Starting phenix.real_space_refine on Mon Apr 6 06:46:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m7e_23710/04_2026/7m7e_23710.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m7e_23710/04_2026/7m7e_23710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m7e_23710/04_2026/7m7e_23710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m7e_23710/04_2026/7m7e_23710.map" model { file = "/net/cci-nas-00/data/ceres_data/7m7e_23710/04_2026/7m7e_23710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m7e_23710/04_2026/7m7e_23710.cif" } resolution = 3.2 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= 0.001 sd= 0.061 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 48 5.16 5 C 10371 2.51 5 N 3016 2.21 5 O 3242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16677 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 6771 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 861} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 6771 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 861} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 2 Chain: "D" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1596 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 2 Time building chain proxies: 3.67, per 1000 atoms: 0.22 Number of scatterers: 16677 At special positions: 0 Unit cell: (94.6, 117.7, 196.9, 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 48 16.00 O 3242 8.00 N 3016 7.00 C 10371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.04 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 216 " 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: 1.40 Conformation dependent library (CDL) restraints added in 687.5 milliseconds 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4024 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 23 sheets defined 33.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'B' and resid 9 through 15 removed outlier: 3.873A pdb=" N ARG B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 105 through 110 removed outlier: 3.891A pdb=" N PHE B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.762A pdb=" N ARG B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 removed outlier: 4.144A pdb=" N GLY B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 221 Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.593A pdb=" N GLN B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 311 through 325 removed outlier: 3.989A pdb=" N GLN B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 removed outlier: 3.875A pdb=" N ILE B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 415 through 419 removed outlier: 4.227A pdb=" N SER B 418 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 419 " --> pdb=" O TRP B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 419' Processing helix chain 'B' and resid 482 through 497 Processing helix chain 'B' and resid 503 through 514 Processing helix chain 'B' and resid 528 through 541 removed outlier: 3.697A pdb=" N ALA B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 583 Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.711A pdb=" N ALA B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 601 No H-bonds generated for 'chain 'B' and resid 599 through 601' Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 620 through 641 Proline residue: B 626 - end of helix Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 667 through 685 removed outlier: 3.809A pdb=" N SER B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 705 Processing helix chain 'B' and resid 728 through 740 Processing helix chain 'B' and resid 759 through 769 removed outlier: 3.737A pdb=" N ARG B 762 " --> pdb=" O GLN B 759 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 808 Processing helix chain 'B' and resid 811 through 821 Processing helix chain 'B' and resid 836 through 845 Processing helix chain 'B' and resid 865 through 878 removed outlier: 3.698A pdb=" N PHE B 869 " --> pdb=" O ASP B 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.558A pdb=" N VAL A 9 " --> pdb=" O ASP A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 32 removed outlier: 3.566A pdb=" N LEU A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.892A pdb=" N PHE A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.762A pdb=" N ARG A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 4.145A pdb=" N GLY A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 221 Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.593A pdb=" N GLN A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.989A pdb=" N GLN A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 removed outlier: 3.874A pdb=" N ILE A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 415 through 419 removed outlier: 4.227A pdb=" N SER A 418 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 419 " --> pdb=" O TRP A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 419' Processing helix chain 'A' and resid 482 through 497 Processing helix chain 'A' and resid 503 through 514 Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.698A pdb=" N ALA A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 583 through 598 removed outlier: 3.711A pdb=" N ALA A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 620 through 641 Proline residue: A 626 - end of helix Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 667 through 685 removed outlier: 3.807A pdb=" N SER A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 760 through 762 No H-bonds generated for 'chain 'A' and resid 760 through 762' Processing helix chain 'A' and resid 763 through 771 removed outlier: 4.165A pdb=" N LEU A 767 " --> pdb=" O VAL A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 811 through 821 Processing helix chain 'A' and resid 836 through 845 Processing helix chain 'A' and resid 865 through 878 removed outlier: 3.876A pdb=" N PHE A 869 " --> pdb=" O ASP A 