Starting phenix.real_space_refine on Fri Sep 11 19:17:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ykv_73059/09_2026/9ykv_73059.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ykv_73059/09_2026/9ykv_73059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ykv_73059/09_2026/9ykv_73059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ykv_73059/09_2026/9ykv_73059.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ykv_73059/09_2026/9ykv_73059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ykv_73059/09_2026/9ykv_73059.map" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 59 5.16 5 C 6953 2.51 5 N 1845 2.21 5 O 2057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10923 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7770 Classifications: {'peptide': 981} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 928} Chain breaks: 3 Chain: "B" Number of atoms: 1869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 1865 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 208} Conformer: "B" Number of residues, atoms: 231, 1865 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 208} bond proxies already assigned to first conformer: 1914 Chain: "C" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 608 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "D" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 608 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'AMP%rna2p': 1, 'IHP': 1, 'POP': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 2.93, per 1000 atoms: 0.27 Number of scatterers: 10923 At special positions: 0 Unit cell: (88.298, 101.626, 126.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 9 15.00 O 2057 8.00 N 1845 7.00 C 6953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS B 188 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 602.0 milliseconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 40.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 70 through 84 removed outlier: 3.540A pdb=" N LEU A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 removed outlier: 3.513A pdb=" N GLY A 102 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 removed outlier: 3.534A pdb=" N VAL A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.551A pdb=" N VAL A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 128 Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.550A pdb=" N ASP A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS A 153 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 177 removed outlier: 3.855A pdb=" N GLN A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.536A pdb=" N LEU A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 307' Processing helix chain 'A' and resid 320 through 340 Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 387 through 408 Processing helix chain 'A' and resid 421 through 427 removed outlier: 4.166A pdb=" N VAL A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.848A pdb=" N ILE A 517 " --> pdb=" O PRO A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.799A pdb=" N ARG A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 633 through 650 Processing helix chain 'A' and resid 651 through 663 Processing helix chain 'A' and resid 668 through 673 Processing helix chain 'A' and resid 683 through 691 removed outlier: 3.822A pdb=" N LYS A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 712 Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.861A pdb=" N LEU A 716 " --> pdb=" O ASN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 769 Processing helix chain 'A' and resid 780 through 782 No H-bonds generated for 'chain 'A' and resid 780 through 782' Processing helix chain 'A' and resid 783 through 789 removed outlier: 4.186A pdb=" N GLU A 789 " --> pdb=" O ASN A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 879 through 889 Processing helix chain 'A' and resid 894 through 914 removed outlier: 3.617A pdb=" N GLY A 914 " --> pdb=" O ILE A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 979 removed outlier: 3.524A pdb=" N TYR A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1015 through 1019 removed outlier: 3.690A pdb=" N GLU A1018 " --> pdb=" O PRO A1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 removed outlier: 3.838A pdb=" N ILE B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.762A pdb=" N MET B 217 " --> pdb=" O ILE B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.585A pdb=" N GLU B 225 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 251 removed outlier: 3.583A pdb=" N GLU B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.736A pdb=" N MET B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 277 removed outlier: 4.042A pdb=" N GLY