Starting phenix.real_space_refine on Thu Aug 6 07:42:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh5_37529/08_2026/8wh5_37529.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh5_37529/08_2026/8wh5_37529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wh5_37529/08_2026/8wh5_37529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh5_37529/08_2026/8wh5_37529.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wh5_37529/08_2026/8wh5_37529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh5_37529/08_2026/8wh5_37529.map" } resolution = 3.58 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= 0.002 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 266 5.49 5 S 29 5.16 5 C 8448 2.51 5 N 2701 2.21 5 O 3219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14663 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 766 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 617 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 662 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "E" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 695 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 706 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 750 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2710 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "J" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2743 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "K" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3604 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 16, 'TRANS': 428} Chain breaks: 1 Time building chain proxies: 3.21, per 1000 atoms: 0.22 Number of scatterers: 14663 At special positions: 0 Unit cell: (135.09, 135.945, 117.99, 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 29 16.00 P 266 15.00 O 3219 8.00 N 2701 7.00 C 8448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 421.0 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 64.7% alpha, 4.1% beta 103 base pairs and 208 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.524A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.911A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.803A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.793A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.567A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.054A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 46 through 75 removed outlier: 4.082A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.625A pdb=" N ILE C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 80 through 108 removed outlier: 3.521A pdb=" N MET D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.604A pdb=" N ILE D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 149 removed outlier: 3.823A pdb=" N SER D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 55 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 87 through 114 removed outlier: 3.680A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.711A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 50 through 75 removed outlier: 4.243A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.636A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 75 removed outlier: 4.423A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG G 72 " --> pdb=" O GLY G 68 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP G 73 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.512A pdb=" N ILE G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'H' and resid 62 through 74 removed outlier: 3.701A pdb=" N LYS H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 109 removed outlier: 4.328A pdb=" N SER H 89 " --> pdb=" O GLY H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 126 Processing helix chain 'H' and resid 129 through 148 removed outlier: 3.927A pdb=" N LYS H 133 " --> pdb=" O GLY H 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 220 Processing helix chain 'K' and resid 233 through 245 removed outlier: 3.789A pdb=" N PHE K 240 " --> pdb=" O GLN K 236 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU K 241 " --> pdb=" O THR K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 249 removed outlier: 4.175A pdb=" N LEU K 249 " --> pdb=" O GLY K 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 246 through 249' Processing helix chain 'K' and resid 258 through 269 Processing helix chain 'K' and resid 285 through 294 removed outlier: 4.216A pdb=" N ARG K 292 " --> pdb=" O ARG K 288 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 317 Processing helix chain 'K' and resid 317 through 323 removed outlier: 4.067A pdb=" N ILE K 321 " --> pdb=" O ASP K 317 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG K 323 " --> pdb=" O LYS K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 339 Processing helix chain 'K' and resid 343 through 352 removed outlier: 3.873A pdb=" N HIS K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 380 Processing helix chain 'K' and resid 416 through 425 removed outlier: 3.652A pdb=" N ILE K 423 " --> pdb=" O LYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 465 Processing helix chain 'K' and resid 467 through 474 removed outlier: 3.534A pdb=" N GLU K 474 " --> pdb=" O ALA K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 499 Processing helix chain 'K' and resid 500 through 508 Processing helix chain 'K' and resid 519 through 522 Processing helix chain 'K' and resid 523 through 536 Processing helix chain 'K' and resid 550 through 564 removed outlier: 3.563A pdb=" N LYS K 563 " --> pdb=" O TYR K 559 " (cutoff:3.500A) Processing helix chain 'K' and resid 575 through 587 Processing helix chain 'K' and resid 604 through 608 removed outlier: 3.520A pdb=" N ILE K 607 " --> pdb=" O GLY K 604 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN K 608 " --> pdb=" O LEU K 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 604 through 608' Processing helix chain 'K' and resid 623 through 635 removed outlier: 4.322A pdb=" N ASP K 627 " --> pdb=" O ASN K 623 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS K 634 " --> pdb=" O ALA K 630 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 674 removed outlier: 3.654A pdb=" N VAL K 672 " --> pdb=" O LEU K 668 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.379A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.401A pdb=" N ARG C 43 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'F' and resid 97 through 98 removed outlier: 3.696A pdb=" N TYR F 98 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.507A pdb=" N ARG G 43 " --> pdb=" O ILE H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 278 through 280 removed outlier: 6.673A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU K 254 " --> pdb=" O VAL K 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 444 through 450 removed outlier: 3.587A pdb=" N MET K 448 " --> pdb=" O ARG K 647 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER K 649 " --> pdb=" O MET K 448 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N CYS K 615 " --> pdb=" O TYR K 646 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU K 648 " --> pdb=" O CYS K 615 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU K 617 " --> pdb=" O LEU K 648 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N THR K 650 " --> pdb=" O LEU K 617 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 568 through 570 removed outlier: 6.350A pdb=" N CYS K 568 " --> pdb=" O LEU K 597 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 500 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 269 hydrogen bonds 530 hydrogen bond angles 0 basepair planarities 103 basepair parallelities 208 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1730 1.28 - 1.42: 4899 1.42 - 1.55: 8153 1.55 - 1.69: 643 1.69 - 1.82: 48 Bond restraints: 15473 Sorted by residual: bond pdb=" C SER K 653 " pdb=" O SER K 653 " ideal model delta sigma weight residual 1.235 1.315 -0.080 1.02e-02 9.61e+03 6.15e+01 bond pdb=" C VAL H 136 " pdb=" O VAL H 136 " ideal model delta sigma weight residual 1.237 1.148 0.089 1.14e-02 7.69e+03 6.11e+01 bond pdb=" C PRO K 258 " pdb=" O PRO K 258 " ideal model delta sigma weight residual 1.235 1.150 0.085 1.30e-02 5.92e+03 4.30e+01 bond pdb=" C ILE K 491 " pdb=" O ILE K 491 " ideal model delta sigma weight residual 1.237 1.185 0.051 9.80e-03 1.04e+04 2.76e+01 bond pdb=" CA SER K 653 " pdb=" C SER K 653 " ideal model delta sigma weight residual 1.524 1.588 -0.064 1.25e-02 6.40e+03 2.59e+01 ... (remaining 15468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 21333 3.47 - 6.94: 652 6.94 - 10.42: 33 10.42 - 13.89: 0 13.89 - 17.36: 2 Bond angle restraints: 22020 Sorted by residual: angle pdb=" N LYS H 104 " pdb=" CA LYS H 104 " pdb=" C LYS H 104 " ideal model delta sigma weight residual 111.28 103.00 8.28 1.09e+00 8.42e-01 5.77e+01 angle pdb=" N GLU K 518 " pdb=" CA GLU K 518 " pdb=" C GLU K 518 " ideal model delta sigma weight residual 114.56 104.94 9.62 1.27e+00 6.20e-01 5.74e+01 angle pdb=" O3' DC I 107 " pdb=" C3' DC I 107 " pdb=" C2' DC I 107 " ideal model delta sigma weight residual 109.40 126.76 -17.36 2.50e+00 1.60e-01 4.82e+01 angle pdb=" N ARG D 107 " pdb=" CA ARG D 107 " pdb=" C ARG D 107 " ideal model delta sigma weight residual 110.97 103.50 7.47 1.09e+00 8.42e-01 4.69e+01 angle pdb=" O3' DG J 112 " pdb=" C3' DG J 112 " pdb=" C2' DG J 112 " ideal