 88)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.061818 restraints weight = 57421.684| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 7.23 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 6.96987 ( 1011) SS BOND : bond 0.00283 ( 34) SS BOND : angle 0.85083 ( 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 : 3.014 Fit side-chains REVERT: A 658 PHE cc_start: 0.8697 (m-80) cc_final: 0.8440 (m-80) REVERT: B 83 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8310 (ttt) REVERT: B 575 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.6965 (m90) REVERT: D 56 ARG cc_start: 0.7802 (mmm160) cc_final: 0.7535 (tpp-160) outliers start: 58 outliers final: 32 residues processed: 129 average time/residue: 0.2853 time to fit residues: 59.4467 Evaluate side-chains 108 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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: 9.9990 chunk 60 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 30.0000 chunk 153 optimal weight: 20.0000 chunk 143 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.096951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.061693 restraints weight = 58142.692| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 7.32 r_work: 0.3147 rms_B_bonded: 7.00 restraints_weight: 2.0000 r_work: 0.3276 rms_B_bonded: 5.38 restraints_weight: 4.0000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14679 Z= 0.229 Angle : 0.660 11.445 19894 Z= 0.338 Chirality : 0.045 0.221 2152 Planarity : 0.004 0.037 2562 Dihedral : 5.297 50.377 1938 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.42 % Allowed : 18.10 % Favored : 77.49 % 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: -1.12 (0.21), residues: 1725 helix: -0.70 (0.31), residues: 283 sheet: -0.27 (0.27), residues: 347 loop : -0.91 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 659 HIS 0.008 0.001 HIS A 444 PHE 0.018 0.002 PHE B 91 TYR 0.016 0.001 TYR A 394 ARG 0.004 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 376) hydrogen bonds : angle 6.67689 ( 1011) SS BOND : bond 0.00361 ( 34) SS BOND : angle 1.50100 ( 68) covalent geometry : bond 0.00519 (14645) covalent geometry : angle 0.65553 (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: 71 poor density : 79 time to evaluate : 1.647 Fit side-chains REVERT: B 83 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8291 (ttt) REVERT: D 52 CYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7642 (m) REVERT: D 56 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7791 (tpp-160) outliers start: 71 outliers final: 44 residues processed: 140 average time/residue: 0.2380 time to fit residues: 53.0536 Evaluate side-chains 121 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 75 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 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 164 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 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: 6.9990 chunk 136 optimal weight: 10.0000 chunk 141 optimal weight: 30.0000 chunk 119 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 97 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 131 optimal weight: 0.4980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 127 HIS ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 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 = 0.4137 r_free = 0.4137 target = 0.098503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.063723 restraints weight = 57349.011| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 7.15 r_work: 0.3210 rms_B_bonded: 6.87 restraints_weight: 2.0000 r_work: 0.3344 rms_B_bonded: 5.40 restraints_weight: 4.0000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14679 Z= 0.109 Angle : 0.596 11.036 19894 Z= 0.297 Chirality : 0.043 0.159 2152 Planarity : 0.004 0.034 2562 Dihedral : 4.934 43.597 1938 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.67 % Allowed : 19.71 % Favored : 77.61 % 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: -0.95 (0.21), residues: 1725 helix: -0.55 (0.32), residues: 283 sheet: -0.05 (0.27), residues: 345 loop : -0.83 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 439 HIS 0.002 0.000 HIS A 444 PHE 0.012 0.001 PHE B 91 TYR 0.014 0.001 TYR B 534 ARG 0.003 0.000 ARG E 55 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 376) hydrogen bonds : angle 6.23351 ( 1011) SS BOND : bond 0.00166 ( 34) SS BOND : angle 0.81303 ( 68) covalent geometry : bond 0.00241 (14645) covalent geometry : angle 0.59508 (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 129 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 513 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7913 (mm) REVERT: D 12 ASP cc_start: 0.9741 (m-30) cc_final: 0.9391 (p0) REVERT: D 52 CYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7451 (m) REVERT: D 56 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7805 (tpp-160) REVERT: F 53 ASP cc_start: 0.8022 (m-30) cc_final: 0.7818 (m-30) outliers start: 43 outliers final: 27 residues processed: 121 average time/residue: 0.2343 time to fit residues: 44.4726 Evaluate side-chains 110 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 315 CYS 