Starting phenix.real_space_refine on Wed Mar 4 01:33:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d3y_27168/03_2026/8d3y_27168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3y_27168/03_2026/8d3y_27168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d3y_27168/03_2026/8d3y_27168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3y_27168/03_2026/8d3y_27168.map" model { file = "/net/cci-nas-00/data/ceres_data/8d3y_27168/03_2026/8d3y_27168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3y_27168/03_2026/8d3y_27168.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians S 58 5.16 5 Be 1 3.05 5 C 6340 2.51 5 N 1646 2.21 5 O 1850 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9898 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7341 Classifications: {'peptide': 982} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 41, 'TRANS': 940} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 11, 'ASP:plan': 9, 'GLN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 187 Chain: "B" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2311 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 264} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 246 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Time building chain proxies: 2.43, per 1000 atoms: 0.25 Number of scatterers: 9898 At special positions: 0 Unit cell: (141.48, 122.04, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 F 3 9.00 O 1850 8.00 N 1646 7.00 C 6340 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " 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: 0.64 Conformation dependent library (CDL) restraints added in 516.4 milliseconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 45.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 54 through 65 removed outlier: 4.250A pdb=" N ALA A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 removed outlier: 4.267A pdb=" N PHE A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 111 removed outlier: 4.097A pdb=" N LEU A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 143 removed outlier: 3.791A pdb=" N GLY A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.802A pdb=" N GLU A 174 " --> pdb=" O ASN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 removed outlier: 4.052A pdb=" N ARG A 254 " --> pdb=" O THR A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.513A pdb=" N PHE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 320 removed outlier: 3.572A pdb=" N VAL A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.992A pdb=" N VAL A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 360 removed outlier: 4.114A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 360' Processing helix chain 'A' and resid 405 through 419 Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.943A pdb=" N ARG A 435 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 456 through 464 removed outlier: 4.026A pdb=" N MET A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 523 through 537 removed outlier: 3.770A pdb=" N GLU A 534 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 removed outlier: 3.696A pdb=" N LEU A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 650 removed outlier: 3.594A pdb=" N ALA A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 661 removed outlier: 3.957A pdb=" N LYS A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 657 through 661' Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 684 through 698 removed outlier: 3.711A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 745 through 771 removed outlier: 3.927A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 786 Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 793 through 803 removed outlier: 3.715A pdb=" N ILE A 797 " --> pdb=" O GLY A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 812 Processing helix chain 'A' and resid 836 through 846 removed outlier: 4.020A pdb=" N GLN A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 865 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 876 through 881 Processing helix chain 'A' and resid 897 through 927 removed outlier: 3.504A pdb=" N ARG A 901 " --> pdb=" O THR A 897 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 959 removed outlier: 4.018A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.837A pdb=" N PHE A 979 " --> pdb=" O SER A 976 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 980 " --> pdb=" O TRP A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'B' and resid 33 through 59 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.930A pdb=" N TYR B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 58 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.520A pdb=" N VAL A 161 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N CYS A 239 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A 241 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 201 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 243 " --> pdb=" O HIS A 199 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 247 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE A 195 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS A 201 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.520A pdb=" N VAL A 161 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N