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 removed outlier: 4.121A pdb=" N THR C 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 4.126A pdb=" N VAL D 104 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 205 through 212 removed outlier: 4.132A pdb=" N LYS D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 197 through 200 removed outlier: 3.967A pdb=" N SER B 39 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU B 277 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE B 37 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA B 291 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY B 295 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 371 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU B 368 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'B' and resid 400 through 401 Processing sheet with id=AA4, first strand: chain 'B' and resid 474 through 480 Processing sheet with id=AA5, first strand: chain 'B' and resid 782 through 783 removed outlier: 7.071A pdb=" N ALA B 647 " --> pdb=" O THR B 782 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 561 " --> pdb=" O PRO B 646 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 648 " --> pdb=" O VAL B 561 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 716 through 717 removed outlier: 4.307A pdb=" N ALA B 716 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 724 " --> pdb=" O ALA B 716 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET B 691 " --> pdb=" O ILE B 749 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 197 through 200 removed outlier: 3.967A pdb=" N SER A 39 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU A 277 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE A 37 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 291 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A 454 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER A 296 " --> pdb=" O HIS A 452 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS A 452 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 298 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN A 450 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A 335 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 440 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 442 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 336 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU A 368 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 401 Processing sheet with id=AB1, first strand: chain 'A' and resid 474 through 480 Processing sheet with id=AB2, first strand: chain 'A' and resid 782 through 783 removed outlier: 7.071A pdb=" N ALA A 647 " --> pdb=" O THR A 782 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 561 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 648 " --> pdb=" O VAL A 561 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 717 removed outlier: 4.307A pdb=" N ALA A 716 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 724 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET A 691 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AB6, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.782A pdb=" N GLY C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 13 through 14 removed outlier: 4.226A pdb=" N TYR C 109 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.756A pdb=" N GLY C 146 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR C 183 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 188 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AC1, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AC2, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.548A pdb=" N TRP D 56 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR D 70 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU D 54 " --> pdb=" O TYR D 70 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.629A pdb=" N LEU D 201 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS D 156 " --> pdb=" O SER D 199 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER D 199 " --> pdb=" O CYS D 156 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 182 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.553A pdb=" N TYR D 195 " --> pdb=" O ASN D 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 167 through 170 removed outlier: 4.159A pdb=" N LYS D 167 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR D 219 " --> pdb=" O LYS D 167 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2893 1.28 - 1.41: 4059 1.41 - 1.55: 9937 1.55 - 1.68: 38 1.68 - 1.81: 78 Bond restraints: 17005 Sorted by residual: bond pdb=" C ARG B 440 " pdb=" O ARG B 440 " ideal model delta sigma weight residual 1.234 1.149 0.085 1.22e-02 6.72e+03 4.83e+01 bond pdb=" C GLU B 456 " pdb=" O GLU B 456 " ideal model delta sigma weight residual 1.235 1.177 0.058 1.14e-02 7.69e+03 2.61e+01 bond pdb=" CA ALA A 439 " pdb=" CB ALA A 439 " ideal model delta sigma weight residual 1.533 1.451 0.082 1.65e-02 3.67e+03 2.45e+01 bond pdb=" CA SER A 442 " pdb=" CB SER A 442 " ideal model delta sigma weight residual 1.532 1.443 0.089 1.82e-02 3.02e+03 2.37e+01 bond pdb=" CA ALA A 335 " pdb=" CB ALA A 335 " ideal model delta sigma weight residual 1.530 1.449 0.082 1.69e-02 3.50e+03 2.33e+01 ... (remaining 17000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 22911 4.76 - 9.52: 199 9.52 - 14.28: 10 14.28 - 19.04: 3 19.04 - 23.80: 2 Bond angle restraints: 23125 Sorted by residual: angle pdb=" C ASP A 334 " pdb=" CA ASP A 334 " pdb=" CB ASP A 334 " ideal model delta sigma weight residual 109.55 87.82 21.73 1.68e+00 3.54e-01 1.67e+02 angle pdb=" C ARG B 790 " pdb=" CA ARG B 790 " pdb=" CB ARG B 790 " ideal model delta sigma weight residual 109.94 86.14 23.80 2.13e+00 2.20e-01 1.25e+02 angle pdb=" CA PHE B 265 " pdb=" CB PHE B 265 " pdb=" CG PHE B 265 " ideal model delta sigma weight residual 113.80 123.68 -9.88 1.00e+00 1.00e+00 9.77e+01 angle pdb=" N ALA A 