Starting phenix.real_space_refine on Thu Sep 18 05:33:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk1_38413/09_2025/8xk1_38413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk1_38413/09_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_38413/09_2025/8xk1_38413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk1_38413/09_2025/8xk1_38413.map" model { file = "/net/cci-nas-00/data/ceres_data/8xk1_38413/09_2025/8xk1_38413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk1_38413/09_2025/8xk1_38413.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.99, per 1000 atoms: 0.28 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: 1.20 Conformation dependent library (CDL) restraints added in 751.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.75 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: 2.89 Time building geometry restraints manager: 1.66 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: 12.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.870 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- 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 : 12.51 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG E 55 TYR 0.014 0.001 TYR B 154 PHE 0.016 0.001 PHE A 658 TRP 0.012 0.001 TRP A 659 HIS 0.003 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00316 (14645) covalent geometry : angle 0.64229 (19826) SS BOND : bond 0.00156 ( 34) SS BOND : angle 0.67128 ( 68) hydrogen bonds : bond 0.23992 ( 376) hydrogen bonds : angle 9.32658 ( 1011) *********************** 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 : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 91 average time/residue: 0.1330 time to fit residues: 17.9187 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 : 0.522 ------------------------------------------------------------------------------- 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 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0060 overall best weight: 2.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN 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 856 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.097359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.062253 restraints weight = 58287.106| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 7.25 r_work: 0.3169 rms_B_bonded: 6.84 restraints_weight: 2.0000 r_work: 0.3293 rms_B_bonded: 5.67 restraints_weight: 4.0000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14679 Z= 0.229 Angle : 0.647 10.338 19894 Z= 0.336 Chirality : 0.045 0.214 2152 Planarity : 0.004 0.035 2562 Dihedral : 5.199 54.452 1940 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.36 % Allowed : 17.66 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.21), residues: 1725 helix: -0.74 (0.31), residues: 283 sheet: -0.03 (0.27), residues: 347 loop : -0.84 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 145 TYR 0.016 0.001 TYR B 428 PHE 0.017 0.002 PHE B 91 TRP 0.010 0.001 TRP B 556 HIS 0.005 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00513 (14645) covalent geometry : angle 0.64619 (19826) SS BOND : bond 0.00405 ( 34) SS BOND : angle 0.75498 ( 68) hydrogen bonds : bond 0.04579 ( 376) hydrogen bonds : angle 7.01052 ( 1011) *********************** 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 135 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 81 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: B 83 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8564 (ttt) REVERT: B 575 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7098 (m90) REVERT: D 46 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7744 (tm-30) REVERT: D 56 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7751 (tpp-160) outliers start: 54 outliers final: 26 residues processed: 126 average time/residue: 0.1070 time to fit residues: 21.3533 Evaluate side-chains 103 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 175 ASN 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 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 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 98 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 72 optimal weight: 50.0000 chunk 132 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 151 optimal weight: 50.0000 chunk 130 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 450 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN B 621 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.097742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.063689 restraints weight = 57726.680| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 6.41 r_work: 0.3183 rms_B_bonded: 6.39 restraints_weight: 2.0000 r_work: 0.3308 rms_B_bonded: 5.00 restraints_weight: 4.0000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1221 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= 0.168 Angle : 0.625 11.515 19894 Z= 0.318 Chirality : 0.044 0.221 2152 Planarity : 0.004 0.035 2562 Dihedral : 5.109 50.067 1938 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.48 % Allowed : 18.28 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.21), residues: 1725 helix: -0.69 (0.31), residues: 289 sheet: -0.16 (0.27), residues: 345 loop : -0.84 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 145 TYR 0.015 0.001 TYR B 806 PHE 0.015 0.001 PHE B 91 TRP 0.013 0.001 TRP B 659 HIS 0.009 0.001 HIS B 575 Details of bonding type rmsd covalent geometry : bond 0.00380 (14645) covalent geometry : angle 0.62013 (19826) SS BOND : bond 0.00242 ( 34) SS BOND : angle 1.43252 ( 68) hydrogen bonds : bond 0.03809 ( 376) hydrogen bonds : angle 6.62262 ( 1011) *********************** 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 138 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 82 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: B 83 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8271 (ttt) REVERT: D 12 ASP cc_start: 0.9751 (m-30) cc_final: 0.9393 (p0) REVERT: D 52 CYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7641 (m) REVERT: D 56 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7895 (tpp-160) outliers start: 56 outliers final: 35 residues processed: 128 average time/residue: 0.1049 time to fit residues: 21.4521 Evaluate side-chains 114 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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 B residue 44 LEU Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 122 optimal weight: 0.0870 chunk 81 optimal weight: 3.9990 chunk 146 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 654 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.096757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.061603 restraints weight = 58149.161| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 7.36 r_work: 0.3151 rms_B_bonded: 6.88 restraints_weight: 2.0000 r_work: 0.3281 rms_B_bonded: 5.30 restraints_weight: 4.0000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14679 Z= 0.217 Angle : 0.653 11.333 19894 Z= 0.329 Chirality : 0.045 0.218 2152 Planarity : 0.004 0.036 2562 Dihedral : 5.248 48.325 1938 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.35 % Allowed : 18.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.21), residues: 1725 helix: -0.66 (0.32), residues: 289 sheet: -0.20 (0.27), residues: 345 loop : -0.90 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 145 TYR 0.015 0.001 TYR A 394 PHE 0.017 0.002 PHE B 91 TRP 0.008 0.001 TRP A 439 HIS 0.008 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00494 (14645) covalent geometry : angle 0.65176 (19826) SS BOND : bond 0.00239 ( 34) SS BOND : angle 0.95042 ( 68) hydrogen bonds : bond 0.03579 ( 376) hydrogen bonds : angle 6.34758 ( 1011) *********************** 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 143 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 73 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 833 MET cc_start: 0.9299 (pmm) cc_final: 0.8961 (pmm) REVERT: B 83 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8615 (ttt) REVERT: D 52 CYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7571 (m) REVERT: D 56 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7839 (tpp-160) REVERT: F 53 ASP cc_start: 0.8018 (m-30) cc_final: 0.7786 (m-30) outliers start: 70 outliers final: 50 residues processed: 133 average time/residue: 0.0957 time to fit residues: 20.5684 Evaluate side-chains 124 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 72 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 486 LEU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 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 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 164 optimal weight: 2.9990 chunk 159 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- 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 424 ASN B 575 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.097582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.062410 restraints weight = 57353.300| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 7.36 r_work: 0.3185 rms_B_bonded: 7.34 restraints_weight: 2.0000 r_work: 0.3311 rms_B_bonded: 5.35 restraints_weight: 4.0000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14679 Z= 0.151 Angle : 0.603 11.268 19894 Z= 0.303 Chirality : 0.043 0.179 2152 Planarity : 0.004 0.035 2562 Dihedral : 5.055 44.258 1938 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.23 % Allowed : 18.66 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.21), residues: 1725 helix: -0.57 (0.32), residues: 289 sheet: -0.10 (0.28), residues: 345 loop : -0.86 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 21 TYR 0.012 0.001 TYR A 259 PHE 0.015 0.001 PHE B 91 TRP 0.011 0.001 TRP A 439 HIS 0.004 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00343 (14645) covalent geometry : angle 0.60218 (19826) SS BOND : bond 0.00177 ( 34) SS BOND : angle 0.70074 ( 68) hydrogen bonds : bond 0.03228 ( 376) hydrogen bonds : angle 6.11432 ( 1011) *********************** 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 151 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 83 time to evaluate : 0.517 Fit side-chains REVERT: A 513 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8022 (mm) REVERT: B 575 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7187 (m90) REVERT: D 12 ASP cc_start: 0.9735 (m-30) cc_final: 0.9377 (p0) REVERT: D 52 CYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7467 (m) REVERT: D 56 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7848 (tpp-160) outliers start: 68 outliers final: 47 residues processed: 139 average time/residue: 0.1004 time to fit residues: 21.9985 Evaluate side-chains 128 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 78 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU 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 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 615 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain 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 306 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 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 575 HIS Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 61 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 89 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.095775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.060677 restraints weight = 57804.693| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 6.66 r_work: 0.3126 rms_B_bonded: 6.59 restraints_weight: 2.0000 r_work: 0.3250 rms_B_bonded: 5.13 restraints_weight: 4.0000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 14679 Z= 0.302 Angle : 0.709 11.496 19894 Z= 0.356 Chirality : 0.046 0.246 2152 Planarity : 0.004 0.038 2562 Dihedral : 5.398 46.635 1938 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 5.22 % Allowed : 17.