CYS A 239 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A 241 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 201 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 243 " --> pdb=" O HIS A 199 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 247 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE A 195 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 348 removed outlier: 5.951A pdb=" N GLY A 721 " --> pdb=" O MET A 738 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU A 740 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA A 723 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 702 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 655 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 383 Processing sheet with id=AA5, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.533A pdb=" N VAL A 422 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 438 " --> pdb=" O VAL A 422 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 466 through 469 removed outlier: 3.717A pdb=" N ALA A 468 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 494 " --> pdb=" O HIS A 483 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A 493 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS A 547 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE A 575 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR A 549 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N LEU A 573 " --> pdb=" O TYR A 549 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU A 573 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLY A 577 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.625A pdb=" N ILE B 299 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 272 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 301 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B 270 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 179 removed outlier: 3.691A pdb=" N ILE B 176 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 260 " --> pdb=" O PHE B 230 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1266 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: 1.45 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3224 1.34 - 1.46: 2195 1.46 - 1.58: 4595 1.58 - 1.70: 0 1.70 - 1.81: 85 Bond restraints: 10099 Sorted by residual: bond pdb=" C BFD A 366 " pdb=" O BFD A 366 " ideal model delta sigma weight residual 1.231 1.807 -0.576 2.00e-02 2.50e+03 8.30e+02 bond pdb=" CB BFD A 366 " pdb=" CG BFD A 366 " ideal model delta sigma weight residual 1.529 1.263 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" OD1 BFD A 366 " pdb="BE BFD A 366 " ideal model delta sigma weight residual 1.737 1.528 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" F1 BFD A 366 " pdb="BE BFD A 366 " ideal model delta sigma weight residual 1.542 1.506 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" F2 BFD A 366 " pdb="BE BFD A 366 " ideal model delta sigma weight residual 1.535 1.513 0.022 2.00e-02 2.50e+03 1.27e+00 ... (remaining 10094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.21: 13715 11.21 - 22.42: 2 22.42 - 33.62: 1 33.62 - 44.83: 0 44.83 - 56.04: 1 Bond angle restraints: 13719 Sorted by residual: angle pdb=" O BFD A 366 " pdb=" C BFD A 366 " pdb=" N LYS A 367 " ideal model delta sigma weight residual 123.00 66.96 56.04 1.60e+00 3.91e-01 1.23e+03 angle pdb=" CA BFD A 366 " pdb=" C BFD A 366 " pdb=" O BFD A 366 " ideal model delta sigma weight residual 120.80 94.22 26.58 1.70e+00 3.46e-01 2.45e+02 angle pdb=" CA BFD A 366 " pdb=" CB BFD A 366 " pdb=" CG BFD A 366 " ideal model delta sigma weight residual 112.84 131.42 -18.58 3.00e+00 1.11e-01 3.84e+01 angle pdb=" CB BFD A 366 " pdb=" CG BFD A 366 " pdb=" OD2 BFD A 366 " ideal model delta sigma weight residual 118.96 102.03 16.93 3.00e+00 1.11e-01 3.19e+01 angle pdb=" CB MET A 581 " pdb=" CG MET A 581 " pdb=" SD MET A 581 " ideal model delta sigma weight residual 112.70 122.54 -9.84 3.00e+00 1.11e-01 1.08e+01 ... (remaining 13714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5099 17.64 - 35.29: 729 35.29 - 52.93: 188 52.93 - 70.58: 30 70.58 - 88.22: 12 Dihedral angle restraints: 6058 sinusoidal: 2327 harmonic: 3731 Sorted by residual: dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 49 " pdb=" CB CYS A 49 " ideal model delta sinusoidal sigma weight residual 93.00 165.45 -72.45 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CA ILE A 285 " pdb=" C ILE A 285 " pdb=" N THR A 286 " pdb=" CA THR A 286 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLY B 30 " pdb=" C GLY B 30 " pdb=" N SER B 31 " pdb=" CA SER B 31 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 6055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1174 0.045 - 0.089: 335 0.089 - 0.134: 73 0.134 - 0.178: 2 0.178 - 0.223: 1 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CB ILE A 926 " pdb=" CA ILE A 926 " pdb=" CG1 ILE A 926 " pdb=" CG2 ILE A 926 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB THR A 233 " pdb=" CA THR A 233 " pdb=" OG1 THR A 233 " pdb=" CG2 THR A 233 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA MET B 121 " pdb=" N MET B 121 " pdb=" C MET B 121 " pdb=" CB MET B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1582 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BFD