Starting phenix.real_space_refine on Fri Jul 3 11:49:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh8_37533/07_2026/8wh8_37533.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh8_37533/07_2026/8wh8_37533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wh8_37533/07_2026/8wh8_37533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh8_37533/07_2026/8wh8_37533.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wh8_37533/07_2026/8wh8_37533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh8_37533/07_2026/8wh8_37533.map" } resolution = 3.6 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= 0.003 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 252 5.49 5 S 29 5.16 5 C 8263 2.51 5 N 2636 2.21 5 O 3124 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14304 Number of models: 1 Model: "" Number of chains: 12 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: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 710 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 700 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} 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: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2544 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2581 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "K" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3592 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 16, 'TRANS': 426} Chain breaks: 1 Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.04, per 1000 atoms: 0.21 Number of scatterers: 14304 At special positions: 0 Unit cell: (131.76, 138.24, 117.72, 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 252 15.00 O 3124 8.00 N 2636 7.00 C 8263 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: 1.24 Conformation dependent library (CDL) restraints added in 426.1 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 63.6% alpha, 4.4% beta 99 base pairs and 194 stacking pairs defined. Time for finding SS restraints: 1.87 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: 4.082A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.911A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.804A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.918A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.566A 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: 4.055A 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: 4.081A 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 109 removed outlier: 3.522A 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: 3.822A 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 132 removed outlier: 3.711A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) 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: 3.961A 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: 3.511A 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: 3.702A pdb=" N LYS H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 109 removed outlier: 3.553A pdb=" N MET H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 4.329A 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: 3.926A pdb=" N LYS H 133 " --> pdb=" O GLY H 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 220 Processing helix chain 'K' and resid 234 through 244 Processing helix chain 'K' and resid 258 through 272 removed outlier: 3.919A pdb=" N LEU K 262 " --> pdb=" O PRO K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 294 removed outlier: 3.957A pdb=" N GLU K 290 " --> pdb=" O ASN K 286 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG K 292 " --> pdb=" O ARG K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 317 Processing helix chain 'K' and resid 317 through 323 removed outlier: 4.068A 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: 3.874A pdb=" N HIS K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 4.229A 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: 3.651A 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 488 through 499 Processing helix chain 'K' and resid 500 through 508 Processing helix chain 'K' and resid 518 through 522 Processing helix chain 'K' and resid 523 through 536 Processing helix chain 'K' and resid 550 through 564 removed outlier: 3.564A 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 623 through 635 removed outlier: 4.161A pdb=" N ASP K 627 " --> pdb=" O ASN K 623 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS K 634 " --> pdb=" O ALA K 630 