B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 289 through 293 removed outlier: 3.733A pdb=" N GLN B 293 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 326 removed outlier: 3.876A pdb=" N LEU B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 124 Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'D' and resid 111 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.238A pdb=" N VAL A 88 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER A 138 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 90 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 64 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N HIS A 91 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 66 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 156 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL A 157 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA A 186 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU A 159 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL A 188 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 removed outlier: 8.104A pdb=" N GLY A 285 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 250 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 228 through 230 removed outlier: 6.435A pdb=" N SER A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 541 removed outlier: 6.234A pdb=" N ILE A 493 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N HIS A 541 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 495 " --> pdb=" O HIS A 541 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 463 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR A 496 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU A 465 " --> pdb=" O THR A 496 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN A 462 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE A 565 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE A 464 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 591 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL A 602 " --> pdb=" O LYS A 922 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS A 922 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 944 through 946 Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.841A pdb=" N TRP A 958 " --> pdb=" O ARG A1044 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N TYR A1046 " --> pdb=" O TRP A 958 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 960 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 986 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.841A pdb=" N TRP A 958 " --> pdb=" O ARG A1044 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N TYR A1046 " --> pdb=" O TRP A 958 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 960 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1038 " --> pdb=" O PHE A1028 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 123 Processing sheet with id=AB1, first strand: chain 'C' and resid 101 through 106 Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.116A pdb=" N ILE D 131 " --> pdb=" O ALA D 159 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3507 1.34 - 1.46: 1529 1.46 - 1.57: 6029 1.57 - 1.69: 12 1.69 - 1.81: 91 Bond restraints: 11168 Sorted by residual: bond pdb=" C1' AMP A1101 " pdb=" C2' AMP A1101 " ideal model delta sigma weight residual 1.526 1.320 0.206 1.50e-02 4.44e+03 1.88e+02 bond pdb=" C1' AMP A1101 " pdb=" O4' AMP A1101 " ideal model delta sigma weight residual 1.415 1.589 -0.174 1.50e-02 4.44e+03 1.34e+02 bond pdb=" C3' AMP A1101 " pdb=" C4' AMP A1101 " ideal model delta sigma weight residual 1.527 1.357 0.170 1.50e-02 4.44e+03 1.29e+02 bond pdb=" C2' AMP A1101 " pdb=" C3' AMP A1101 " ideal model delta sigma weight residual 1.525 1.632 -0.107 1.50e-02 4.44e+03 5.10e+01 bond pdb=" C4 AMP A1101 " pdb=" C5 AMP A1101 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.25e+01 ... (remaining 11163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 15060 3.60 - 7.20: 62 7.20 - 10.79: 13 10.79 - 14.39: 1 14.39 - 17.99: 1 Bond angle restraints: 15137 Sorted by residual: angle pdb=" P1 POP A1103 " pdb=" O POP A1103 " pdb=" P2 POP A1103 " ideal model delta sigma weight residual 139.66 121.67 17.99 3.00e+00 1.11e-01 3.60e+01 angle pdb=" C1' AMP A1101 " pdb=" O4' AMP A1101 " pdb=" C4' AMP A1101 " ideal model delta sigma weight residual 109.70 104.39 5.31 1.00e+00 1.00e+00 2.82e+01 angle pdb=" C2' AMP A1101 " pdb=" C3' AMP A1101 " pdb=" C4' AMP A1101 " ideal model delta sigma weight residual 102.60 107.11 -4.51 1.00e+00 1.00e+00 2.04e+01 angle pdb=" O2P AMP A1101 " pdb=" P AMP A1101 " pdb=" O3P AMP A1101 " ideal model delta sigma weight residual 119.90 106.88 13.02 3.00e+00 1.11e-01 1.88e+01 angle pdb=" C3' AMP A1101 " pdb=" C2' AMP A1101 " pdb=" O2' AMP