A 366 " 0.222 2.00e-02 2.50e+03 3.06e-01 9.38e+02 pdb=" C BFD A 366 " -0.495 2.00e-02 2.50e+03 pdb=" O BFD A 366 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 367 " 0.285 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 73 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO B 74 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 74 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 74 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 430 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 431 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.022 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 859 2.74 - 3.28: 10133 3.28 - 3.82: 15922 3.82 - 4.36: 17798 4.36 - 4.90: 31014 Nonbonded interactions: 75726 Sorted by model distance: nonbonded pdb=" O THR A 607 " pdb=" OG1 THR A 683 " model vdw 2.198 3.040 nonbonded pdb=" OE2 GLU A 33 " pdb=" OH TYR A 45 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 892 " pdb=" O SER B 62 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLN A 846 " pdb=" OH TYR A 991 " model vdw 2.258 3.040 nonbonded pdb=" O ARG B 150 " pdb=" OH TYR B 242 " model vdw 2.264 3.040 ... (remaining 75721 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.007 0.576 10102 Z= 0.358 Angle : 0.813 56.037 13725 Z= 0.442 Chirality : 0.041 0.223 1585 Planarity : 0.008 0.306 1766 Dihedral : 17.343 88.219 3655 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.19 % Allowed : 34.00 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.14 (0.24), residues: 1289 helix: 1.24 (0.24), residues: 517 sheet: -0.56 (0.47), residues: 123 loop : -1.12 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 492 TYR 0.010 0.001 TYR G 32 PHE 0.019 0.001 PHE A 296 TRP 0.005 0.001 TRP A 896 HIS 0.002 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00734 (10099) covalent geometry : angle 0.81356 (13719) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.41620 ( 6) hydrogen bonds : bond 0.19141 ( 428) hydrogen bonds : angle 6.87823 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.270 Fit side-chains REVERT: A 973 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8311 (pp) outliers start: 2 outliers final: 0 residues processed: 139 average time/residue: 0.0666 time to fit residues: 14.8242 Evaluate side-chains 134 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 973 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 0.0070 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 140 GLN A 169 GLN A 696 GLN A 895 GLN A 900 GLN B 69 GLN B 82 GLN B 256 GLN G 31 HIS G 35 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113233 restraints weight = 16707.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112867 restraints weight = 10840.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113527 restraints weight = 8288.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114691 restraints weight = 7149.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114576 restraints weight = 6184.788| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10102 Z= 0.108 Angle : 0.541 7.460 13725 Z= 0.278 Chirality : 0.040 0.144 1585 Planarity : 0.004 0.043 1766 Dihedral : 4.065 47.160 1389 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.42 % Allowed : 30.86 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.13 (0.24), residues: 1289 helix: 1.61 (0.24), residues: 524 sheet: -0.39 (0.47), residues: 128 loop : -1.14 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.012 0.001 TYR A 121 PHE 0.015 0.001 PHE B 230 TRP 0.005 0.001 TRP B 155 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd covalent geometry : bond 0.00233 (10099) covalent geometry : angle 0.54101 (13719) SS BOND : bond 0.00415 ( 3) SS BOND : angle 0.53411 ( 6) hydrogen bonds : bond 0.04164 ( 428) hydrogen bonds : angle 4.87469 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.403 Fit side-chains REVERT: A 923 ASP cc_start: 0.8908 (t0) cc_final: 0.8704 (t70) REVERT: B 229 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6558 (m-80) REVERT: B 275 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.5895 (pt0) outliers start: 36 outliers final: 14 residues processed: 172 average time/residue: 0.0721 time to fit residues: 19.3403 Evaluate side-chains 150 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 98 optimal weight: 0.0060 chunk 116 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 HIS B 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107660 restraints weight = 17014.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108624 restraints weight = 13428.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109320 restraints weight = 11211.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109654 restraints weight = 8379.