model delta sigma weight residual 109.40 126.00 -16.60 2.50e+00 1.60e-01 4.41e+01 ... (remaining 22015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 7380 35.56 - 71.12: 1198 71.12 - 106.68: 26 106.68 - 142.25: 5 142.25 - 177.81: 5 Dihedral angle restraints: 8614 sinusoidal: 5274 harmonic: 3340 Sorted by residual: dihedral pdb=" CA VAL B 81 " pdb=" C VAL B 81 " pdb=" N THR B 82 " pdb=" CA THR B 82 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" C4' DC I 110 " pdb=" C3' DC I 110 " pdb=" O3' DC I 110 " pdb=" P DC I 111 " ideal model delta sinusoidal sigma weight residual -140.00 37.81 -177.81 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 3 " pdb=" C3' DC I 3 " pdb=" O3' DC I 3 " pdb=" P DG I 4 " ideal model delta sinusoidal sigma weight residual -140.00 29.39 -169.39 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 8611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 2446 0.177 - 0.355: 51 0.355 - 0.532: 0 0.532 - 0.710: 0 0.710 - 0.887: 2 Chirality restraints: 2499 Sorted by residual: chirality pdb=" C3' DG J 112 " pdb=" C4' DG J 112 " pdb=" O3' DG J 112 " pdb=" C2' DG J 112 " both_signs ideal model delta sigma weight residual False -2.73 -1.84 -0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" C3' DC I 107 " pdb=" C4' DC I 107 " pdb=" O3' DC I 107 " pdb=" C2' DC I 107 " both_signs ideal model delta sigma weight residual False -2.73 -1.96 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" CA LEU K 372 " pdb=" N LEU K 372 " pdb=" C LEU K 372 " pdb=" CB LEU K 372 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2496 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 148 " 0.024 2.00e-02 2.50e+03 4.70e-02 2.21e+01 pdb=" C SER H 148 " -0.081 2.00e-02 2.50e+03 pdb=" O SER H 148 " 0.030 2.00e-02 2.50e+03 pdb=" N SER H 149 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 376 " 0.021 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C LEU K 376 " -0.076 2.00e-02 2.50e+03 pdb=" O LEU K 376 " 0.028 2.00e-02 2.50e+03 pdb=" N ASN K 377 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 85 " 0.021 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C GLN A 85 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN A 85 " 0.025 2.00e-02 2.50e+03 pdb=" N SER A 86 " 0.024 2.00e-02 2.50e+03 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2326 2.76 - 3.29: 14097 3.29 - 3.83: 25940 3.83 - 4.36: 32559 4.36 - 4.90: 45781 Nonbonded interactions: 120703 Sorted by model distance: nonbonded pdb=" O SER K 620 " pdb=" OD1 ASP K 621 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP K 621 " pdb=" OD1 ASP K 627 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASN K 368 " pdb=" N SER K 370 " model vdw 2.319 3.120 nonbonded pdb=" O LYS K 294 " pdb=" NZ LYS K 294 " model vdw 2.325 3.120 nonbonded pdb=" O GLU G 92 " pdb=" OG SER G 95 " model vdw 2.351 3.040 ... (remaining 120698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 50 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 100) selection = (chain 'F' and resid 25 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 21 through 108) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 61 through 149) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.430 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.012 0.089 15473 Z= 0.924 Angle : 1.369 17.360 22020 Z= 1.026 Chirality : 0.075 0.887 2499 Planarity : 0.008 0.047 1858 Dihedral : 25.452 177.808 6458 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.39 % Favored : 91.81 % Rotamer: Outliers : 0.91 % Allowed : 6.30 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.21), residues: 1136 helix: -1.56 (0.17), residues: 691 sheet: -3.21 (0.55), residues: 55 loop : -3.36 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 431 TYR 0.041 0.003 TYR K 329 PHE 0.028 0.003 PHE D 67 TRP 0.015 0.002 TRP K 482 HIS 0.015 0.002 HIS H 74 Details of bonding type rmsd/Z covalent geometry : bond 0.01225 / 0.92 (15473) covalent geometry : angle 1.36856 / 1.03 (22020) hydrogen bonds : bond 0.22449 / 14.88 ( 769) hydrogen bonds : angle 9.65229 / 6.95 ( 2006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 328 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8930 (pt) cc_final: 0.8554 (mt) REVERT: A 73 GLU cc_start: 0.8019 (tt0) cc_final: 0.7760 (tt0) REVERT: B 25 ASN cc_start: 0.5358 (m110) cc_final: 0.4648 (m-40) REVERT: D 81 SER cc_start: 0.8822 (t) cc_final: 0.8571 (p) REVERT: E 97 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7157 (mt-10) REVERT: E 123 ASP cc_start: 0.8469 (m-30) cc_final: 0.8235 (m-30) REVERT: G 74 ASN cc_start: 0.8122 (t0) cc_final: 0.7855 (t0) REVERT: K 373 TRP cc_start: 0.5573 (t60) cc_final: 0.5302 (t-100) REVERT: K 432 MET cc_start: 0.8212 (mmm) cc_final: 0.7497 (ttm) REVERT: K 615 CYS cc_start: 0.7641 (m) cc_final: 0.7157 (m) REVERT: K 631 MET cc_start: 0.9284 (mtp) cc_final: 0.9074 (mtp) outliers start: 9 outliers final: 0 residues processed: 334 average time/residue: 0.1704 time to fit residues: 75.9512 Evaluate side-chains 172 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 40.0000 chunk 55 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 72 GLN E 85 GLN G 90 ASN G 105 ASN G 111 ASN K 295 HIS K 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.096385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.069063 restraints weight = 52166.