Starting phenix.real_space_refine on Fri Feb 14 06:36:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d3y_27168/02_2025/8d3y_27168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3y_27168/02_2025/8d3y_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_27168/02_2025/8d3y_27168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3y_27168/02_2025/8d3y_27168.map" model { file = "/net/cci-nas-00/data/ceres_data/8d3y_27168/02_2025/8d3y_27168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3y_27168/02_2025/8d3y_27168.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 11} 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: {'GLU:plan': 2, 'ASP:plan': 1} 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: 5.55, per 1000 atoms: 0.56 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: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.24 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: 3.51 Time building geometry restraints manager: 2.91 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: 0.690 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.690 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.840 ------------------------------------------------------------------------------- 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 10099 Z= 0.371 Angle : 0.814 56.037 13719 Z= 0.443 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 : 10.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (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 TRP 0.005 0.001 TRP A 896 HIS 0.002 0.001 HIS A 909 PHE 0.019 0.001 PHE A 296 TYR 0.010 0.001 TYR G 32 ARG 0.011 0.000 ARG A 492 *********************** 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 : 1.026 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: 0.1620 time to fit residues: 35.1668 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 : 1.145 ------------------------------------------------------------------------------- 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 108 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.145806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.111580 restraints weight = 16598.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110869 restraints weight = 10698.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111789 restraints weight = 8760.785| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10099 Z= 0.196 Angle : 0.554 7.525 13719 Z= 0.285 Chirality : 0.041 0.145 1585 Planarity : 0.004 0.046 1766 Dihedral : 4.152 46.475 1389 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.46 % Allowed : 30.01 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1289 helix: 1.54 (0.24), residues: 524 sheet: -0.57 (0.46), residues: 135 loop : -1.16 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 977 HIS 0.002 0.001 HIS A 610 PHE 0.016 0.001 PHE B 230 TYR 0.013 0.001 TYR A 121 ARG 0.003 0.000 ARG A 492 *********************** 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 191 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 1.127 Fit side-chains REVERT: A 260 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7470 (mt) REVERT: A 341 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7864 (mtp) REVERT: A 446 LEU cc_start: 0.8815 (tt) cc_final: 0.8453 (mt) REVERT: A 973 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8406 (pp) REVERT: B 229 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.6656 (m-80) REVERT: B 275 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.5906 (pt0) outliers start: 47 outliers final: 24 residues processed: 175 average time/residue: 0.1681 time to fit residues: 45.8921 Evaluate side-chains 161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 260 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 689 LEU 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 A residue 973 LEU Chi-restraints excluded: chain B residue 78 THR 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 40 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 42 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110212 restraints weight = 16858.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110004 restraints weight = 10930.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110539 restraints weight = 8957.756| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10099 Z= 0.220 Angle : 0.558 7.515 13719 Z= 0.284 Chirality : 0.042 0.144 1585 Planarity : 0.004 0.041 1766 Dihedral : 4.132 41.266 1389 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 5.89 % Allowed : 29.72 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1289 helix: 1.62 (0.24), residues: 520 sheet: -0.78 (0.43), residues: 145 loop : -1.18 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 155 HIS 0.003 0.001 HIS A 909 PHE 0.013 0.001 PHE B 230 TYR 0.014 0.001 TYR A 532 ARG 0.002 0.000 ARG A 492 *********************** 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 202 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 140 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 283 GLN cc_start: 0.6078 (OUTLIER) cc_final: 0.5619 (mp10) REVERT: A 446 LEU cc_start: 0.8813 (tt) cc_final: 0.8478 (mt) REVERT: A 973 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8422 (pp) REVERT: B 229 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: B 275 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.5920 (pt0) outliers start: 62 outliers final: 45 residues processed: 182 average time/residue: 0.1777 time to fit residues: 49.0526 Evaluate side-chains 186 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 75 THR 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 155 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 267 LEU 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 510 THR Chi-restraints excluded: chain A residue 566 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 973 LEU 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 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 43 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** A 909 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106845 restraints weight = 16767.