A1101 " ideal model delta sigma weight residual 114.60 108.35 6.25 1.50e+00 4.44e-01 1.73e+01 ... (remaining 15132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.82: 6500 32.82 - 65.64: 269 65.64 - 98.47: 22 98.47 - 131.29: 5 131.29 - 164.11: 3 Dihedral angle restraints: 6799 sinusoidal: 2818 harmonic: 3981 Sorted by residual: dihedral pdb=" C5' AMP A1101 " pdb=" O5' AMP A1101 " pdb=" P AMP A1101 " pdb=" O3P AMP A1101 " ideal model delta sinusoidal sigma weight residual -60.00 -160.15 100.15 1 2.00e+01 2.50e-03 2.82e+01 dihedral pdb=" C6 IHP A1102 " pdb=" C1 IHP A1102 " pdb=" C2 IHP A1102 " pdb=" O12 IHP A1102 " ideal model delta sinusoidal sigma weight residual 61.05 -103.06 164.11 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O12 IHP A1102 " pdb=" C2 IHP A1102 " pdb=" C3 IHP A1102 " pdb=" O13 IHP A1102 " ideal model delta sinusoidal sigma weight residual 64.08 -90.17 154.25 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 6796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.991: 1693 0.991 - 1.981: 0 1.981 - 2.972: 0 2.972 - 3.962: 0 3.962 - 4.953: 3 Chirality restraints: 1696 Sorted by residual: chirality pdb=" C4 IHP A1102 " pdb=" C3 IHP A1102 " pdb=" C5 IHP A1102 " pdb=" O14 IHP A1102 " both_signs ideal model delta sigma weight residual False 2.48 -2.47 4.95 2.00e-01 2.50e+01 6.13e+02 chirality pdb=" C1 IHP A1102 " pdb=" C2 IHP A1102 " pdb=" C6 IHP A1102 " pdb=" O11 IHP A1102 " both_signs ideal model delta sigma weight residual False 2.32 -2.42 4.74 2.00e-01 2.50e+01 5.61e+02 chirality pdb=" C2 IHP A1102 " pdb=" C1 IHP A1102 " pdb=" C3 IHP A1102 " pdb=" O12 IHP A1102 " both_signs ideal model delta sigma weight residual False -2.52 2.16 -4.68 2.00e-01 2.50e+01 5.48e+02 ... (remaining 1693 not shown) Planarity restraints: 1934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 293 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 294 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 513 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO A 514 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 514 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 514 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 430 " -0.036 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 431 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " -0.030 5.00e-02 4.00e+02 ... (remaining 1931 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 244 2.70 - 3.25: 10538 3.25 - 3.80: 17693 3.80 - 4.35: 23323 4.35 - 4.90: 38736 Nonbonded interactions: 90534 Sorted by model distance: nonbonded pdb=" OH TYR A 710 " pdb=" O31 IHP A1102 " model vdw 2.148 3.040 nonbonded pdb=" OG SER A 108 " pdb=" OD1 ASP A 110 " model vdw 2.173 3.040 nonbonded pdb=" OD2 ASP A 499 " pdb=" O2' AMP A1101 " model vdw 2.214 3.040 nonbonded pdb=" OE2 GLU A 435 " pdb=" OG1 THR A 453 " model vdw 2.220 3.040 nonbonded pdb=" O ARG A 615 " pdb=" OG1 THR C 129 " model vdw 2.246 3.040 ... (remaining 90529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.610 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.005 0.208 11171 Z= 0.355 Angle : 0.645 17.991 15139 Z= 0.301 Chirality : 0.206 4.953 1696 Planarity : 0.005 0.103 1934 Dihedral : 18.003 164.110 4218 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 0.33 % Allowed : 21.79 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.23), residues: 1357 helix: 1.71 (0.24), residues: 470 sheet: 0.28 (0.35), residues: 209 loop : -0.32 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 164 TYR 0.007 0.001 TYR A 979 PHE 0.024 0.001 PHE A 510 TRP 0.006 0.001 TRP A 192 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.28 (11168) covalent geometry : angle 0.64453 / 0.30 (15137) SS BOND : bond 0.00178 / 0.09 ( 1) SS BOND : angle 0.40413 / 0.24 ( 2) hydrogen bonds : bond 0.13861 / 9.46 ( 433) hydrogen bonds : angle 6.12858 / 4.47 ( 1188) Misc. bond : bond 0.16350 / 7.95 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.400 Fit side-chains REVERT: A 724 LEU cc_start: 0.8425 (mt) cc_final: 0.8202 (mt) REVERT: A 998 MET cc_start: 0.3920 (ptm) cc_final: 0.3613 (pp-130) REVERT: D 118 MET cc_start: 0.6156 (ptp) cc_final: 0.5526 (mpm) outliers start: 2 outliers final: 2 residues processed: 98 average time/residue: 0.5290 time to fit residues: 56.4725 Evaluate side-chains 95 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 844 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 143 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127163 restraints weight = 11358.448| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.21 r_work: 0.3436 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11171 Z= 0.154 Angle : 0.588 11.450 15139 Z= 0.278 Chirality : 0.047 0.588 1696 Planarity : 0.005 