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071221 restraints weight = 25438.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.072530 restraints weight = 16884.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073318 restraints weight = 13532.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.073741 restraints weight = 12112.563| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15473 Z= 0.219 Angle : 0.850 13.151 22020 Z= 0.475 Chirality : 0.053 0.312 2499 Planarity : 0.006 0.046 1858 Dihedral : 29.590 172.651 4149 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.84 % Favored : 94.81 % Rotamer: Outliers : 2.95 % Allowed : 15.04 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.24), residues: 1136 helix: 0.59 (0.19), residues: 701 sheet: -2.55 (0.61), residues: 57 loop : -2.90 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 17 TYR 0.016 0.002 TYR K 663 PHE 0.013 0.002 PHE K 427 TRP 0.014 0.002 TRP K 265 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.22 (15473) covalent geometry : angle 0.85016 / 0.47 (22020) hydrogen bonds : bond 0.08579 / 5.76 ( 769) hydrogen bonds : angle 4.32207 / 3.10 ( 2006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 105 ASN cc_start: 0.7690 (t0) cc_final: 0.7482 (t0) REVERT: E 105 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7745 (tm-30) REVERT: G 74 ASN cc_start: 0.8058 (t0) cc_final: 0.7699 (t0) REVERT: G 93 GLU cc_start: 0.8352 (mp0) cc_final: 0.7879 (mt-10) REVERT: H 101 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7740 (mm-30) REVERT: K 315 MET cc_start: 0.8386 (tmm) cc_final: 0.8119 (tmm) outliers start: 29 outliers final: 14 residues processed: 206 average time/residue: 0.1090 time to fit residues: 33.1356 Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 87 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 overall best weight: 3.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.093257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.065449 restraints weight = 50141.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.067063 restraints weight = 26291.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067915 restraints weight = 16274.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068043 restraints weight = 15488.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068062 restraints weight = 14193.134| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15473 Z= 0.207 Angle : 0.741 11.684 22020 Z= 0.427 Chirality : 0.049 0.432 2499 Planarity : 0.005 0.046 1858 Dihedral : 29.462 167.353 4149 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.46 % Favored : 94.28 % Rotamer: Outliers : 3.86 % Allowed : 17.07 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1136 helix: 1.36 (0.20), residues: 705 sheet: -1.90 (0.63), residues: 57 loop : -2.61 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 17 TYR 0.016 0.002 TYR K 618 PHE 0.018 0.002 PHE D 67 TRP 0.014 0.002 TRP K 265 HIS 0.010 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 (15473) covalent geometry : angle 0.74089 / 0.43 (22020) hydrogen bonds : bond 0.07857 / 5.30 ( 769) hydrogen bonds : angle 4.00572 / 2.87 ( 2006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8125 (tt0) cc_final: 0.7916 (tt0) REVERT: C 105 ASN cc_start: 0.8074 (t0) cc_final: 0.7450 (t0) REVERT: D 101 GLU cc_start: 0.8139 (tp30) cc_final: 0.7744 (tp30) REVERT: E 105 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7936 (tm-30) REVERT: G 63 VAL cc_start: 0.8896 (t) cc_final: 0.8260 (t) REVERT: G 74 ASN cc_start: 0.8149 (t0) cc_final: 0.7732 (t0) REVERT: G 85 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8325 (tm-30) REVERT: G 93 GLU cc_start: 0.8485 (mp0) cc_final: 0.7978 (mt-10) REVERT: G 94 LEU cc_start: 0.9055 (mt) cc_final: 0.8381 (mt) REVERT: H 60 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7942 (mm-30) REVERT: H 101 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7653 (mm-30) REVERT: K 296 MET cc_start: 0.8567 (ptp) cc_final: 0.7972 (pmm) outliers start: 38 outliers final: 23 residues processed: 195 average time/residue: 0.1048 time to fit residues: 30.1489 Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 464 VAL Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 556 MET Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 626 MET Chi-restraints excluded: chain K residue 668 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 104 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN C 90 ASN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.093679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.066138 restraints weight = 49506.