16 " pdb=" CA ALA A 16 " pdb=" C ALA A 16 " ideal model delta sigma weight residual 113.88 104.06 9.82 1.23e+00 6.61e-01 6.37e+01 angle pdb=" C PHE B 265 " pdb=" CA PHE B 265 " pdb=" CB PHE B 265 " ideal model delta sigma weight residual 110.45 96.95 13.50 1.73e+00 3.34e-01 6.09e+01 ... (remaining 23120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 9198 17.71 - 35.41: 560 35.41 - 53.12: 241 53.12 - 70.83: 151 70.83 - 88.54: 25 Dihedral angle restraints: 10175 sinusoidal: 3884 harmonic: 6291 Sorted by residual: dihedral pdb=" C ARG B 790 " pdb=" N ARG B 790 " pdb=" CA ARG B 790 " pdb=" CB ARG B 790 " ideal model delta harmonic sigma weight residual -122.60 -89.88 -32.72 0 2.50e+00 1.60e-01 1.71e+02 dihedral pdb=" C ASP A 334 " pdb=" N ASP A 334 " pdb=" CA ASP A 334 " pdb=" CB ASP A 334 " ideal model delta harmonic sigma weight residual -122.60 -97.57 -25.03 0 2.50e+00 1.60e-01 1.00e+02 dihedral pdb=" N ARG B 790 " pdb=" C ARG B 790 " pdb=" CA ARG B 790 " pdb=" CB ARG B 790 " ideal model delta harmonic sigma weight residual 122.80 98.86 23.94 0 2.50e+00 1.60e-01 9.17e+01 ... (remaining 10172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2453 0.109 - 0.219: 122 0.219 - 0.328: 17 0.328 - 0.437: 8 0.437 - 0.547: 3 Chirality restraints: 2603 Sorted by residual: chirality pdb=" CA HIS A 339 " pdb=" N HIS A 339 " pdb=" C HIS A 339 " pdb=" CB HIS A 339 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.47e+00 chirality pdb=" CA ARG B 790 " pdb=" N ARG B 790 " pdb=" C ARG B 790 " pdb=" CB ARG B 790 " both_signs ideal model delta sigma weight residual False 2.51 3.05 -0.54 2.00e-01 2.50e+01 7.30e+00 chirality pdb=" CB VAL B 763 " pdb=" CA VAL B 763 " pdb=" CG1 VAL B 763 " pdb=" CG2 VAL B 763 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.91e+00 ... (remaining 2600 not shown) Planarity restraints: 3080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 800 " 0.833 9.50e-02 1.11e+02 3.73e-01 8.56e+01 pdb=" NE ARG A 800 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 800 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 800 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 800 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 798 " -0.031 2.00e-02 2.50e+03 6.32e-02 3.99e+01 pdb=" C ASP B 798 " 0.109 2.00e-02 2.50e+03 pdb=" O ASP B 798 " -0.043 2.00e-02 2.50e+03 pdb=" N ALA B 799 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 864 " -0.023 2.00e-02 2.50e+03 4.83e-02 2.34e+01 pdb=" C GLY A 864 " 0.084 2.00e-02 2.50e+03 pdb=" O GLY A 864 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP A 865 " -0.029 2.00e-02 2.50e+03 ... (remaining 3077 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 507 2.70 - 3.25: 15325 3.25 - 3.80: 24938 3.80 - 4.35: 32359 4.35 - 4.90: 55204 Nonbonded interactions: 128333 Sorted by model distance: nonbonded pdb=" O THR A 771 " pdb=" OG1 THR A 771 " model vdw 2.151 3.040 nonbonded pdb=" O THR B 771 " pdb=" OG1 THR B 771 " model vdw 2.151 3.040 nonbonded pdb=" O GLY C 111 " pdb=" OG SER D 64 " model vdw 2.213 3.040 nonbonded pdb=" NH2 ARG A 711 " pdb=" O VAL A 724 " model vdw 2.272 3.120 nonbonded pdb=" OG SER C 19 " pdb=" OD1 ASN C 88 " model vdw 2.272 3.040 ... (remaining 128328 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 4 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 911)) selection = (chain 'B' and (resid 4 through 439 or (resid 440 and (name N or name CA or name \ C or name O or name CB )) or resid 441 through 911)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 2.390 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.850 Find NCS groups from input model: 0.240 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 0.006 0.089 17008 Z= 0.395 Angle : 1.086 23.800 23131 Z= 0.683 Chirality : 0.062 0.547 2603 Planarity : 0.011 0.373 3080 Dihedral : 16.734 88.536 6142 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 9.50 % Allowed : 3.94 % Favored : 86.57 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 3.42 % 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 are not related in a simple way. whole: -1.47 (0.17), residues: 2214 helix: -0.08 (0.20), residues: 702 sheet: -0.32 (0.26), residues: 410 loop : -1.85 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 764 TYR 0.051 0.002 TYR B 753 PHE 0.057 0.001 PHE B 265 TRP 0.019 0.001 TRP B 430 HIS 0.017 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00585 (17005) covalent geometry : angle 1.08585 (23125) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.53742 ( 6) hydrogen bonds : bond 0.15318 ( 674) hydrogen bonds : angle 6.50549 ( 1926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 236 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 VAL cc_start: 0.7764 (OUTLIER) cc_final: 0.7508 (t) REVERT: B 12 TYR cc_start: 0.8049 (m-10) cc_final: 0.7752 (m-80) REVERT: B 201 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6755 (m-30) REVERT: B 225 MET cc_start: 0.7856 (mtt) cc_final: 0.7514 (mtm) REVERT: B 265 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.6464 (p90) REVERT: B 409 GLU cc_start: 0.5691 (OUTLIER) cc_final: 0.5251 (pm20) REVERT: B 415 ASP cc_start: 0.6145 (OUTLIER) cc_final: 0.5726 (t0) REVERT: B 464 ARG cc_start: 0.2601 (OUTLIER) cc_final: 0.2258 (tpt90) REVERT: B 465 GLU cc_start: -0.3181 (OUTLIER) cc_final: -0.3414 (tp30) REVERT: B 557 ASP cc_start: 0.5082 (OUTLIER) cc_final: 0.4691 (t0) REVERT: B 764 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7386 (ttt90) REVERT: B 800 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7274 (mmt90) REVERT: A 11 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6444 (tp30) REVERT: A 60 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.5966 (mp0) REVERT: A 63 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: A 100 ASP cc_start: 0.7536 (t0) cc_final: 0.7269 (t70) REVERT: A 201 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7245 (t0) REVERT: A 247 ARG