0.074 1934 Dihedral : 8.550 95.919 1525 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 2.65 % Allowed : 20.71 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.23), residues: 1357 helix: 1.38 (0.24), residues: 489 sheet: 0.26 (0.35), residues: 212 loop : -0.32 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 166 TYR 0.010 0.001 TYR A 979 PHE 0.022 0.001 PHE A 510 TRP 0.006 0.001 TRP A 735 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.15 (11168) covalent geometry : angle 0.58774 / 0.28 (15137) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 0.54936 / 0.32 ( 2) hydrogen bonds : bond 0.04151 / 2.80 ( 433) hydrogen bonds : angle 5.01855 / 3.62 ( 1188) Misc. bond : bond 0.00080 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.347 Fit side-chains REVERT: A 248 ARG cc_start: 0.5119 (OUTLIER) cc_final: 0.4641 (ppt-90) REVERT: A 420 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: A 724 LEU cc_start: 0.8534 (mt) cc_final: 0.8246 (mt) REVERT: A 1010 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.6295 (t-90) REVERT: B 268 ARG cc_start: 0.6197 (tpp-160) cc_final: 0.5366 (tpt170) REVERT: B 283 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6019 (mp0) REVERT: C 104 LEU cc_start: 0.4864 (OUTLIER) cc_final: 0.4624 (pp) outliers start: 30 outliers final: 14 residues processed: 125 average time/residue: 0.5182 time to fit residues: 70.4012 Evaluate side-chains 118 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 123 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN D 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.185526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126201 restraints weight = 11466.866| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.20 r_work: 0.3421 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11171 Z= 0.162 Angle : 0.572 11.166 15139 Z= 0.275 Chirality : 0.046 0.441 1696 Planarity : 0.005 0.064 1934 Dihedral : 8.523 96.205 1521 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.17 % Rotamer: Outliers : 3.89 % Allowed : 20.71 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1357 helix: 1.19 (0.24), residues: 495 sheet: 0.24 (0.34), residues: 217 loop : -0.41 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 869 TYR 0.011 0.001 TYR A 979 PHE 0.019 0.001 PHE A 510 TRP 0.007 0.001 TRP A 192 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (11168) covalent geometry : angle 0.57226 / 0.27 (15137) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 0.51477 / 0.30 ( 2) hydrogen bonds : bond 0.03972 / 2.68 ( 433) hydrogen bonds : angle 4.87804 / 3.50 ( 1188) Misc. bond : bond 0.00068 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.396 Fit side-chains REVERT: A 177 GLN cc_start: 0.6124 (OUTLIER) cc_final: 0.5880 (pt0) REVERT: A 248 ARG cc_start: 0.5182 (OUTLIER) cc_final: 0.4824 (ppt-90) REVERT: A 339 TYR cc_start: 0.8047 (m-80) cc_final: 0.7825 (m-80) REVERT: A 420 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7482 (pm20) REVERT: A 724 LEU cc_start: 0.8525 (mt) cc_final: 0.8232 (mt) REVERT: A 1010 HIS cc_start: 0.6379 (OUTLIER) cc_final: 0.6162 (t-90) REVERT: B 164 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7206 (mpp-170) REVERT: B 268 ARG cc_start: 0.6262 (tpp-160) cc_final: 0.5406 (tpt170) REVERT: B 283 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.5965 (mp0) REVERT: B 325 LEU cc_start: 0.4558 (OUTLIER) cc_final: 0.4355 (mm) REVERT: C 104 LEU cc_start: 0.5110 (OUTLIER) cc_final: 0.4868 (pp) outliers start: 45 outliers final: 23 residues processed: 135 average time/residue: 0.4862 time to fit residues: 71.6358 Evaluate side-chains 130 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 998 MET Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 151 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN A 348 GLN A 759 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.186153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127298 restraints weight = 11471.899| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.20 r_work: 0.3433 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11171 Z= 0.134 Angle : 0.541 11.186 15139 Z= 0.261 Chirality : 0.043 0.395 1696 Planarity : 0.004 0.057 1934 Dihedral : 8.602 96.268 1521 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.17 % Rotamer: Outliers : 3.65 % Allowed : 20.96 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.23), residues: 1357 helix: 1.17 (0.24), residues: 502 sheet: 0.22 (0.34), residues: 217 loop : -0.42 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 869 TYR 0.010 0.001 TYR A 979 PHE 0.020 0.001 PHE A 510 TRP 0.006 0.001 TRP A 660 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (11168) covalent geometry : angle 0.54064 / 0.26 (15137) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 0.40480 / 0.24 ( 2) hydrogen bonds : bond 0.03570 / 2.40 ( 433) hydrogen bonds : angle 4.73177 / 3.39 ( 1188) Misc. bond : bond 0.00050 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.444 Fit side-chains REVERT: A 248 ARG cc_start: 0.5210 (OUTLIER) cc_final: 0.4846 (ppt-90) REVERT: A 280 GLU cc_start: 0.3624 (OUTLIER) cc_final: 0.3423 (pm20) REVERT: A 420 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7438 (pm20) REVERT: A 724 LEU cc_start: 0.8540 (mt) cc_final: 0.8247 (mt) REVERT: B 268 ARG cc_start: 0.6397 (tpp-160) cc_final: 0.5525 (tpt170) REVERT: C 104 LEU cc_start: 0.5098 (OUTLIER) cc_final: 0.4894 (pp) outliers start: 42 outliers final: 20 residues processed: 133 average time/residue: 0.5534 time to fit residues: 80.1966 Evaluate side-chains 124 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 998 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 151 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 29 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 39 optimal weight: 0.0050 chunk 119 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN A 251 ASN A 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.188276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129891 restraints weight = 11409.677| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.19 r_work: 0.3466 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11171 Z= 0.101 Angle : 0.512 11.404 15139 Z= 0.245 Chirality : 0.042 0.350 1696 Planarity : 0.004 0.052 1934 Dihedral : 8.470 95.152 1521 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 3.56 % Allowed : 21.13 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1357 helix: 1.63 (0.24), residues: 482 sheet: 0.17 (0.35), residues: 212 loop : -0.34 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 101 TYR 0.008 0.001 TYR A 979 PHE 0.025 0.001 PHE A 510 TRP 0.005 0.001 TRP A 660 HIS 0.003 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (11168) covalent geometry : angle 0.51187 / 0.25 (15137) SS BOND : bond 0.00077 / 0.04 ( 1) SS BOND : angle 0.26863 / 0.16 ( 2) hydrogen bonds : bond 0.03120 / 2.09 ( 433) hydrogen bonds : angle 4.54344 / 3.26 ( 1188) Misc. bond : bond 0.00031 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.451 Fit side-chains REVERT: A 248 ARG cc_start: 0.5229 (OUTLIER) cc_final: 0.4942 (ppt-90) REVERT: A 510 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.6104 (p90) REVERT: A 724 LEU cc_start: 0.8544 (mt) cc_final: 0.8252 (mt) REVERT: A 1007 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6043 (pp) REVERT: B 268 ARG cc_start: 0.6401 (tpp-160) cc_final: 0.5514 (tpt170) outliers start: 41 outliers final: 21 residues processed: 131 average time/residue: 0.5273 time to fit residues: 75.5840 Evaluate side-chains 126 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 998 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 151 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.189006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130453 restraints weight = 11385.984| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.20 r_work: 0.3472 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11171 Z= 0.099 Angle : 0.507 10.889 15139 Z= 0.243 Chirality : 0.042 0.351 1696 Planarity : 0.004 0.049 1934 Dihedral : 8.420 94.639 1521 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 3.81 % Allowed : 21.13 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.23), residues: 1357 helix: 1.68 (0.24), residues: 482 sheet: 0.20 (0.35), residues: 212 loop : -0.31 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 101 TYR 0.008 0.001 TYR A 979 PHE 0.024 0.001 PHE A 510 TRP 0.005 0.001 TRP A 660 HIS 0.002 0.000 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (11168) covalent geometry : angle 0.50678 / 0.24 (15137) SS BOND : bond 0.00076 / 0.04 ( 1) SS BOND : angle 0.25424 / 0.15 ( 2) hydrogen bonds : bond 0.03047 / 2.04 ( 433) hydrogen bonds : angle 4.48255 / 3.22 ( 1188) Misc. bond : bond 0.00030 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 0.382 Fit side-chains REVERT: A 248 ARG cc_start: 0.5214 (OUTLIER) cc_final: 0.4930 (ppt-90) REVERT: A 510 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.6237 (p90) REVERT: A 724 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8220 (mt) REVERT: A 1007 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6025 (pp) REVERT: B 268 ARG cc_start: 0.6403 (tpp-160) cc_final: 0.5513 (tpt170) REVERT: B 325 LEU cc_start: 0.4559 (OUTLIER) cc_final: 0.4349 (mm) outliers start: 44 outliers final: 28 residues processed: 132 average time/residue: 0.4833 time to fit residues: 70.1577 Evaluate side-chains 136 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 