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 676 removed outlier: 3.654A pdb=" N VAL K 672 " --> pdb=" O LEU K 668 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN K 675 " --> pdb=" O VAL K 671 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY K 676 " --> pdb=" O VAL K 672 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.148A 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 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.462A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.400A pdb=" N ARG C 43 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, 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=AA6 Processing sheet with id=AA7, 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=AA7 Processing sheet with id=AA8, first strand: chain 'K' and resid 278 through 280 removed outlier: 6.609A pdb=" N ILE K 279 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU K 254 " --> pdb=" O VAL K 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 443 through 450 removed outlier: 3.586A 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: 7.289A pdb=" N CYS K 615 " --> pdb=" O TYR K 646 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU K 648 " --> pdb=" O CYS K 615 " (cutoff:3.500A) removed outlier: 6.905A 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: 6.298A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 567 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=AB1 500 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 508 hydrogen bond angles 0 basepair planarities 99 basepair parallelities 194 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1702 1.28 - 1.42: 4706 1.42 - 1.55: 7948 1.55 - 1.69: 671 1.69 - 1.82: 48 Bond restraints: 15075 Sorted by residual: bond pdb=" C SER K 653 " pdb=" O SER K 653 " ideal model delta sigma weight residual 1.235 1.316 -0.081 1.02e-02 9.61e+03 6.26e+01 bond pdb=" C ILE K 235 " pdb=" O ILE K 235 " ideal model delta sigma weight residual 1.236 1.142 0.094 1.19e-02 7.06e+03 6.23e+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 6.04e+01 bond pdb=" N ASN K 222 " pdb=" CA ASN K 222 " ideal model delta sigma weight residual 1.457 1.538 -0.081 1.29e-02 6.01e+03 3.92e+01 bond pdb=" C1' DC I 125 " pdb=" N1 DC I 125 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.40e+01 ... (remaining 15070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 20649 3.47 - 6.93: 715 6.93 - 10.40: 48 10.40 - 13.86: 2 13.86 - 17.33: 2 Bond angle restraints: 21416 Sorted by residual: angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" C ARG F 17 " ideal model delta sigma weight residual 111.14 101.23 9.91 1.08e+00 8.57e-01 8.41e+01 angle pdb=" N LEU K 259 " pdb=" CA LEU K 259 " pdb=" C LEU K 259 " ideal model delta sigma weight residual 111.14 119.57 -8.43 1.08e+00 8.57e-01 6.09e+01 angle pdb=" N LYS H 104 " pdb=" CA LYS H 104 " pdb=" C LYS H 104 " ideal model delta sigma weight residual 111.28 103.01 8.27 1.09e+00 8.42e-01 5.75e+01 angle pdb=" O3' DC I 107 " pdb=" C3' DC I 107 " pdb=" C2' DC I 107 " ideal model delta sigma weight residual 109.40 126.73 -17.33 2.50e+00 1.60e-01 4.81e+01 angle pdb=" N GLU K 517 " pdb=" CA GLU K 517 " pdb=" C GLU K 517 " ideal model delta sigma weight residual 113.38 105.39 7.99 1.17e+00 7.31e-01 4.66e+01 ... (remaining 21411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.66: 7149 33.66 - 67.32: 1220 67.32 - 100.97: 32 100.97 - 134.63: 4 134.63 - 168.29: 5 Dihedral angle restraints: 8410 sinusoidal: 5091 harmonic: 3319 Sorted by residual: dihedral pdb=" O2A ADP K 801 " pdb=" O3A ADP K 801 " pdb=" PA ADP K 801 " pdb=" PB ADP K 801 " ideal model delta sinusoidal sigma weight residual 300.00 164.37 135.63 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" C4' ADP K 801 " pdb=" C5' ADP K 801 " pdb=" O5' ADP K 801 " pdb=" PA ADP K 801 " ideal model delta sinusoidal sigma weight residual 180.00 92.83 87.17 1 2.00e+01 2.50e-03 2.28e+01 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 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 8407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 2338 0.162 - 0.323: 87 0.323 - 0.485: 1 0.485 - 0.646: 0 0.646 - 0.808: 2 Chirality restraints: 2428 Sorted by residual: chirality pdb=" C3' DT J 50 " pdb=" C4' DT J 50 " pdb=" O3' DT J 50 " pdb=" C2' DT J 50 " both_signs ideal model delta sigma weight residual False -2.73 -1.92 -0.81 2.00e-01 2.50e+01 1.63e+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 