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106147 restraints weight = 10913.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107013 restraints weight = 9501.870| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10099 Z= 0.320 Angle : 0.614 7.569 13719 Z= 0.314 Chirality : 0.043 0.142 1585 Planarity : 0.004 0.038 1766 Dihedral : 4.373 30.505 1389 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.14 % Favored : 92.79 % Rotamer: Outliers : 7.79 % Allowed : 28.40 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1289 helix: 1.45 (0.23), residues: 522 sheet: -1.17 (0.40), residues: 155 loop : -1.30 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 977 HIS 0.004 0.001 HIS A 909 PHE 0.017 0.002 PHE B 230 TYR 0.014 0.002 TYR A 532 ARG 0.005 0.000 ARG A 259 *********************** 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 220 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 138 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 126 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9130 (mp) REVERT: A 215 GLN cc_start: 0.8601 (mp10) cc_final: 0.8363 (mp10) REVERT: A 260 ILE cc_start: 0.7977 (mt) cc_final: 0.7731 (mp) REVERT: A 446 LEU cc_start: 0.8747 (tt) cc_final: 0.8422 (mt) REVERT: A 529 GLN cc_start: 0.8305 (tp-100) cc_final: 0.8023 (tp40) REVERT: A 591 ASP cc_start: 0.7917 (t0) cc_final: 0.7679 (t0) REVERT: A 973 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8503 (pp) REVERT: B 187 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8549 (ptpt) REVERT: B 229 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: B 275 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.5788 (pt0) outliers start: 82 outliers final: 61 residues processed: 198 average time/residue: 0.1702 time to fit residues: 51.5438 Evaluate side-chains 198 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 132 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 61 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 126 LEU 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 276 ILE 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 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 607 THR Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 642 VAL 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 720 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 774 ILE 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 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 A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 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 134 LYS 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 227 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110107 restraints weight = 16681.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110496 restraints weight = 10453.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111447 restraints weight = 7761.792| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10099 Z= 0.164 Angle : 0.554 10.635 13719 Z= 0.276 Chirality : 0.041 0.155 1585 Planarity : 0.004 0.039 1766 Dihedral : 4.092 30.180 1389 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.60 % Allowed : 30.58 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1289 helix: 1.62 (0.24), residues: 528 sheet: -0.90 (0.42), residues: 145 loop : -1.19 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 977 HIS 0.001 0.000 HIS A 610 PHE 0.013 0.001 PHE B 230 TYR 0.013 0.001 TYR A 532 ARG 0.002 0.000 ARG A 492 *********************** 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 211 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 126 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8939 (mp) REVERT: A 260 ILE cc_start: 0.8076 (mt) cc_final: 0.7678 (mp) REVERT: A 446 LEU cc_start: 0.8757 (tt) cc_final: 0.8486 (mt) REVERT: A 591 ASP cc_start: 0.7901 (t0) cc_final: 0.7617 (t0) REVERT: A 973 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8396 (pp) REVERT: B 229 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.6690 (m-80) REVERT: B 275 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.5705 (pt0) outliers start: 59 outliers final: 45 residues processed: 192 average time/residue: 0.1751 time to fit residues: 50.9236 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 : 1.231 ------------------------------------------------------------------------------- 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 61 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 151 PHE 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 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 335 THR 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 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 626 GLU 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 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 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 973 LEU 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 134 LYS 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 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 5 optimal weight: 0.0870 chunk 81 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.146457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112376 restraints weight = 16769.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112036 restraints weight = 10364.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112680 restraints weight = 7236.226| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10099 Z= 0.146 Angle : 0.537 8.952 13719 Z= 0.268 Chirality : 0.040 0.156 1585 Planarity : 0.004 0.040 1766 Dihedral : 3.917 29.778 1389 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 5.60 % Allowed : 31.62 % Favored : 62.