998 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 151 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.188976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130218 restraints weight = 11400.772| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.21 r_work: 0.3467 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11171 Z= 0.102 Angle : 0.511 10.992 15139 Z= 0.246 Chirality : 0.042 0.350 1696 Planarity : 0.004 0.048 1934 Dihedral : 8.409 94.564 1521 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 3.56 % Allowed : 21.46 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1357 helix: 1.71 (0.24), residues: 482 sheet: 0.23 (0.35), residues: 212 loop : -0.32 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 101 TYR 0.008 0.001 TYR A 979 PHE 0.024 0.001 PHE A 510 TRP 0.005 0.001 TRP A 660 HIS 0.002 0.000 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (11168) covalent geometry : angle 0.51128 / 0.25 (15137) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 0.25638 / 0.15 ( 2) hydrogen bonds : bond 0.03039 / 2.03 ( 433) hydrogen bonds : angle 4.44846 / 3.20 ( 1188) Misc. bond : bond 0.00028 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.421 Fit side-chains REVERT: A 248 ARG cc_start: 0.5236 (OUTLIER) cc_final: 0.4937 (ppt-90) REVERT: A 253 MET cc_start: 0.3072 (mtt) cc_final: 0.2842 (mtt) REVERT: A 280 GLU cc_start: 0.3529 (OUTLIER) cc_final: 0.3301 (pm20) REVERT: A 724 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8243 (mt) REVERT: A 1007 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6044 (pp) REVERT: B 268 ARG cc_start: 0.6433 (tpp-160) cc_final: 0.5505 (tpt170) REVERT: B 283 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: B 325 LEU cc_start: 0.4574 (OUTLIER) cc_final: 0.4357 (mm) outliers start: 41 outliers final: 28 residues processed: 133 average time/residue: 0.4985 time to fit residues: 72.8214 Evaluate side-chains 138 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 998 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 132 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 98 optimal weight: 0.0000 chunk 122 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 30.0000 chunk 24 optimal weight: 6.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.186504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.127513 restraints weight = 11441.493| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.20 r_work: 0.3433 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11171 Z= 0.140 Angle : 0.539 10.961 15139 Z= 0.260 Chirality : 0.043 0.372 1696 Planarity : 0.004 0.048 1934 Dihedral : 8.618 97.189 1521 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.17 % Rotamer: Outliers : 3.81 % Allowed : 21.04 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.23), residues: 1357 helix: 1.54 (0.24), residues: 482 sheet: 0.25 (0.34), residues: 217 loop : -0.38 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 101 TYR 0.009 0.001 TYR A 979 PHE 0.028 0.001 PHE A 510 TRP 0.008 0.001 TRP A 660 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (11168) covalent geometry : angle 0.53870 / 0.26 (15137) SS BOND : bond 0.00105 / 0.06 ( 1) SS BOND : angle 0.38040 / 0.22 ( 2) hydrogen bonds : bond 0.03530 / 2.36 ( 433) hydrogen bonds : angle 4.59979 / 3.30 ( 1188) Misc. bond : bond 0.00045 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 0.440 Fit side-chains REVERT: A 248 ARG cc_start: 0.5177 (OUTLIER) cc_final: 0.4833 (ppt-90) REVERT: A 280 GLU cc_start: 0.3480 (OUTLIER) cc_final: 0.3226 (pm20) REVERT: A 724 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8275 (mt) REVERT: A 967 THR cc_start: 0.5955 (OUTLIER) cc_final: 0.5540 (t) REVERT: A 1007 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.5938 (pp) REVERT: B 268 ARG cc_start: 0.6386 (tpp-160) cc_final: 0.5454 (tpt170) REVERT: B 283 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: B 325 LEU cc_start: 0.4826 (OUTLIER) cc_final: 0.4569 (mm) outliers start: 44 outliers final: 26 residues processed: 131 average time/residue: 0.4957 time to fit residues: 71.3728 Evaluate side-chains 134 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 132 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 56 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.188475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129992 restraints weight = 11343.655| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.19 r_work: 0.3465 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11171 Z= 0.105 Angle : 0.515 11.037 15139 Z= 0.248 Chirality : 0.042 0.348 1696 Planarity : 0.004 0.047 1934 Dihedral : 8.532 95.842 1521 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 3.15 % Allowed : 21.79 