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 786 PHE Chi-restraints excluded: chain A residue 813 CYS 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 173 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 832 THR 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: 3.9990 chunk 170 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 HIS A 662 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN ** B 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.094163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.058433 restraints weight = 57977.197| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 7.10 r_work: 0.3072 rms_B_bonded: 6.90 restraints_weight: 2.0000 r_work: 0.3201 rms_B_bonded: 5.36 restraints_weight: 4.0000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.071 14679 Z= 0.487 Angle : 0.892 13.125 19894 Z= 0.453 Chirality : 0.051 0.291 2152 Planarity : 0.005 0.042 2562 Dihedral : 5.993 48.601 1938 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 5.72 % Allowed : 17.85 % Favored : 76.43 % 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: -1.58 (0.20), residues: 1725 helix: -0.98 (0.31), residues: 279 sheet: -0.53 (0.28), residues: 337 loop : -1.26 (0.20), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 556 HIS 0.017 0.002 HIS A 444 PHE 0.024 0.003 PHE A 454 TYR 0.036 0.002 TYR B 428 ARG 0.006 0.001 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 376) hydrogen bonds : angle 6.71498 ( 1011) SS BOND : bond 0.00528 ( 34) SS BOND : angle 1.32227 ( 68) covalent geometry : bond 0.01107 (14645) covalent geometry : angle 0.89066 (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 162 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 70 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8221 (ttt) REVERT: B 575 HIS cc_start: 0.8049 (OUTLIER) cc_final: 0.7410 (m90) REVERT: D 56 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7788 (tpp-160) outliers start: 92 outliers final: 67 residues processed: 152 average time/residue: 0.2367 time to fit residues: 55.9587 Evaluate side-chains 137 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 68 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain A residue 97 GLU 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 422 ILE 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 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 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 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 93 VAL 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 238 GLU 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 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 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 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 12 ASP 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: 9.9990 chunk 152 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 68 optimal weight: 20.0000 chunk 157 optimal weight: 40.0000 chunk 87 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 A 290 HIS ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.097537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.062528 restraints weight = 57680.281| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 6.84 r_work: 0.3187 rms_B_bonded: 6.59 restraints_weight: 2.0000 r_work: 0.3309 rms_B_bonded: 5.19 restraints_weight: 4.0000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14679 Z= 0.123 Angle : 0.642 10.874 19894 Z= 0.319 Chirality : 0.044 0.166 2152 Planarity : 0.004 0.041 2562 Dihedral : 5.247 42.446 1938 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.48 % Allowed : 20.15 % Favored : 76.37 % 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: -1.18 (0.21), residues: 1725 helix: -0.68 (0.32), residues: 285 sheet: -0.26 (0.28), residues: 347 loop : -0.99 (0.20), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 439 HIS 0.023 0.001 HIS B 575 PHE 0.022 0.001 PHE B 285 TYR 0.016 0.001 TYR A 259 ARG 0.004 0.000 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 376) hydrogen bonds : angle 6.19494 ( 1011) SS BOND : bond 0.00167 ( 34) SS BOND : angle 0.68651 ( 68) covalent geometry : bond 0.00277 (14645) covalent geometry : angle 0.64208 (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 136 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 80 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8245 (ttt) REVERT: B 238 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6425 (mm-30) REVERT: D 12 ASP cc_start: 0.9741 (m-30) cc_final: 0.9396 (p0) outliers start: 56 outliers final: 39 residues processed: 126 average time/residue: 0.2397 time to fit residues: 46.3822 Evaluate side-chains 118 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 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 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 581 ARG 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 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 238 GLU 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 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 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 D residue 43 ILE 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: 0.9980 chunk 43 