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.21), residues: 1725 helix: -0.76 (0.31), residues: 291 sheet: -0.38 (0.27), residues: 352 loop : -1.05 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 145 TYR 0.021 0.002 TYR B 428 PHE 0.020 0.002 PHE B 91 TRP 0.009 0.002 TRP B 556 HIS 0.018 0.001 HIS B 575 Details of bonding type rmsd covalent geometry : bond 0.00690 (14645) covalent geometry : angle 0.70837 (19826) SS BOND : bond 0.00301 ( 34) SS BOND : angle 0.91726 ( 68) hydrogen bonds : bond 0.03604 ( 376) hydrogen bonds : angle 6.22413 ( 1011) *********************** 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 157 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 73 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8342 (ttt) REVERT: D 52 CYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7611 (m) outliers start: 84 outliers final: 63 residues processed: 145 average time/residue: 0.1160 time to fit residues: 25.9324 Evaluate side-chains 134 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 69 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 486 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 581 ARG Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 57 LEU 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 162 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.4108 r_free = 0.4108 target = 0.096962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.061605 restraints weight = 57311.308| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 7.38 r_work: 0.3175 rms_B_bonded: 7.36 restraints_weight: 2.0000 r_work: 0.3290 rms_B_bonded: 5.41 restraints_weight: 4.0000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14679 Z= 0.167 Angle : 0.642 11.070 19894 Z= 0.320 Chirality : 0.044 0.190 2152 Planarity : 0.004 0.035 2562 Dihedral : 5.172 43.957 1938 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.48 % Allowed : 18.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.21), residues: 1725 helix: -0.71 (0.31), residues: 296 sheet: -0.23 (0.28), residues: 347 loop : -1.01 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 506 TYR 0.013 0.001 TYR A 259 PHE 0.018 0.001 PHE B 91 TRP 0.012 0.001 TRP A 439 HIS 0.006 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00380 (14645) covalent geometry : angle 0.64154 (19826) SS BOND : bond 0.00193 ( 34) SS BOND : angle 0.70435 ( 68) hydrogen bonds : bond 0.03253 ( 376) hydrogen bonds : angle 6.02049 ( 1011) *********************** 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 147 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 75 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: B 575 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7743 (m170) REVERT: B 725 GLU cc_start: 0.8190 (pm20) cc_final: 0.7936 (pm20) outliers start: 72 outliers final: 59 residues processed: 134 average time/residue: 0.1117 time to fit residues: 23.3502 Evaluate side-chains 131 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 71 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 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 615 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 THR 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 199 THR 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 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 575 HIS Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 48 CYS 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 Chi-restraints excluded: chain F residue 14 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 13 optimal weight: 4.9990 chunk 127 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.097846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.063110 restraints weight = 56964.011| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 6.44 r_work: 0.3182 rms_B_bonded: 6.40 restraints_weight: 2.0000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14679 Z= 0.125 Angle : 0.626 10.767 19894 Z= 0.310 Chirality : 0.043 0.163 2152 Planarity : 0.003 0.034 2562 Dihedral : 5.011 40.303 1938 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.10 % Allowed : 18.35 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.21), residues: 1725 helix: -0.67 (0.31), residues: 296 sheet: -0.16 (0.28), residues: 352 loop : -0.94 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 506 TYR 0.014 0.001 TYR A 259 PHE 0.016 0.001 PHE B 91 TRP 0.020 0.001 TRP B 659 HIS 0.004 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00284 (14645) covalent geometry : angle 0.62589 (19826) SS BOND : bond 0.00159 ( 34) SS BOND : angle 0.60884 ( 68) hydrogen bonds : bond 0.03041 ( 376) hydrogen bonds : angle 5.90015 ( 1011) *********************** 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 146 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 80 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.8564 (ttt) cc_final: 0.8219 (ttt) REVERT: B 321 MET cc_start: 0.8341 (tpt) cc_final: 0.7847 (tpp) REVERT: D 56 ARG cc_start: 0.7996 (mmm160) cc_final: 0.7720 (tpp-160) outliers start: 66 outliers final: 56 residues processed: 133 average time/residue: 0.1077 time to fit residues: 22.9812 Evaluate side-chains 131 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 75 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 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 516 TRP Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 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 621 ASN Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 14 LEU 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 86 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 71 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.097260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.062402 restraints weight = 57216.599| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 6.59 r_work: 0.3162 rms_B_bonded: 6.47 restraints_weight: 2.0000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14679 Z= 0.167 Angle : 0.661 10.821 19894 Z= 0.328 Chirality : 0.044 0.193 2152 Planarity : 0.004 0.080 2562 Dihedral : 5.092 39.805 1938 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.17 % Allowed : 18.