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1357 helix: 1.65 (0.24), residues: 482 sheet: 0.22 (0.34), residues: 217 loop : -0.36 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 101 TYR 0.008 0.001 TYR A 979 PHE 0.026 0.001 PHE A 510 TRP 0.005 0.001 TRP A 192 HIS 0.002 0.000 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11168) covalent geometry : angle 0.51474 / 0.25 (15137) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 0.29404 / 0.17 ( 2) hydrogen bonds : bond 0.03110 / 2.07 ( 433) hydrogen bonds : angle 4.47170 / 3.21 ( 1188) Misc. bond : bond 0.00031 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.375 Fit side-chains REVERT: A 248 ARG cc_start: 0.5216 (OUTLIER) cc_final: 0.4883 (ppt-90) REVERT: A 280 GLU cc_start: 0.3408 (OUTLIER) cc_final: 0.3192 (pm20) REVERT: A 510 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.6184 (p90) REVERT: A 724 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8248 (mt) REVERT: A 967 THR cc_start: 0.5933 (OUTLIER) cc_final: 0.5526 (t) REVERT: A 1007 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.5948 (pp) REVERT: B 268 ARG cc_start: 0.6385 (tpp-160) cc_final: 0.5455 (tpt170) REVERT: B 325 LEU cc_start: 0.4803 (OUTLIER) cc_final: 0.4552 (mm) outliers start: 36 outliers final: 24 residues processed: 128 average time/residue: 0.4645 time to fit residues: 65.5275 Evaluate side-chains 133 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 132 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 56 optimal weight: 0.0270 overall best weight: 1.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN C 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.187679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128824 restraints weight = 11384.165| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.20 r_work: 0.3452 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11171 Z= 0.120 Angle : 0.526 10.902 15139 Z= 0.253 Chirality : 0.043 0.354 1696 Planarity : 0.004 0.048 1934 Dihedral : 8.598 96.539 1521 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 2.82 % Allowed : 22.12 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1357 helix: 1.61 (0.24), residues: 482 sheet: 0.24 (0.34), residues: 217 loop : -0.36 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 101 TYR 0.009 0.001 TYR B 279 PHE 0.027 0.001 PHE A 510 TRP 0.007 0.001 TRP A 660 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (11168) covalent geometry : angle 0.52570 / 0.25 (15137) SS BOND : bond 0.00079 / 0.04 ( 1) SS BOND : angle 0.34057 / 0.20 ( 2) hydrogen bonds : bond 0.03299 / 2.20 ( 433) hydrogen bonds : angle 4.52685 / 3.25 ( 1188) Misc. bond : bond 0.00033 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.426 Fit side-chains REVERT: A 248 ARG cc_start: 0.5249 (OUTLIER) cc_final: 0.4896 (ppt-90) REVERT: A 724 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8280 (mt) REVERT: A 967 THR cc_start: 0.6004 (OUTLIER) cc_final: 0.5590 (t) REVERT: A 1007 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.5949 (pp) REVERT: B 268 ARG cc_start: 0.6433 (tpp-160) cc_final: 0.5538 (tpt170) REVERT: B 325 LEU cc_start: 0.4802 (OUTLIER) cc_final: 0.4535 (mm) outliers start: 32 outliers final: 25 residues processed: 123 average time/residue: 0.5023 time to fit residues: 68.0891 Evaluate side-chains 130 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 132 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 93 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN C 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.189156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130867 restraints weight = 11390.163| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.20 r_work: 0.3470 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11171 Z= 0.101 Angle : 0.517 11.046 15139 Z= 0.249 Chirality : 0.042 0.341 1696 Planarity : 0.004 0.047 1934 Dihedral : 8.541 95.607 1521 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.53 % Rotamer: Outliers : 2.73 % Allowed : 22.20 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1357 helix: 1.69 (0.24), residues: 482 sheet: 0.20 (0.35), residues: 212 loop : -0.34 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 101 TYR 0.010 0.001 TYR B 279 PHE 0.029 0.001 PHE A 510 TRP 0.005 0.001 TRP A 192 HIS 0.002 0.000 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (11168) covalent geometry : angle 0.51742 / 0.25 (15137) SS BOND : bond 0.00061 / 0.03 ( 1) SS BOND : angle 0.26320 / 0.15 ( 2) hydrogen bonds : bond 0.03039 / 2.03 ( 433) hydrogen bonds : angle 4.46444 / 3.20 ( 1188) Misc. bond : bond 0.00028 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4330.99 seconds wall clock time: 74 minutes 33.89 seconds (4473.89 seconds total)