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1289 helix: 1.77 (0.24), residues: 524 sheet: -0.88 (0.42), residues: 145 loop : -1.10 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 896 HIS 0.002 0.000 HIS A 909 PHE 0.013 0.001 PHE B 230 TYR 0.016 0.001 TYR A 532 ARG 0.005 0.000 ARG B 273 *********************** 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 202 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 143 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 260 ILE cc_start: 0.7977 (mt) cc_final: 0.7618 (mp) REVERT: A 591 ASP cc_start: 0.8032 (t0) cc_final: 0.7719 (t0) REVERT: A 711 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6937 (t70) REVERT: A 827 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8632 (ptt-90) REVERT: A 973 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8366 (pp) REVERT: B 223 LYS cc_start: 0.8058 (tptt) cc_final: 0.7694 (tppt) REVERT: B 229 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.6849 (m-80) REVERT: B 272 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.6942 (tp) REVERT: B 275 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.5743 (pt0) outliers start: 59 outliers final: 43 residues processed: 185 average time/residue: 0.1823 time to fit residues: 51.4282 Evaluate side-chains 188 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 75 THR Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 VAL 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 458 LYS 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 697 ARG Chi-restraints excluded: chain A residue 711 ASP 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 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 41 ILE 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 70 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.141961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107594 restraints weight = 17098.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107106 restraints weight = 10716.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107434 restraints weight = 9243.598| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 10099 Z= 0.294 Angle : 0.603 8.470 13719 Z= 0.303 Chirality : 0.043 0.188 1585 Planarity : 0.004 0.038 1766 Dihedral : 4.141 30.514 1389 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.21 % Favored : 93.72 % Rotamer: Outliers : 7.12 % Allowed : 30.39 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.24), residues: 1289 helix: 1.63 (0.24), residues: 525 sheet: -1.12 (0.40), residues: 155 loop : -1.18 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 896 HIS 0.002 0.001 HIS A 909 PHE 0.016 0.001 PHE B 230 TYR 0.016 0.001 TYR A 892 ARG 0.005 0.000 ARG B 273 *********************** 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 219 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 144 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 260 ILE cc_start: 0.8143 (mt) cc_final: 0.7743 (mt) REVERT: A 263 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7275 (mp) REVERT: A 591 ASP cc_start: 0.8014 (t0) cc_final: 0.7666 (t0) REVERT: A 697 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8027 (ptp-110) REVERT: A 711 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6892 (t0) REVERT: A 827 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8704 (ptt-90) REVERT: A 973 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8475 (pp) REVERT: B 57 MET cc_start: 0.8146 (tmm) cc_final: 0.7908 (tmm) REVERT: B 229 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: B 275 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.5818 (pt0) outliers start: 75 outliers final: 55 residues processed: 195 average time/residue: 0.1774 time to fit residues: 53.1613 Evaluate side-chains 203 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 141 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 62 LEU 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 232 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 267 LEU 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 301 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 317 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 458 LYS 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 697 ARG Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 ILE 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 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 973 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 227 VAL 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 101 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.145191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110083 restraints weight = 16967.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110472 restraints weight = 9920.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111001 restraints weight = 7294.992| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10099 Z= 0.161 Angle : 0.558 8.754 13719 Z= 0.277 Chirality : 0.041 0.208 1585 Planarity : 0.004 0.038 1766 Dihedral : 3.979 29.672 1389 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 4.84 % Allowed : 32.10 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1289 helix: 1.77 (0.24), residues: 525 sheet: -0.94 (0.42), residues: 145 loop : -1.11 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 880 HIS 0.001 0.000 HIS A 909 PHE 0.014 0.001 PHE A 296 TYR 0.017 0.001 TYR A 532 ARG 0.004 0.000 ARG B 273 *********************** 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 192 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 141 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 591 ASP cc_start: 0.7988 (t0) cc_final: 0.7684 (t0) REVERT: A 711 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6905 (t70) REVERT: A 827 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8721 (ptt-90) REVERT: A 973 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8420 (pp) REVERT: B 229 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: B 275 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.5908 (pt0) outliers start: 51 outliers final: 44 residues processed: 177 average time/residue: 0.1816 time to fit residues: 48.3469 Evaluate side-chains 185 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 VAL 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 437 VAL Chi-restraints excluded: chain A residue 458 LYS 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 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 ARG 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 973 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 227 VAL 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 263 PHE 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 57 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 109 optimal weight: 0.0170 chunk 60 optimal weight: 8.