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.21), residues: 1725 helix: -0.69 (0.32), residues: 296 sheet: -0.19 (0.28), residues: 354 loop : -0.95 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 21 TYR 0.015 0.001 TYR B 806 PHE 0.016 0.001 PHE B 91 TRP 0.011 0.001 TRP A 439 HIS 0.006 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00384 (14645) covalent geometry : angle 0.65588 (19826) SS BOND : bond 0.00190 ( 34) SS BOND : angle 1.48728 ( 68) hydrogen bonds : bond 0.03196 ( 376) hydrogen bonds : angle 5.90615 ( 1011) *********************** 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 138 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 71 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.8626 (ttt) cc_final: 0.8295 (ttt) REVERT: A 321 MET cc_start: 0.8404 (tpp) cc_final: 0.7835 (tpp) REVERT: B 321 MET cc_start: 0.8369 (tpt) cc_final: 0.7646 (tpp) REVERT: D 56 ARG cc_start: 0.8047 (mmm160) cc_final: 0.7806 (tpp-160) REVERT: F 12 ASP cc_start: 0.9686 (m-30) cc_final: 0.9406 (p0) outliers start: 67 outliers final: 62 residues processed: 129 average time/residue: 0.1025 time to fit residues: 21.5020 Evaluate side-chains 133 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 71 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 516 TRP Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 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 85 THR 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 273 TYR 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 475 THR Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 14 LEU 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 138 optimal weight: 0.0670 chunk 172 optimal weight: 0.7980 chunk 126 optimal weight: 8.9990 chunk 170 optimal weight: 0.0170 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS A 303 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.098629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063631 restraints weight = 57169.940| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 6.94 r_work: 0.3210 rms_B_bonded: 6.78 restraints_weight: 2.0000 r_work: 0.3340 rms_B_bonded: 5.24 restraints_weight: 4.0000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14679 Z= 0.104 Angle : 0.636 10.598 19894 Z= 0.312 Chirality : 0.043 0.159 2152 Planarity : 0.004 0.061 2562 Dihedral : 4.842 32.550 1938 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.92 % Allowed : 19.40 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.21), residues: 1725 helix: -0.66 (0.31), residues: 296 sheet: -0.07 (0.28), residues: 348 loop : -0.86 (0.20), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 21 TYR 0.016 0.001 TYR A 259 PHE 0.014 0.001 PHE B 91 TRP 0.018 0.001 TRP B 439 HIS 0.004 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00235 (14645) covalent geometry : angle 0.63461 (19826) SS BOND : bond 0.00149 ( 34) SS BOND : angle 0.98495 ( 68) hydrogen bonds : bond 0.02990 ( 376) hydrogen bonds : angle 5.76035 ( 1011) ********************** 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 121 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 74 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.8445 (ttt) cc_final: 0.8086 (ttt) REVERT: A 321 MET cc_start: 0.8287 (tpp) cc_final: 0.7650 (tpp) REVERT: B 321 MET cc_start: 0.8222 (tpt) cc_final: 0.7823 (tpp) REVERT: B 725 GLU cc_start: 0.8147 (pm20) cc_final: 0.6949 (tm-30) REVERT: F 12 ASP cc_start: 0.9647 (m-30) cc_final: 0.9333 (p0) REVERT: F 53 ASP cc_start: 0.8087 (m-30) cc_final: 0.7864 (m-30) outliers start: 47 outliers final: 42 residues processed: 112 average time/residue: 0.1030 time to fit residues: 18.6194 Evaluate side-chains 116 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 74 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 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 575 HIS Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 48 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 542 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 30.0000 chunk 147 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 138 optimal weight: 0.0470 chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN B 575 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.098904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.064031 restraints weight = 57467.851| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 7.02 r_work: 0.3225 rms_B_bonded: 6.81 restraints_weight: 2.0000 r_work: 0.3353 rms_B_bonded: 5.33 restraints_weight: 4.0000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14679 Z= 0.103 Angle : 0.635 11.375 19894 Z= 0.307 Chirality : 0.043 0.234 2152 Planarity : 0.004 0.052 2562 Dihedral : 4.673 24.297 1938 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.74 % Allowed : 19.84 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.21), residues: 1725 helix: -0.63 (0.32), residues: 297 sheet: 0.01 (0.28), residues: 348 loop : -0.82 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 21 TYR 0.014 0.001 TYR A 259 PHE 0.014 0.001 PHE B 91 TRP 0.015 0.001 TRP B 439 HIS 0.003 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00233 (14645) covalent geometry : angle 0.63427 (19826) SS BOND : bond 0.00148 ( 34) SS BOND : angle 0.83492 ( 68) hydrogen bonds : bond 0.02875 ( 376) hydrogen bonds : angle 5.65208 ( 1011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6704.34 seconds wall clock time: 114 minutes 45.59 seconds (6885.59 seconds total)