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109777 restraints weight = 7345.492| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10102 Z= 0.215 Angle : 0.618 7.538 13725 Z= 0.317 Chirality : 0.044 0.145 1585 Planarity : 0.004 0.045 1766 Dihedral : 4.222 37.636 1387 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.83 % Favored : 93.10 % Rotamer: Outliers : 6.08 % Allowed : 30.48 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.21 (0.24), residues: 1289 helix: 1.36 (0.23), residues: 533 sheet: -1.07 (0.40), residues: 155 loop : -1.28 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 931 TYR 0.015 0.002 TYR A 892 PHE 0.015 0.002 PHE B 230 TRP 0.007 0.001 TRP B 155 HIS 0.004 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00514 (10099) covalent geometry : angle 0.61792 (13719) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.67724 ( 6) hydrogen bonds : bond 0.04540 ( 428) hydrogen bonds : angle 4.65557 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 133 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: B 229 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.6790 (m-80) REVERT: B 275 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5819 (pt0) outliers start: 64 outliers final: 44 residues processed: 176 average time/residue: 0.0749 time to fit residues: 20.2404 Evaluate side-chains 177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 38 optimal weight: 10.0000 chunk 108 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 94 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.146056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111802 restraints weight = 16913.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111276 restraints weight = 10658.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111933 restraints weight = 8911.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112764 restraints weight = 8016.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112714 restraints weight = 6853.666| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10102 Z= 0.103 Angle : 0.533 7.435 13725 Z= 0.270 Chirality : 0.040 0.142 1585 Planarity : 0.004 0.040 1766 Dihedral : 3.996 36.703 1387 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.13 % Allowed : 30.86 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.04 (0.24), residues: 1289 helix: 1.60 (0.23), residues: 535 sheet: -0.98 (0.43), residues: 133 loop : -1.18 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 259 TYR 0.009 0.001 TYR A 121 PHE 0.013 0.001 PHE B 230 TRP 0.006 0.001 TRP A 977 HIS 0.002 0.000 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00228 (10099) covalent geometry : angle 0.53280 (13719) SS BOND : bond 0.00253 ( 3) SS BOND : angle 0.65598 ( 6) hydrogen bonds : bond 0.03681 ( 428) hydrogen bonds : angle 4.27969 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 0.262 Fit side-chains REVERT: A 529 GLN cc_start: 0.8592 (tp40) cc_final: 0.8386 (tp-100) REVERT: A 734 GLN cc_start: 0.8500 (pp30) cc_final: 0.8252 (pp30) REVERT: B 229 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.6701 (m-80) REVERT: B 275 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.5828 (pt0) outliers start: 54 outliers final: 36 residues processed: 182 average time/residue: 0.0672 time to fit residues: 19.2977 Evaluate side-chains 177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 91 optimal weight: 1.9990 chunk 108 optimal weight: 0.1980 chunk 92 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 118 optimal weight: 0.0270 chunk 93 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112227 restraints weight = 16834.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112373 restraints weight = 10097.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112614 restraints weight = 8079.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112899 restraints weight = 7255.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113105 restraints weight = 6550.957| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10102 Z= 0.099 Angle : 0.534 9.942 13725 Z= 0.267 Chirality : 0.040 0.144 1585 Planarity : 0.003 0.041 1766 Dihedral : 3.808 30.055 1387 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.22 % Allowed : 31.05 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.06 (0.24), residues: 1289 helix: 1.58 (0.23), residues: 542 sheet: -0.83 (0.43), residues: 145 loop : -1.20 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 259 TYR 0.009 0.001 TYR B 243 PHE 0.015 0.001 PHE G 44 TRP 0.006 0.001 TRP A 977 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00221 (10099) covalent geometry : angle 0.53382 (13719) SS BOND : bond 0.00233 ( 3) SS BOND : angle 0.68166 ( 6) hydrogen bonds : bond 0.03382 ( 428) hydrogen bonds : angle 4.09208 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 923 ASP cc_start: 0.8890 (t0) cc_final: 0.8626 (t70) REVERT: B 229 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: B 275 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.5851 (pt0) outliers start: 55 outliers final: 43 residues processed: 186 average time/residue: 0.0649 time to fit residues: 18.8174 Evaluate side-chains 184 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 77 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.147774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113206 restraints weight = 16821.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112996 restraints weight = 10838.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113333 restraints weight = 8203.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113847 restraints weight = 7121.