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.144322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.109943 restraints weight = 16971.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110780 restraints weight = 12282.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111968 restraints weight = 9190.422| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10099 Z= 0.194 Angle : 0.576 9.849 13719 Z= 0.284 Chirality : 0.042 0.233 1585 Planarity : 0.004 0.040 1766 Dihedral : 3.944 29.752 1389 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 5.70 % Allowed : 31.81 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1289 helix: 1.73 (0.24), residues: 529 sheet: -0.95 (0.42), residues: 145 loop : -1.10 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 977 HIS 0.002 0.000 HIS A 909 PHE 0.015 0.001 PHE A 296 TYR 0.017 0.001 TYR A 532 ARG 0.004 0.000 ARG B 273 *********************** 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 199 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 591 ASP cc_start: 0.8041 (t0) cc_final: 0.7696 (t0) REVERT: A 638 LEU cc_start: 0.6755 (pt) cc_final: 0.6329 (tp) REVERT: A 697 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7912 (ptp-110) REVERT: A 711 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6940 (t70) REVERT: A 827 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8741 (ptt-90) REVERT: A 973 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8413 (pp) REVERT: B 229 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: B 268 MET cc_start: 0.7744 (mpp) cc_final: 0.7357 (mtm) REVERT: B 275 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.5949 (pt0) outliers start: 60 outliers final: 52 residues processed: 180 average time/residue: 0.1823 time to fit residues: 50.0331 Evaluate side-chains 197 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 139 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 62 LEU 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 283 GLN 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 335 THR Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 LYS 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 660 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 804 THR 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 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 973 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 227 VAL 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 96 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.145842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113385 restraints weight = 16842.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111903 restraints weight = 12651.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112826 restraints weight = 9287.707| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10099 Z= 0.160 Angle : 0.559 8.489 13719 Z= 0.276 Chirality : 0.041 0.229 1585 Planarity : 0.004 0.039 1766 Dihedral : 3.859 29.539 1389 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 5.03 % Allowed : 32.48 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1289 helix: 1.76 (0.24), residues: 529 sheet: -1.03 (0.43), residues: 146 loop : -0.99 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 977 HIS 0.002 0.000 HIS A 909 PHE 0.013 0.001 PHE A 296 TYR 0.017 0.001 TYR A 532 ARG 0.004 0.000 ARG B 273 ********************** 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 192 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 591 ASP cc_start: 0.7998 (t0) cc_final: 0.7698 (t0) REVERT: A 638 LEU cc_start: 0.6639 (pt) cc_final: 0.6262 (tp) REVERT: A 711 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6871 (t70) REVERT: A 827 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8787 (ptt-90) REVERT: A 973 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8407 (pp) REVERT: B 229 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.6820 (m-80) REVERT: B 268 MET cc_start: 0.7808 (mpp) cc_final: 0.7469 (mtm) REVERT: B 275 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.5964 (pt0) outliers start: 53 outliers final: 46 residues processed: 177 average time/residue: 0.1796 time to fit residues: 48.6505 Evaluate side-chains 188 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 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 437 VAL Chi-restraints excluded: chain A residue 458 LYS 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 660 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 804 THR 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 973 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 227 VAL 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 10 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 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 = 0.3702 r_free = 0.3702 target = 0.140818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.106767 restraints weight = 17026.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106146 restraints weight = 10718.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106736 restraints weight = 9329.797| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10099 Z= 0.336 Angle : 0.644 9.499 13719 Z= 0.325 Chirality : 0.045 0.240 1585 Planarity : 0.004 0.040 1766 Dihedral : 4.246 30.480 1389 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.44 % Favored : 93.48 % Rotamer: Outliers : 5.41 % Allowed : 31.91 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1289 helix: 1.52 (0.24), residues: 530 sheet: -0.70 (0.45), residues: 121 loop : -1.25 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 977 HIS 0.002 0.001 HIS A 483 PHE 0.020 0.002 PHE A 296 TYR 0.019 0.002 TYR A 892 ARG 0.004 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.97 seconds wall clock time: 53 minutes 3.79 seconds (3183.79 seconds total)