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068180 restraints weight = 25426.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068629 restraints weight = 15209.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.068760 restraints weight = 15133.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068854 restraints weight = 13951.520| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15473 Z= 0.156 Angle : 0.659 10.003 22020 Z= 0.383 Chirality : 0.045 0.286 2499 Planarity : 0.004 0.048 1858 Dihedral : 29.255 168.995 4149 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.49 % Favored : 95.25 % Rotamer: Outliers : 3.25 % Allowed : 18.29 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1136 helix: 1.89 (0.20), residues: 704 sheet: -1.22 (0.66), residues: 57 loop : -2.44 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 82 TYR 0.012 0.001 TYR K 663 PHE 0.021 0.001 PHE G 34 TRP 0.016 0.002 TRP K 265 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.16 (15473) covalent geometry : angle 0.65918 / 0.38 (22020) hydrogen bonds : bond 0.06770 / 4.55 ( 769) hydrogen bonds : angle 3.64014 / 2.61 ( 2006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: C 105 ASN cc_start: 0.8079 (t0) cc_final: 0.7651 (t0) REVERT: D 101 GLU cc_start: 0.8104 (tp30) cc_final: 0.7737 (tp30) REVERT: G 74 ASN cc_start: 0.8137 (t0) cc_final: 0.7687 (t0) REVERT: G 85 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8196 (tm-30) REVERT: G 93 GLU cc_start: 0.8361 (mp0) cc_final: 0.7933 (mt-10) REVERT: H 60 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7811 (tp30) REVERT: H 101 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7581 (mm-30) REVERT: K 432 MET cc_start: 0.7257 (mmp) cc_final: 0.6384 (tpp) REVERT: K 582 GLN cc_start: 0.8679 (mt0) cc_final: 0.8185 (tt0) outliers start: 32 outliers final: 18 residues processed: 172 average time/residue: 0.1115 time to fit residues: 29.0610 Evaluate side-chains 158 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain K residue 317 ASP Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 77 optimal weight: 40.0000 chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 134 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.091764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.064109 restraints weight = 49983.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066077 restraints weight = 26012.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066345 restraints weight = 16014.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066675 restraints weight = 15357.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.066633 restraints weight = 13941.331| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15473 Z= 0.180 Angle : 0.670 13.231 22020 Z= 0.383 Chirality : 0.044 0.277 2499 Planarity : 0.005 0.048 1858 Dihedral : 29.244 172.908 4149 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.49 % Favored : 95.25 % Rotamer: Outliers : 3.25 % Allowed : 19.21 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1136 helix: 1.98 (0.20), residues: 704 sheet: -0.87 (0.66), residues: 57 loop : -2.37 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 82 TYR 0.038 0.002 TYR K 513 PHE 0.012 0.001 PHE E 67 TRP 0.016 0.002 TRP K 265 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (15473) covalent geometry : angle 0.67024 / 0.38 (22020) hydrogen bonds : bond 0.06911 / 4.68 ( 769) hydrogen bonds : angle 3.64760 / 2.61 ( 2006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: C 105 ASN cc_start: 0.8182 (t0) cc_final: 0.7617 (t0) REVERT: D 101 GLU cc_start: 0.8184 (tp30) cc_final: 0.7813 (tp30) REVERT: G 74 ASN cc_start: 0.8115 (t0) cc_final: 0.7655 (t0) REVERT: G 85 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8265 (tm-30) REVERT: H 101 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7595 (mm-30) REVERT: K 432 MET cc_start: 0.7462 (mmp) cc_final: 0.6612 (tpp) outliers start: 32 outliers final: 24 residues processed: 170 average time/residue: 0.1036 time to fit residues: 27.1120 Evaluate side-chains 160 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 668 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 101 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 87 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 75 HIS G 111 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.090391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.062383 restraints weight = 49204.