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114065 restraints weight = 6382.608| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10102 Z= 0.096 Angle : 0.529 8.677 13725 Z= 0.265 Chirality : 0.040 0.149 1585 Planarity : 0.003 0.040 1766 Dihedral : 3.723 25.752 1387 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 4.65 % Allowed : 31.91 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 (0.24), residues: 1289 helix: 1.78 (0.24), residues: 528 sheet: -0.92 (0.44), residues: 133 loop : -1.02 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.008 0.001 TYR B 243 PHE 0.012 0.001 PHE B 230 TRP 0.007 0.001 TRP A 977 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00216 (10099) covalent geometry : angle 0.52902 (13719) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.74481 ( 6) hydrogen bonds : bond 0.03194 ( 428) hydrogen bonds : angle 3.97684 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 923 ASP cc_start: 0.8906 (t0) cc_final: 0.8611 (t70) REVERT: B 223 LYS cc_start: 0.8032 (tptt) cc_final: 0.7805 (tptt) REVERT: B 229 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: B 275 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.5794 (pt0) outliers start: 49 outliers final: 41 residues processed: 175 average time/residue: 0.0686 time to fit residues: 19.0222 Evaluate side-chains 180 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108993 restraints weight = 17088.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109508 restraints weight = 13675.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110821 restraints weight = 10642.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110950 restraints weight = 7836.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111066 restraints weight = 7334.820| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10102 Z= 0.179 Angle : 0.591 8.032 13725 Z= 0.297 Chirality : 0.043 0.196 1585 Planarity : 0.004 0.041 1766 Dihedral : 3.923 27.483 1387 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 5.41 % Allowed : 31.43 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.01 (0.24), residues: 1289 helix: 1.59 (0.24), residues: 536 sheet: -1.06 (0.40), residues: 155 loop : -1.18 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 273 TYR 0.013 0.001 TYR A 892 PHE 0.015 0.001 PHE B 230 TRP 0.008 0.001 TRP A 978 HIS 0.002 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00432 (10099) covalent geometry : angle 0.59116 (13719) SS BOND : bond 0.00203 ( 3) SS BOND : angle 0.75472 ( 6) hydrogen bonds : bond 0.03795 ( 428) hydrogen bonds : angle 4.12796 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 137 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 263 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7237 (mp) REVERT: A 827 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8663 (ptt-90) REVERT: B 187 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8536 (ptpt) REVERT: B 229 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.6798 (m-80) REVERT: B 275 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6035 (pt0) outliers start: 57 outliers final: 45 residues processed: 175 average time/residue: 0.0658 time to fit residues: 18.2175 Evaluate side-chains 182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 109 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109364 restraints weight = 16880.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109909 restraints weight = 10807.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110635 restraints weight = 8093.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111010 restraints weight = 7021.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111293 restraints weight = 6066.758| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10102 Z= 0.133 Angle : 0.565 7.995 13725 Z= 0.283 Chirality : 0.042 0.219 1585 Planarity : 0.004 0.039 1766 Dihedral : 3.882 25.815 1387 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 5.32 % Allowed : 31.15 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.06 (0.24), residues: 1289 helix: 1.65 (0.24), residues: 531 sheet: -1.08 (0.40), residues: 155 loop : -1.12 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.017 0.001 TYR A 532 PHE 0.014 0.001 PHE B 230 TRP 0.006 0.001 TRP A 977 HIS 0.002 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00320 (10099) covalent geometry : angle 0.56517 (13719) SS BOND : bond 0.00227 ( 3) SS BOND : angle 0.74192 ( 6) hydrogen bonds : bond 0.03600 ( 428) hydrogen bonds : angle 4.05986 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 138 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 263 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7130 (mp) REVERT: A 827 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8678 (ptt-90) REVERT: B 229 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.6750 (m-80) REVERT: B 268 MET cc_start: 0.7800 (mpp) cc_final: 0.7507 (mtm) REVERT: B 272 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7040 (tp) REVERT: B 275 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.5903 (pt0) outliers start: 56 outliers final: 44 residues processed: 176 average time/residue: 0.0710 time to fit residues: 19.5863 Evaluate side-chains 184 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 92 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 25 optimal weight: 0.0570 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.145927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.111481 restraints weight = 16884.