cc_start: 0.8054 (mtt90) cc_final: 0.7616 (mtt180) REVERT: A 337 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7003 (mm-30) REVERT: A 415 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6356 (m-30) REVERT: A 465 GLU cc_start: -0.3621 (OUTLIER) cc_final: -0.5378 (tm-30) REVERT: A 495 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6434 (mp0) REVERT: A 557 ASP cc_start: 0.5865 (OUTLIER) cc_final: 0.5438 (t0) REVERT: A 669 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: A 752 ASP cc_start: 0.7606 (t0) cc_final: 0.7406 (t0) REVERT: A 808 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6220 (pm20) REVERT: C 84 TYR cc_start: 0.7897 (m-80) cc_final: 0.7581 (m-80) REVERT: C 99 TYR cc_start: 0.7067 (m-80) cc_final: 0.6851 (m-80) outliers start: 164 outliers final: 27 residues processed: 358 average time/residue: 0.1963 time to fit residues: 94.4997 Evaluate side-chains 210 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 764 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 841 GLU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 53 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.0040 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 0.5980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 GLN A 81 HIS ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.198950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.143150 restraints weight = 20801.481| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.44 r_work: 0.3762 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17008 Z= 0.135 Angle : 0.583 6.421 23131 Z= 0.306 Chirality : 0.044 0.173 2603 Planarity : 0.005 0.061 3080 Dihedral : 8.641 92.686 2548 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.18 % Allowed : 9.09 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 are not related in a simple way. whole: -1.04 (0.17), residues: 2214 helix: 0.48 (0.20), residues: 730 sheet: -0.10 (0.26), residues: 401 loop : -1.78 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 764 TYR 0.024 0.002 TYR A 803 PHE 0.013 0.001 PHE C 31 TRP 0.013 0.001 TRP C 110 HIS 0.006 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00309 (17005) covalent geometry : angle 0.58351 (23125) SS BOND : bond 0.00255 ( 3) SS BOND : angle 0.43767 ( 6) hydrogen bonds : bond 0.03969 ( 674) hydrogen bonds : angle 4.62335 ( 1926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 TYR cc_start: 0.8141 (m-10) cc_final: 0.7937 (m-80) REVERT: B 201 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7053 (m-30) REVERT: B 225 MET cc_start: 0.8569 (mtt) cc_final: 0.8322 (mtm) REVERT: B 265 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7625 (p90) REVERT: B 337 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: B 415 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6534 (t0) REVERT: B 440 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.6034 (mpp80) REVERT: B 464 ARG cc_start: 0.3033 (OUTLIER) cc_final: 0.2791 (mmt180) REVERT: B 465 GLU cc_start: -0.3272 (OUTLIER) cc_final: -0.3538 (tp30) REVERT: B 557 ASP cc_start: 0.5722 (OUTLIER) cc_final: 0.5466 (t0) REVERT: B 696 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6802 (mp) REVERT: B 800 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6757 (mmt90) REVERT: A 60 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6668 (mt-10) REVERT: A 178 VAL cc_start: 0.8751 (m) cc_final: 0.8544 (t) REVERT: A 201 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.6842 (m-30) REVERT: A 247 ARG cc_start: 0.8478 (mtt90) cc_final: 0.8061 (mtt180) REVERT: A 281 GLU cc_start: 0.8106 (mp0) cc_final: 0.7620 (mt-10) REVERT: A 415 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6563 (t0) REVERT: A 495 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7061 (mp0) REVERT: A 674 LEU cc_start: 0.7543 (mt) cc_final: 0.7307 (mt) outliers start: 55 outliers final: 18 residues processed: 217 average time/residue: 0.1706 time to fit residues: 52.2411 Evaluate side-chains 176 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 53 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 215 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 GLN A 81 HIS ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.188974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.132894 restraints weight = 20922.559| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.39 r_work: 0.3624 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17008 Z= 0.194 Angle : 0.621 7.664 23131 Z= 0.326 Chirality : 0.046 0.179 2603 Planarity : 0.005 0.067 3080 Dihedral : 6.864 83.883 2486 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.32 % Allowed : 11.75 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 are not related in a simple way. whole: -0.99 (0.17), residues: 2214 helix: 0.55 (0.20), residues: 727 sheet: -0.03 (0.26), residues: 404 loop : -1.80 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 78 TYR 0.020 0.002 TYR B 358 PHE 0.019 0.002 PHE A 152 TRP 0.014 0.002 TRP A 802 HIS 0.005 0.001 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00484 (17005) covalent geometry : angle 0.62102 (23125) SS BOND : bond 0.00216 ( 3) SS BOND : angle 0.39489 ( 6) hydrogen bonds : bond 0.04963 ( 674) hydrogen bonds : angle 4.51148 ( 1926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 TYR cc_start: 0.8229 (m-10) cc_final: 0.7979 (m-80) REVERT: B 180 PRO cc_start: 0.8928 (Cg_endo) cc_final: 0.8704 (Cg_exo) REVERT: B 201 ASP cc_start: 0.7982 (t0) cc_final: 0.7374 (m-30) REVERT: B 415 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7518 (t0) REVERT: B 440 ARG cc_start: 0.6926 (mpp80) cc_final: 0.6289 (mpp80) REVERT: B 465 GLU cc_start: -0.3013 (OUTLIER) cc_final: -0.3324 (tp30) REVERT: B 698 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6904 (tm-30) REVERT: B 705 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5939 (tp) REVERT: B 738 ASP cc_start: 0.7700 (m-30) cc_final: 0.7395 (p0) REVERT: B 800 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6915 (mmm160) REVERT: A 15 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7890 (tpp-160) REVERT: A 201 ASP cc_start: 0.8365 (t0) cc_final: 0.8046 (t70) REVERT: A 247 ARG cc_start: 0.8547 (mtt90) cc_final: 0.8161 (mtt180) REVERT: A 281 GLU cc_start: 0.8110 (mp0) cc_final: 0.7694 (mm-30) REVERT: A 301 ASP cc_start: 0.7900 (m-30) cc_final: 0.7589 (m-30) REVERT: A 495 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7293 (mm-30) REVERT: C 69 LYS cc_start: 0.5500 (tppt) cc_final: 0.5150 (tppt) REVERT: C 108 ASP cc_start: 0.8805 (t0) cc_final: 0.8535 (t0) outliers start: 40 outliers final: 21 residues processed: 194 average time/residue: 0.1673 time to fit residues: 46.3534 Evaluate side-chains 170 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 53 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 2 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 122 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 GLN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.192226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.136148 restraints weight = 20656.256| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.34 r_work: 0.3624 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17008 Z= 0.111 Angle : 0.507 8.151 23131 Z= 0.266 Chirality : 0.042 0.167 2603 Planarity : 0.004 0.054 3080 Dihedral : 5.895 78.780 2465 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.37 % Allowed : 13.09 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 are not related in a simple way. whole: -0.66 (0.18), residues: 2214 helix: 0.91 (0.20), residues: 728 sheet: 0.16 (0.26), residues: 393 loop : -1.65 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 591 TYR 0.017 0.001 TYR B 358 PHE 0.013 0.001 PHE A 152 TRP 0.009 0.001 TRP A 639 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00260 (17005) covalent geometry : angle 0.50749 (23125) SS BOND : bond 0.00278 ( 3) SS BOND : angle 0.19318 ( 6) hydrogen bonds : bond 0.03455 ( 674) hydrogen bonds : angle 4.15141 ( 1926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 TYR cc_start: 0.8134 (m-10) cc_final: 0.7885 (m-80) REVERT: B 60 GLU cc_start: 0.6395 (mm-30) cc_final: 0.6172 (mm-30) REVERT: B 180 PRO cc_start: 0.8867 (Cg_endo) cc_final: 0.8662 (Cg_exo) REVERT: B 201 ASP cc_start: 0.7976 (t0) cc_final: 0.7491 (m-30) REVERT: B 337 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6811 (mm-30) REVERT: B 415 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7837 (t0) REVERT: B 440 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6539 (mpp80) REVERT: B 465 GLU cc_start: -0.2833 (OUTLIER) cc_final: -0.3064 (tp30) REVERT: B 674 LEU cc_start: 0.6160 (mm) cc_final: 0.5904 (mm) REVERT: B 698 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6675 (tm-30) REVERT: B 705 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5487 (tp) REVERT: B 738 ASP cc_start: 0.7640 (m-30) cc_final: 0.7280 (p0) REVERT: B 800 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6813 (mmt90) REVERT: A 201 ASP cc_start: 0.8293 (t0) cc_final: 0.8010 (t70) REVERT: A 247 ARG cc_start: 0.8423 (mtt90) cc_final: 0.8037 (mtt180) REVERT: A 281 GLU cc_start: 0.8042 (mp0) cc_final: 0.7626 (mm-30) REVERT: A 301 ASP cc_start: 0.7767 (m-30) cc_final: 0.7541 (m-30) REVERT: A 495 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7291 (mm-30) REVERT: A 696 LEU cc_start: 0.4379 (OUTLIER) cc_final: 0.4143 (tt) REVERT: C 69 LYS cc_start: 0.5433 (tppt) cc_final: 0.5069 (tppt) REVERT: C 213 LYS cc_start: 0.6980 (mttt) cc_final: 0.6149 (tptt) outliers start: 41 outliers final: 24 residues processed: 193 average time/residue: 0.1609 time to fit residues: 44.5979 Evaluate side-chains 169 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain D residue 53 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 13 optimal weight: 0.0020 chunk 6 optimal weight: 0.0270 chunk 106 optimal weight: 0.0270 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 194 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 216 optimal weight: 20.0000 overall best weight: 0.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.194676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.139223 restraints weight = 20635.554| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.30 r_work: 0.3732 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17008 Z= 0.089 Angle : 0.478 8.282 23131 Z= 0.248 Chirality : 0.041 0.158 2603 Planarity : 0.004 0.051 3080 Dihedral : 5.177 56.250 2462 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.61 % Allowed : 13.61 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 are not related in a simple way. whole: -0.34 (0.18), residues: 2214 helix: 1.24 (0.20), residues: 727 sheet: 0.29 (0.26), residues: 411 loop : -1.52 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.018 0.001 TYR B 358 PHE 0.009 0.001 PHE B 243 TRP 0.009 0.001 TRP A 55 HIS 0.005 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00200 (17005) covalent geometry : angle 0.47756 (23125) SS BOND : bond 0.00251 ( 3) SS BOND : angle 0.20784 ( 6) hydrogen bonds : bond 0.02930 ( 674) hydrogen bonds : angle 3.93322 ( 1926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8069 (tmm160) REVERT: B 86 ASN cc_start: 0.6707 (t0) cc_final: 0.6236 (p0) REVERT: B 201 ASP cc_start: 0.7983 (t0) cc_final: 0.7597 (m-30) REVERT: B 337 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: B 415 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7967 (t70) REVERT: B 440 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6381 (mpp80) REVERT: B 465 GLU cc_start: -0.2591 (OUTLIER) cc_final: -0.2820 (tp30) REVERT: B 487 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7343 (mtt-85) REVERT: B 597 MET cc_start: 0.7039 (mtt) cc_final: 0.5834 (ttm) REVERT: B 674 LEU cc_start: 0.6625 (mm) cc_final: 0.6310 (mm) REVERT: B 698 