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.064145 restraints weight = 25953.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.064957 restraints weight = 16104.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.064969 restraints weight = 14846.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065066 restraints weight = 13869.627| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15473 Z= 0.188 Angle : 0.666 8.108 22020 Z= 0.384 Chirality : 0.044 0.264 2499 Planarity : 0.005 0.044 1858 Dihedral : 29.269 173.933 4149 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 3.96 % Allowed : 19.11 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.26), residues: 1136 helix: 1.93 (0.20), residues: 710 sheet: -0.42 (0.70), residues: 57 loop : -2.45 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 430 TYR 0.027 0.002 TYR D 108 PHE 0.012 0.001 PHE G 34 TRP 0.023 0.002 TRP K 265 HIS 0.011 0.001 HIS K 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (15473) covalent geometry : angle 0.66614 / 0.38 (22020) hydrogen bonds : bond 0.06965 / 4.66 ( 769) hydrogen bonds : angle 3.58849 / 2.54 ( 2006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8099 (mp0) cc_final: 0.7700 (mp0) REVERT: C 105 ASN cc_start: 0.8299 (t0) cc_final: 0.7941 (t0) REVERT: D 101 GLU cc_start: 0.8197 (tp30) cc_final: 0.7840 (tp30) REVERT: G 74 ASN cc_start: 0.8267 (t0) cc_final: 0.7824 (t0) REVERT: G 85 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8252 (tm-30) REVERT: G 93 GLU cc_start: 0.8488 (mp0) cc_final: 0.7747 (mt-10) REVERT: H 60 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7569 (tm-30) REVERT: H 101 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7580 (mm-30) REVERT: K 582 GLN cc_start: 0.8789 (mt0) cc_final: 0.8271 (tt0) outliers start: 39 outliers final: 23 residues processed: 170 average time/residue: 0.1077 time to fit residues: 27.7384 Evaluate side-chains 167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain K residue 317 ASP Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 105 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 111 ASN K 341 HIS ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.091432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.063625 restraints weight = 49074.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065378 restraints weight = 25371.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065614 restraints weight = 15642.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.065836 restraints weight = 15311.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.065977 restraints weight = 14257.636| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15473 Z= 0.141 Angle : 0.611 8.063 22020 Z= 0.358 Chirality : 0.041 0.259 2499 Planarity : 0.004 0.044 1858 Dihedral : 29.104 177.039 4149 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.14 % Favored : 95.60 % Rotamer: Outliers : 3.05 % Allowed : 20.83 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.26), residues: 1136 helix: 2.20 (0.20), residues: 708 sheet: -0.71 (0.65), residues: 65 loop : -2.20 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 117 TYR 0.025 0.002 TYR D 108 PHE 0.009 0.001 PHE D 67 TRP 0.024 0.002 TRP K 217 HIS 0.004 0.001 HIS H 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (15473) covalent geometry : angle 0.61135 / 0.36 (22020) hydrogen bonds : bond 0.06105 / 4.08 ( 769) hydrogen bonds : angle 3.35764 / 2.41 ( 2006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.9023 (pt) cc_final: 0.8592 (mt) REVERT: C 105 ASN cc_start: 0.8327 (t0) cc_final: 0.7987 (t0) REVERT: D 101 GLU cc_start: 0.8147 (tp30) cc_final: 0.7824 (tp30) REVERT: G 74 ASN cc_start: 0.8245 (t0) cc_final: 0.7752 (t0) REVERT: G 85 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8235 (tm-30) REVERT: G 93 GLU cc_start: 0.8443 (mp0) cc_final: 0.7866 (mt-10) REVERT: H 101 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7637 (mm-30) REVERT: K 296 MET cc_start: 0.8602 (ptp) cc_final: 0.7805 (pmm) REVERT: K 582 GLN cc_start: 0.8728 (mt0) cc_final: 0.8179 (tt0) REVERT: K 618 TYR cc_start: 0.9137 (t80) cc_final: 0.8763 (t80) outliers start: 30 outliers final: 19 residues processed: 169 average time/residue: 0.0930 time to fit residues: 24.0072 Evaluate side-chains 160 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain K residue 317 ASP Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 77 optimal weight: 40.0000 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN H 88 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.091558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.063996 restraints weight = 49987.