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.4144 ------------------------------------------------------------------------------- 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** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.096352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.062899 restraints weight = 58166.695| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 5.58 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14679 Z= 0.218 Angle : 0.669 11.112 19894 Z= 0.334 Chirality : 0.044 0.194 2152 Planarity : 0.004 0.036 2562 Dihedral : 5.319 44.411 1938 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.98 % Allowed : 19.59 % Favored : 76.43 % 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: -1.30 (0.21), residues: 1725 helix: -0.80 (0.31), residues: 297 sheet: -0.33 (0.27), residues: 347 loop : -1.07 (0.20), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 439 HIS 0.008 0.001 HIS A 444 PHE 0.019 0.002 PHE B 91 TYR 0.021 0.001 TYR B 457 ARG 0.003 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 376) hydrogen bonds : angle 6.12815 ( 1011) SS BOND : bond 0.00236 ( 34) SS BOND : angle 0.73589 ( 68) covalent geometry : bond 0.00500 (14645) covalent geometry : angle 0.66871 (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 139 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 75 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7937 (ttt) REVERT: F 12 ASP cc_start: 0.9710 (m-30) cc_final: 0.9488 (p0) outliers start: 64 outliers final: 51 residues processed: 130 average time/residue: 0.3128 time to fit residues: 62.6561 Evaluate side-chains 125 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 73 time to evaluate : 2.916 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 171 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 492 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 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 = 0.4107 r_free = 0.4107 target = 0.097038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.063097 restraints weight = 57057.498| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 5.79 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14679 Z= 0.154 Angle : 0.649 10.789 19894 Z= 0.324 Chirality : 0.044 0.163 2152 Planarity : 0.004 0.074 2562 Dihedral : 5.196 42.386 1938 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.98 % Allowed : 19.22 % 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: -1.21 (0.21), residues: 1725 helix: -0.76 (0.31), residues: 297 sheet: -0.28 (0.27), residues: 352 loop : -0.99 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 659 HIS 0.006 0.001 HIS A 444 PHE 0.017 0.001 PHE B 91 TYR 0.041 0.001 TYR B 457 ARG 0.012 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 376) hydrogen bonds : angle 6.03978 ( 1011) SS BOND : bond 0.00180 ( 34) SS BOND : angle 0.64746 ( 68) covalent geometry : bond 0.00353 (14645) covalent geometry : angle 0.64865 (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 138 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 74 time to evaluate : 1.517 Fit side-chains REVERT: B 321 MET cc_start: 0.8196 (tpt) cc_final: 0.7707 (tpp) REVERT: B 456 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.7613 (t-170) REVERT: B 725 GLU cc_start: 0.8008 (pm20) cc_final: 0.7698 (pm20) outliers start: 64 outliers final: 51 residues processed: 127 average time/residue: 0.2358 time to fit residues: 47.0988 Evaluate side-chains 125 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 73 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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 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 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 196 CYS Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 342 LEU 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 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 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 57 LEU 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: 2.9990 chunk 15 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 159 optimal weight: 0.0170 chunk 45 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- 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 303 GLN ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.095935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.067773 restraints weight = 57198.798| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 6.53 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14679 Z= 0.247 Angle : 0.712 10.920 19894 Z= 0.357 Chirality : 0.045 0.207 2152 Planarity : 0.004 0.080 2562 Dihedral : 5.399 44.598 1938 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 4.04 % Allowed : 19.09 % 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: -1.34 (0.21), residues: 1725 helix: -0.80 (0.31), residues: 296 sheet: -0.43 (0.27), residues: 359 loop : -1.08 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 439 HIS 0.010 0.001 HIS A 444 PHE 0.019 0.002 PHE B 91 TYR 0.031 0.002 TYR B 457 ARG 0.013 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 376) hydrogen bonds : angle 6.11559 ( 1011) SS BOND : bond 0.00267 ( 34) SS BOND : angle 1.60961 ( 68) covalent