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6628 (tm-30) REVERT: B 705 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5689 (tt) REVERT: B 738 ASP cc_start: 0.7704 (m-30) cc_final: 0.7299 (p0) REVERT: A 15 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7862 (tpm170) REVERT: A 201 ASP cc_start: 0.8006 (t0) cc_final: 0.7719 (t70) REVERT: A 247 ARG cc_start: 0.8366 (mtt90) cc_final: 0.8006 (mtt180) REVERT: A 281 GLU cc_start: 0.8029 (mp0) cc_final: 0.7676 (mm-30) REVERT: A 301 ASP cc_start: 0.7707 (m-30) cc_final: 0.7486 (m-30) REVERT: A 495 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7150 (mm-30) REVERT: A 696 LEU cc_start: 0.4476 (OUTLIER) cc_final: 0.4265 (tt) REVERT: A 873 MET cc_start: 0.8280 (mtt) cc_final: 0.8021 (mtt) REVERT: C 69 LYS cc_start: 0.5543 (tppt) cc_final: 0.5151 (tppt) REVERT: C 122 SER cc_start: 0.5213 (p) cc_final: 0.4834 (t) REVERT: C 213 LYS cc_start: 0.7079 (mttt) cc_final: 0.6292 (tptt) outliers start: 45 outliers final: 21 residues processed: 191 average time/residue: 0.1689 time to fit residues: 45.9041 Evaluate side-chains 169 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain C residue 22 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 135 optimal weight: 0.0970 chunk 191 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 GLN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.190600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.134392 restraints weight = 20528.792| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.33 r_work: 0.3652 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17008 Z= 0.135 Angle : 0.531 8.694 23131 Z= 0.276 Chirality : 0.043 0.159 2603 Planarity : 0.004 0.060 3080 Dihedral : 4.967 59.271 2454 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.55 % Allowed : 14.53 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 are not related in a simple way. whole: -0.30 (0.18), residues: 2214 helix: 1.20 (0.20), residues: 723 sheet: 0.30 (0.26), residues: 417 loop : -1.43 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 360 TYR 0.015 0.002 TYR B 358 PHE 0.018 0.001 PHE A 152 TRP 0.012 0.001 TRP A 55 HIS 0.004 0.001 HIS D 47 Details of bonding type rmsd covalent geometry : bond 0.00330 (17005) covalent geometry : angle 0.53132 (23125) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.23749 ( 6) hydrogen bonds : bond 0.03907 ( 674) hydrogen bonds : angle 4.03590 ( 1926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6606 (mm-30) REVERT: B 201 ASP cc_start: 0.8146 (t0) cc_final: 0.7631 (m-30) REVERT: B 337 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: B 440 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6444 (mpp80) REVERT: B 487 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7487 (mtt-85) REVERT: B 674 LEU cc_start: 0.6666 (mm) cc_final: 0.6203 (mt) REVERT: B 698 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6752 (tm-30) REVERT: A 15 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7932 (tpm170) REVERT: A 79 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.6883 (tt) REVERT: A 201 ASP cc_start: 0.8365 (t0) cc_final: 0.8072 (t70) REVERT: A 247 ARG cc_start: 0.8448 (mtt90) cc_final: 0.8110 (mtt180) REVERT: A 281 GLU cc_start: 0.8042 (mp0) cc_final: 0.7663 (mm-30) REVERT: A 301 ASP cc_start: 0.7883 (m-30) cc_final: 0.7632 (m-30) REVERT: A 355 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 495 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7279 (mm-30) REVERT: A 600 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7410 (ptm) REVERT: C 69 LYS cc_start: 0.5655 (tppt) cc_final: 0.5278 (tppt) REVERT: C 122 SER cc_start: 0.5316 (p) cc_final: 0.4960 (t) REVERT: C 213 LYS cc_start: 0.7008 (mttt) cc_final: 0.6211 (tptt) REVERT: D 63 GLN cc_start: 0.6747 (pm20) cc_final: 0.6432 (pm20) outliers start: 44 outliers final: 26 residues processed: 179 average time/residue: 0.1708 time to fit residues: 43.7950 Evaluate side-chains 173 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 22 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 204 optimal weight: 0.3980 chunk 156 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 88 optimal weight: 0.0770 chunk 210 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 86 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.191297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.135611 restraints weight = 20616.530| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.32 r_work: 0.3664 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17008 Z= 0.129 Angle : 0.524 9.005 23131 Z= 0.272 Chirality : 0.043 0.149 2603 Planarity : 0.004 0.057 3080 Dihedral : 4.570 59.840 2445 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.20 % Allowed : 15.17 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 are not related in a simple way. whole: -0.24 (0.18), residues: 2214 helix: 1.23 (0.20), residues: 724 sheet: 0.37 (0.26), residues: 414 loop : -1.40 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 78 TYR 0.023 0.001 TYR D 162 PHE 0.016 0.001 PHE A 152 TRP 0.011 0.001 TRP A 55 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00316 (17005) covalent geometry : angle 0.52440 (23125) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.18801 ( 6) hydrogen bonds : bond 0.03669 ( 674) hydrogen bonds : angle 4.00396 ( 1926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.8390 (ttp80) cc_final: 0.8048 (tmm160) REVERT: B 86 ASN cc_start: 0.6861 (t0) cc_final: 0.6349 (m-40) REVERT: B 201 ASP cc_start: 0.8342 (t0) cc_final: 0.7778 (m-30) REVERT: B 202 THR cc_start: 0.8516 (m) cc_final: 0.8259 (m) REVERT: B 337 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7116 (mm-30) REVERT: B 440 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6403 (mpp80) REVERT: B 487 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7455 (mtt-85) REVERT: B 674 LEU cc_start: 0.6544 (mm) cc_final: 0.6153 (mt) REVERT: B 698 