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.065710 restraints weight = 26123.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.066161 restraints weight = 16332.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066341 restraints weight = 15580.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066392 restraints weight = 14498.271| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15473 Z= 0.140 Angle : 0.604 8.178 22020 Z= 0.351 Chirality : 0.041 0.254 2499 Planarity : 0.004 0.043 1858 Dihedral : 29.119 176.808 4149 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.79 % Favored : 95.95 % Rotamer: Outliers : 2.74 % Allowed : 21.44 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.26), residues: 1136 helix: 2.21 (0.20), residues: 709 sheet: -0.69 (0.64), residues: 70 loop : -2.08 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 117 TYR 0.030 0.002 TYR K 663 PHE 0.006 0.001 PHE G 34 TRP 0.026 0.002 TRP K 217 HIS 0.004 0.001 HIS H 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (15473) covalent geometry : angle 0.60378 / 0.35 (22020) hydrogen bonds : bond 0.05866 / 3.93 ( 769) hydrogen bonds : angle 3.27992 / 2.35 ( 2006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8100 (mp0) cc_final: 0.7722 (mp0) REVERT: C 105 ASN cc_start: 0.8354 (t0) cc_final: 0.8042 (t0) REVERT: D 101 GLU cc_start: 0.8172 (tp30) cc_final: 0.7881 (tp30) REVERT: G 74 ASN cc_start: 0.8154 (t0) cc_final: 0.7645 (t0) REVERT: G 85 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8217 (tm-30) REVERT: G 93 GLU cc_start: 0.8473 (mp0) cc_final: 0.7836 (mt-10) REVERT: H 60 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7554 (tm-30) REVERT: H 101 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7657 (mm-30) REVERT: K 354 MET cc_start: 0.7861 (tpp) cc_final: 0.7571 (tpt) REVERT: K 582 GLN cc_start: 0.8750 (mt0) cc_final: 0.8215 (tt0) REVERT: K 618 TYR cc_start: 0.9196 (t80) cc_final: 0.8775 (t80) REVERT: K 626 MET cc_start: 0.8834 (mmt) cc_final: 0.8587 (mmm) outliers start: 27 outliers final: 22 residues processed: 171 average time/residue: 0.0949 time to fit residues: 24.5628 Evaluate side-chains 166 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 309 THR Chi-restraints excluded: chain K residue 317 ASP Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 83 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 79 optimal weight: 50.0000 chunk 82 optimal weight: 30.0000 chunk 22 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 111 ASN H 134 HIS K 336 HIS ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.088442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.059980 restraints weight = 49943.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061563 restraints weight = 26648.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061876 restraints weight = 17484.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.062202 restraints weight = 15998.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.062247 restraints weight = 14918.396| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 15473 Z= 0.249 Angle : 0.716 9.351 22020 Z= 0.400 Chirality : 0.045 0.280 2499 Planarity : 0.005 0.056 1858 Dihedral : 29.283 176.571 4149 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.58 % Favored : 95.07 % Rotamer: Outliers : 3.05 % Allowed : 21.44 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.26), residues: 1136 helix: 1.91 (0.20), residues: 709 sheet: -0.12 (0.71), residues: 63 loop : -2.24 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 117 TYR 0.023 0.002 TYR K 663 PHE 0.019 0.002 PHE E 67 TRP 0.024 0.002 TRP K 217 HIS 0.008 0.002 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.25 (15473) covalent geometry : angle 0.71591 / 0.40 (22020) hydrogen bonds : bond 0.07381 / 4.98 ( 769) hydrogen bonds : angle 3.68710 / 2.61 ( 2006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8209 (mp0) cc_final: 0.7844 (mp0) REVERT: C 105 ASN cc_start: 0.8314 (t0) cc_final: 0.8071 (t0) REVERT: D 101 GLU cc_start: 0.8239 (tp30) cc_final: 0.7894 (tp30) REVERT: G 85 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8296 (tm-30) REVERT: G 93 GLU cc_start: 0.8529 (mp0) cc_final: 0.7629 (mt-10) REVERT: H 60 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7642 (tm-30) REVERT: H 101 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7661 (mm-30) REVERT: H 118 GLU cc_start: 0.7774 (mp0) cc_final: 0.7558 (mp0) REVERT: H 131 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8125 (mp) REVERT: K 354 MET cc_start: 0.7834 (tpp) cc_final: 0.7556 (tpt) REVERT: K 626 MET cc_start: 0.8854 (mmt) cc_final: 0.8605 (mmm) outliers start: 30 outliers final: 22 residues processed: 160 average time/residue: 0.1036 time to fit residues: 25.3266 Evaluate side-chains 158 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 78 optimal weight: 50.0000 chunk 116 optimal weight: 0.0170 chunk 16 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 111 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.090606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.062753 restraints weight = 49579.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.064324 restraints weight = 26940.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.064694 restraints weight = 16933.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.064975 restraints weight = 15560.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064973 restraints weight = 14561.228| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 15473 Z= 0.148 Angle : 0.629 9.403 22020 Z= 0.363 Chirality : 0.043 0.486 2499 Planarity : 0.004 0.041 1858 Dihedral : 29.103 177.623 4149 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.61 % Favored : 96.13 % Rotamer: Outliers : 2.03 % Allowed : 22.05 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.26), residues: 1136 helix: 2.16 (0.20), residues: 709 sheet: -0.28 (0.69), residues: 68 loop : -2.16 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 580 TYR 0.025 0.001 TYR K 663 PHE 0.010 0.001 PHE B 100 TRP 0.026 0.002 TRP K 217 HIS 0.011 0.001 HIS K 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (15473) covalent geometry : angle 0.62927 / 0.36 (22020) hydrogen bonds : bond 0.06101 / 4.09 ( 769) hydrogen bonds : angle 3.31864 / 2.38 ( 2006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: C 105 ASN cc_start: 0.8317 (t0) cc_final: 0.8057 (t0) REVERT: D 101 GLU cc_start: 0.8144 (tp30) cc_final: 0.7852 (tp30) REVERT: G 74 ASN cc_start: 0.8214 (t0) cc_final: 0.7750 (t0) REVERT: G 85 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8258 (tm-30) REVERT: G 93 GLU cc_start: 0.8462 (mp0) cc_final: 0.7847 (mt-10) REVERT: H 101 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7583 (mm-30) REVERT: K 296 MET cc_start: 0.8519 (ptp) cc_final: 0.7762 (pmm) REVERT: K 354 MET cc_start: 0.7794 (tpp) cc_final: 0.7550 (tpt) REVERT: K 486 LEU cc_start: 0.8616 (tp) cc_final: 0.8351 (pp) REVERT: K 582 GLN cc_start: 0.8764 (mt0) cc_final: 0.8199 (tt0) REVERT: K 618 TYR cc_start: 0.9172 (t80) cc_final: 0.8730 (t80) REVERT: K 626 MET cc_start: 0.8821 (mmt) cc_final: 0.8591 (mmm) outliers start: 20 outliers final: 16 residues processed: 161 average time/residue: 0.1136 time to fit residues: 27.8840 Evaluate side-chains 161 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain K residue 309 THR Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 609 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 59 optimal weight: 0.4980 chunk 130 optimal weight: 8.9990 chunk 78 optimal weight: 50.0000 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 111 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.090656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.062636 restraints weight = 49374.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.064383 restraints weight = 26648.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064702 restraints weight = 16447.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064991 restraints weight = 15713.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.065011 restraints weight = 14478.891| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15473 Z= 0.144 Angle : 0.618 9.672 22020 Z= 0.356 Chirality : 0.041 0.261 2499 Planarity : 0.004 0.048 1858 Dihedral : 29.099 177.871 4149 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.33 % Rotamer: Outliers : 2.03 % Allowed : 22.15 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.26), residues: 1136 helix: 2.21 (0.20), residues: 708 sheet: -0.26 (0.68), residues: 68 loop : -2.11 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.024 0.001 TYR K 663 PHE 0.017 0.001 PHE B 100 TRP 0.034 0.002 TRP K 217 HIS 0.006 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (15473) covalent geometry : angle 0.61849 / 0.36 (22020) hydrogen bonds : bond 0.05952 / 3.99 ( 769) hydrogen bonds : angle 3.30452 / 2.36 ( 2006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.52 seconds wall clock time: 40 minutes 15.68 seconds (2415.68 seconds total)