geometry : bond 0.00567 (14645) covalent geometry : angle 0.70741 (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 140 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 75 time to evaluate : 1.648 Fit side-chains revert: symmetry clash REVERT: A 580 MET cc_start: 0.7500 (mmm) cc_final: 0.7210 (mmt) REVERT: B 321 MET cc_start: 0.8396 (tpt) cc_final: 0.7625 (tpp) REVERT: B 456 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7633 (t-170) outliers start: 65 outliers final: 61 residues processed: 129 average time/residue: 0.2172 time to fit residues: 44.9771 Evaluate side-chains 134 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 72 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 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 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 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 177 ASP Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 LEU 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 591 ILE 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 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 47 CYS Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 24 TYR Chi-restraints excluded: chain F residue 57 LEU 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 43 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 chunk 134 optimal weight: 0.0570 chunk 109 optimal weight: 0.9980 overall best weight: 0.7898 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.097832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.062588 restraints weight = 56931.836| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 7.34 r_work: 0.3184 rms_B_bonded: 7.15 restraints_weight: 2.0000 r_work: 0.3313 rms_B_bonded: 5.31 restraints_weight: 4.0000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14679 Z= 0.118 Angle : 0.647 10.777 19894 Z= 0.320 Chirality : 0.043 0.158 2152 Planarity : 0.004 0.053 2562 Dihedral : 5.040 37.598 1938 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.48 % Allowed : 19.84 % 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: -1.12 (0.21), residues: 1725 helix: -0.54 (0.32), residues: 284 sheet: -0.23 (0.27), residues: 359 loop : -0.98 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 439 HIS 0.005 0.001 HIS A 444 PHE 0.016 0.001 PHE B 91 TYR 0.029 0.001 TYR B 457 ARG 0.012 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 376) hydrogen bonds : angle 5.88801 ( 1011) SS BOND : bond 0.00167 ( 34) SS BOND : angle 1.03973 ( 68) covalent geometry : bond 0.00271 (14645) covalent geometry : angle 0.64500 (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 135 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 79 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 321 MET cc_start: 0.8332 (tpt) cc_final: 0.7915 (tpp) REVERT: B 456 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.7961 (t-170) REVERT: D 12 ASP cc_start: 0.9750 (m-30) cc_final: 0.9425 (p0) REVERT: F 12 ASP cc_start: 0.9661 (m-30) cc_final: 0.9333 (p0) outliers start: 56 outliers final: 50 residues processed: 125 average time/residue: 0.2341 time to fit residues: 47.4096 Evaluate side-chains 127 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 76 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 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 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 173 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 342 LEU 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 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 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 47 CYS Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 57 LEU 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: 0.0020 chunk 48 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 50 optimal weight: 0.0770 chunk 15 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 overall best weight: 1.7750 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.096928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.061475 restraints weight = 57577.526| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 7.09 r_work: 0.3162 rms_B_bonded: 6.90 restraints_weight: 2.0000 r_work: 0.3282 rms_B_bonded: 5.25 restraints_weight: 4.0000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14679 Z= 0.171 Angle : 0.661 10.747 19894 Z= 0.327 Chirality : 0.044 0.169 2152 Planarity : 0.004 0.056 2562 Dihedral : 5.094 38.414 1938 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.67 % Allowed : 19.78 % Favored : 76.55 % 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: -1.13 (0.21), residues: 1725 helix: -0.57 (0.32), residues: 290 sheet: -0.27 (0.27), residues: 359 loop : -0.97 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 439 HIS 0.007 0.001 HIS A 444 PHE 0.018 0.001 PHE B 91 TYR 0.025 0.001 TYR B 457 ARG 0.012 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 376) hydrogen bonds : angle 5.87627 ( 1011) SS BOND : bond 0.00195 ( 34) SS BOND : angle 0.95574 ( 68) covalent geometry : bond 0.00394 (14645) covalent geometry : angle 0.66020 (19826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13137.64 seconds wall clock time: 232 minutes 23.74 seconds (13943.74 seconds total)