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6699 (tm-30) REVERT: A 15 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7932 (tpm170) REVERT: A 79 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6815 (tt) REVERT: A 201 ASP cc_start: 0.8424 (t0) cc_final: 0.8110 (t70) REVERT: A 247 ARG cc_start: 0.8420 (mtt90) cc_final: 0.8055 (mtt180) REVERT: A 281 GLU cc_start: 0.8038 (mp0) cc_final: 0.7686 (mm-30) REVERT: A 301 ASP cc_start: 0.7863 (m-30) cc_final: 0.7614 (m-30) REVERT: A 355 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7969 (mp) REVERT: A 495 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7203 (mm-30) REVERT: A 600 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7501 (ptm) REVERT: C 69 LYS cc_start: 0.5579 (tppt) cc_final: 0.5171 (tppt) REVERT: C 122 SER cc_start: 0.5308 (p) cc_final: 0.4962 (t) REVERT: C 213 LYS cc_start: 0.6979 (mttt) cc_final: 0.6233 (tptt) REVERT: D 63 GLN cc_start: 0.6728 (pm20) cc_final: 0.6402 (pm20) outliers start: 38 outliers final: 24 residues processed: 175 average time/residue: 0.1632 time to fit residues: 40.9246 Evaluate side-chains 169 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 22 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 40 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 197 optimal weight: 20.0000 chunk 83 optimal weight: 0.0170 chunk 139 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 784 HIS A 81 HIS A 86 ASN ** D 22 GLN ** 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 = 0.4115 r_free = 0.4115 target = 0.174109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.115693 restraints weight = 20550.645| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.04 r_work: 0.3264 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17008 Z= 0.096 Angle : 0.489 8.874 23131 Z= 0.254 Chirality : 0.041 0.143 2603 Planarity : 0.004 0.049 3080 Dihedral : 4.329 59.816 2445 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.08 % Allowed : 15.58 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 are not related in a simple way. whole: -0.05 (0.18), residues: 2214 helix: 1.45 (0.20), residues: 726 sheet: 0.50 (0.26), residues: 397 loop : -1.31 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 78 TYR 0.028 0.001 TYR D 162 PHE 0.012 0.001 PHE A 152 TRP 0.011 0.001 TRP A 55 HIS 0.003 0.000 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00222 (17005) covalent geometry : angle 0.48946 (23125) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.15619 ( 6) hydrogen bonds : bond 0.03003 ( 674) hydrogen bonds : angle 3.84815 ( 1926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7867 (tmm160) REVERT: B 86 ASN cc_start: 0.6731 (t0) cc_final: 0.6264 (m-40) REVERT: B 201 ASP cc_start: 0.8036 (t0) cc_final: 0.7351 (m-30) REVERT: B 234 MET cc_start: 0.7987 (mtt) cc_final: 0.7357 (mtm) REVERT: B 337 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: B 440 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6376 (mpp80) REVERT: B 487 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6696 (mtt-85) REVERT: B 674 LEU cc_start: 0.6154 (mm) cc_final: 0.5734 (mt) REVERT: B 698 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6371 (tm-30) REVERT: A 60 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6457 (mp0) REVERT: A 79 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6177 (tt) REVERT: A 119 MET cc_start: 0.7765 (mtt) cc_final: 0.7543 (mtp) REVERT: A 201 ASP cc_start: 0.8303 (t0) cc_final: 0.8020 (t0) REVERT: A 247 ARG cc_start: 0.7992 (mtt90) cc_final: 0.7609 (mtt180) REVERT: A 281 GLU cc_start: 0.7774 (mp0) cc_final: 0.7480 (mm-30) REVERT: A 301 ASP cc_start: 0.7476 (m-30) cc_final: 0.7141 (m-30) REVERT: A 355 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7053 (mp) REVERT: A 495 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6650 (mm-30) REVERT: A 600 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7433 (ptm) REVERT: A 842 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7142 (mm-30) REVERT: C 122 SER cc_start: 0.5414 (p) cc_final: 0.5057 (t) REVERT: C 213 LYS cc_start: 0.6936 (mttt) cc_final: 0.6271 (tptt) REVERT: D 63 GLN cc_start: 0.6436 (pm20) cc_final: 0.6116 (pm20) outliers start: 36 outliers final: 22 residues processed: 176 average time/residue: 0.1772 time to fit residues: 44.0218 Evaluate side-chains 166 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 22 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 22 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 199 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 HIS A 246 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.132909 restraints weight = 20689.762| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.41 r_work: 0.3579 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17008 Z= 0.123 Angle : 0.520 7.499 23131 Z= 0.268 Chirality : 0.043 0.147 2603 Planarity : 0.004 0.053 3080 Dihedral : 4.425 59.817 2445 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.97 % Allowed : 15.75 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 are not related in a simple way. whole: -0.02 (0.18), residues: 2214 helix: 1.47 (0.20), residues: 721 sheet: 0.51 (0.26), residues: 406 loop : -1.28 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 78 TYR 0.028 0.002 TYR D 162 PHE 0.016 0.001 PHE A 152 TRP 0.012 0.001 TRP A 55 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00300 (17005) covalent geometry : angle 0.51987 (23125) SS BOND : bond 0.00191 ( 3) SS BOND : angle 0.21359 ( 6) hydrogen bonds : bond 0.03597 ( 674) hydrogen bonds : angle 3.90723 ( 1926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.8386 (ttp80) cc_final: 0.7991 (tmm160) REVERT: B 86 ASN cc_start: 0.7169 (t0) cc_final: 0.6758 (m-40) REVERT: B 201 ASP cc_start: 0.8160 (t0) cc_final: 0.7623 (m-30) REVERT: B 234 MET cc_start: 0.8175 (mtt) cc_final: 0.7548 (mtm) REVERT: B 337 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7196 (mm-30) REVERT: B 409 GLU cc_start: 0.7607 (pm20) cc_final: 0.7124 (pt0) REVERT: B 440 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6357 (mpp80) REVERT: B 487 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7361 (mtt-85) REVERT: B 674 LEU cc_start: 0.6546 (mm) cc_final: 0.6132 (mt) REVERT: B 698 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6525 (tm-30) REVERT: A 79 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6863 (tt) REVERT: A 201 ASP cc_start: 0.8449 (t0) cc_final: 0.8097 (t70) REVERT: A 247 ARG cc_start: 0.8386 (mtt90) cc_final: 0.7885 (mtt180) REVERT: A 281 GLU cc_start: 0.7943 (mp0) cc_final: 0.7586 (mm-30) REVERT: A 301 ASP cc_start: 0.7848 (m-30) cc_final: 0.7599 (m-30) REVERT: A 355 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7966 (mp) REVERT: A 495 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7149 (mm-30) REVERT: A 600 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7564 (ptm) REVERT: C 69 LYS cc_start: 0.5525 (tppt) cc_final: 0.5024 (tppt) REVERT: C 84 TYR cc_start: 0.7522 (m-10) cc_final: 0.7290 (m-10) REVERT: C 99 TYR cc_start: 0.6977 (m-10) cc_final: 0.6750 (m-10) REVERT: C 122 SER cc_start: 0.5487 (p) cc_final: 0.4566 (t) REVERT: C 124 LYS cc_start: 0.6880 (tptp) cc_final: 0.6635 (mttp) REVERT: C 213 LYS cc_start: 0.6989 (mttt) cc_final: 0.6271 (tptt) REVERT: D 63 GLN cc_start: 0.6666 (pm20) cc_final: 0.6314 (pm20) outliers start: 34 outliers final: 26 residues processed: 170 average time/residue: 0.1651 time to fit residues: 39.5890 Evaluate side-chains 171 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 102 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 181 optimal weight: 0.0670 chunk 97 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.189057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.133664 restraints weight = 20500.937| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.38 r_work: 0.3594 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17008 Z= 0.113 Angle : 0.517 10.954 23131 Z= 0.268 Chirality : 0.042 0.147 2603 Planarity : 0.004 0.052 3080 Dihedral : 4.359 58.877 2445 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.91 % Allowed : 15.92 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 are not related in a simple way. whole: 0.03 (0.18), residues: 2214 helix: 1.53 (0.20), residues: 720 sheet: 0.55 (0.26), residues: 400 loop : -1.27 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 78 TYR 0.026 0.001 TYR D 162 PHE 0.014 0.001 PHE A 152 TRP 0.012 0.001 TRP A 55 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00272 (17005) covalent geometry : angle 0.51736 (23125) SS BOND : bond 0.00210 ( 3) SS BOND : angle 0.20006 ( 6) hydrogen bonds : bond 0.03357 ( 674) hydrogen bonds : angle 3.86942 ( 1926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.8393 (ttp80) cc_final: 0.7994 (tmm160) REVERT: B 86 ASN cc_start: 0.7140 (t0) cc_final: 0.6873 (p0) REVERT: B 201 ASP cc_start: 0.8129 (t0) cc_final: 0.7653 (m-30) REVERT: B 234 MET cc_start: 0.8143 (mtt) cc_final: 0.7505 (mtm) REVERT: B 337 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: B 409 GLU cc_start: 0.7617 (pm20) cc_final: 0.7177 (pt0) REVERT: B 440 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6346 (mpp80) REVERT: B 487 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7327 (mtt-85) REVERT: B 674 LEU cc_start: 0.6533 (mm) cc_final: 0.6094 (mt) REVERT: B 698 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6510 (tm-30) REVERT: A 79 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6951 (tt) REVERT: A 201 ASP cc_start: 0.8414 (t0) cc_final: 0.8164 (t0) REVERT: A 247 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7861 (mtt180) REVERT: A 281 GLU cc_start: 0.7928 (mp0) cc_final: 0.7569 (mm-30) REVERT: A 301 ASP cc_start: 0.7823 (m-30) cc_final: 0.7582 (m-30) REVERT: A 355 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7843 (mp) REVERT: A 495 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7110 (mm-30) REVERT: A 600 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7576 (ptm) REVERT: C 69 LYS cc_start: 0.5631 (tppt) cc_final: 0.5077 (tppt) REVERT: C 84 TYR cc_start: 0.7429 (m-10) cc_final: 0.6904 (m-10) REVERT: C 122 SER cc_start: 0.5513 (p) cc_final: 0.4606 (t) REVERT: C 124 LYS cc_start: 0.6919 (tptp) cc_final: 0.6622 (mttp) REVERT: C 213 LYS cc_start: 0.6978 (mttt) cc_final: 0.6278 (tptt) REVERT: D 63 GLN cc_start: 0.6632 (pm20) cc_final: 0.6304 (pm20) outliers start: 33 outliers final: 25 residues processed: 168 average time/residue: 0.1647 time to fit residues: 39.0772 Evaluate side-chains 169 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 33 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.170931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.112759 restraints weight = 20530.100| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.97 r_work: 0.3214 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17008 Z= 0.138 Angle : 0.545 12.565 23131 Z= 0.282 Chirality : 0.043 0.149 2603 Planarity : 0.004 0.056 3080 Dihedral : 4.486 58.741 2445 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.97 % Allowed : 15.81 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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 are not related in a simple way. whole: -0.03 (0.18), residues: 2214 helix: 1.46 (0.20), residues: 719 sheet: 0.57 (0.26), residues: 395 loop : -1.30 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 78 TYR 0.026 0.002 TYR D 162 PHE 0.017 0.001 PHE A 152 TRP 0.011 0.001 TRP A 639 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00338 (17005) covalent geometry : angle 0.54522 (23125) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.22113 ( 6) hydrogen bonds : bond 0.03805 ( 674) hydrogen bonds : angle 3.95947 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5216.48 seconds wall clock time: 89 minutes 27.65 seconds (5367.65 seconds total)