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111877 restraints weight = 10828.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112682 restraints weight = 8207.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113033 restraints weight = 6867.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113354 restraints weight = 6052.671| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10102 Z= 0.107 Angle : 0.558 8.038 13725 Z= 0.276 Chirality : 0.041 0.219 1585 Planarity : 0.003 0.039 1766 Dihedral : 3.761 22.754 1387 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 5.22 % Allowed : 31.43 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.19 (0.24), residues: 1289 helix: 1.75 (0.24), residues: 531 sheet: -0.94 (0.43), residues: 145 loop : -1.08 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.018 0.001 TYR A 532 PHE 0.013 0.001 PHE B 230 TRP 0.007 0.001 TRP B 155 HIS 0.002 0.000 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00252 (10099) covalent geometry : angle 0.55841 (13719) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.69382 ( 6) hydrogen bonds : bond 0.03348 ( 428) hydrogen bonds : angle 3.97295 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 263 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7019 (mp) REVERT: A 711 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6769 (t70) REVERT: A 827 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8679 (ptt-90) REVERT: B 229 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: B 268 MET cc_start: 0.7815 (mpp) cc_final: 0.7513 (mtm) REVERT: B 272 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.6976 (tp) REVERT: B 275 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.5862 (pt0) outliers start: 55 outliers final: 42 residues processed: 178 average time/residue: 0.0706 time to fit residues: 19.8640 Evaluate side-chains 184 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 122 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 0.1980 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.108594 restraints weight = 16930.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107871 restraints weight = 10956.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108503 restraints weight = 9500.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108969 restraints weight = 8097.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109443 restraints weight = 6922.461| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 10102 Z= 0.181 Angle : 0.615 9.202 13725 Z= 0.307 Chirality : 0.043 0.256 1585 Planarity : 0.004 0.039 1766 Dihedral : 3.950 27.714 1387 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.44 % Favored : 93.48 % Rotamer: Outliers : 5.03 % Allowed : 31.53 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 (0.24), residues: 1289 helix: 1.61 (0.24), residues: 532 sheet: -1.20 (0.40), residues: 155 loop : -1.18 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.018 0.001 TYR A 532 PHE 0.015 0.001 PHE B 230 TRP 0.012 0.001 TRP A 977 HIS 0.002 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00442 (10099) covalent geometry : angle 0.61457 (13719) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.73256 ( 6) hydrogen bonds : bond 0.03879 ( 428) hydrogen bonds : angle 4.13893 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 263 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7267 (mp) REVERT: A 711 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6838 (t0) REVERT: B 223 LYS cc_start: 0.7955 (tptp) cc_final: 0.7675 (tptp) REVERT: B 229 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.6848 (m-80) REVERT: B 268 MET cc_start: 0.7810 (mpp) cc_final: 0.7548 (mtm) REVERT: B 275 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.5785 (pt0) outliers start: 53 outliers final: 46 residues processed: 174 average time/residue: 0.0755 time to fit residues: 20.5190 Evaluate side-chains 184 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108245 restraints weight = 17003.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107251 restraints weight = 11246.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108076 restraints weight = 9315.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108787 restraints weight = 8363.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108814 restraints weight = 7241.368| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10102 Z= 0.172 Angle : 0.613 9.602 13725 Z= 0.306 Chirality : 0.043 0.237 1585 Planarity : 0.004 0.037 1766 Dihedral : 4.066 28.144 1387 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 5.13 % Allowed : 31.62 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 (0.24), residues: 1289 helix: 1.58 (0.24), residues: 530 sheet: -1.05 (0.42), residues: 142 loop : -1.25 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.017 0.001 TYR A 532 PHE 0.016 0.001 PHE G 44 TRP 0.006 0.001 TRP B 32 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00416 (10099) covalent geometry : angle 0.61315 (13719) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.80645 ( 6) hydrogen bonds : bond 0.03894 ( 428) hydrogen bonds : angle 4.17012 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1540.22 seconds wall clock time: 27 minutes 15.86 seconds (1635.86 seconds total)