2.84 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 2425 not shown) Planarity restraints: 1833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 148 " 0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C SER H 148 " -0.082 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 4.35e-02 1.89e+01 pdb=" C LEU K 376 " -0.075 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 ASN K 277 " -0.020 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C ASN K 277 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN K 277 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA K 278 " -0.025 2.00e-02 2.50e+03 ... (remaining 1830 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3714 2.82 - 3.34: 13538 3.34 - 3.86: 25280 3.86 - 4.38: 30863 4.38 - 4.90: 43590 Nonbonded interactions: 116985 Sorted by model distance: nonbonded pdb=" CG2 VAL K 516 " pdb=" CG1 ILE K 519 " model vdw 2.300 3.860 nonbonded pdb=" CD1 ILE B 50 " pdb=" CG2 ILE E 119 " model vdw 2.307 3.880 nonbonded pdb=" O SER K 547 " pdb=" OG1 THR K 600 " model vdw 2.311 3.040 nonbonded pdb=" OD1 ASN K 368 " pdb=" N SER K 370 " model vdw 2.319 3.120 nonbonded pdb=" O ASN K 466 " pdb=" OG1 THR K 467 " model vdw 2.325 3.040 ... (remaining 116980 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: 0.910 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.790 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.013 0.109 15075 Z= 0.969 Angle : 1.420 17.330 21416 Z= 1.051 Chirality : 0.076 0.808 2428 Planarity : 0.008 0.047 1833 Dihedral : 25.117 168.290 6268 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.44 % Favored : 91.67 % Rotamer: Outliers : 0.72 % Allowed : 6.86 % Favored : 92.43 % Cbeta Deviations : 0.09 % 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: -3.35 (0.21), residues: 1129 helix: -1.60 (0.17), residues: 677 sheet: -2.93 (0.58), residues: 62 loop : -3.03 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 430 TYR 0.040 0.003 TYR K 329 PHE 0.028 0.003 PHE D 67 TRP 0.038 0.003 TRP K 217 HIS 0.016 0.002 HIS H 74 Details of bonding type rmsd/Z covalent geometry : bond 0.01299 / 0.97 (15075) covalent geometry : angle 1.42023 / 1.05 (21416) hydrogen bonds : bond 0.22102 / 14.89 ( 756) hydrogen bonds : angle 8.67054 / 5.95 ( 1990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 326 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.6445 (m110) cc_final: 0.5761 (m-40) REVERT: C 65 GLU cc_start: 0.7509 (tp30) cc_final: 0.7297 (tp30) REVERT: C 75 LYS cc_start: 0.8499 (mttp) cc_final: 0.8234 (tmtt) REVERT: E 54 TYR cc_start: 0.8331 (m-80) cc_final: 0.7823 (m-80) REVERT: E 123 ASP cc_start: 0.8983 (m-30) cc_final: 0.8733 (m-30) REVERT: F 52 GLU cc_start: 0.7781 (tp30) cc_final: 0.7317 (tp30) REVERT: G 36 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8702 (mtpt) REVERT: H 113 THR cc_start: 0.9186 (m) cc_final: 0.8891 (p) REVERT: H 141 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8211 (mtmt) REVERT: K 269 ILE cc_start: 0.8514 (tt) cc_final: 0.8306 (mt) REVERT: K 296 MET cc_start: 0.8179 (mtp) cc_final: 0.7514 (mmp) REVERT: K 432 MET cc_start: 0.6988 (mmm) cc_final: 0.6731 (tpt) REVERT: K 446 ILE cc_start: 0.7555 (mt) cc_final: 0.7058 (tp) REVERT: K 452 MET cc_start: 0.7877 (ttp) cc_final: 0.7651 (ttt) REVERT: K 626 MET cc_start: 0.8521 (mmt) cc_final: 0.8311 (mmm) REVERT: K 667 LYS cc_start: 0.6950 (mtpt) cc_final: 0.6737 (mptt) REVERT: K 669 GLU cc_start: 0.8623 (tp30) cc_final: 0.8339 (tp30) outliers start: 7 outliers final: 1 residues processed: 328 average time/residue: 0.1675 time to fit residues: 72.9986 Evaluate side-chains 169 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 211 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 120 GLN E 85 GLN K 206 GLN K 286 ASN K 366 GLN K 462 HIS ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.107527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.070722 restraints weight = 40016.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.072798 restraints weight = 20138.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.074127 restraints weight = 13705.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.074837 restraints weight = 11161.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.075281 restraints weight = 10073.591| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 15075 Z= 0.307 Angle : 0.869 9.181 21416 Z= 0.482 Chirality : 0.055 0.345 2428 Planarity : 0.006 0.055 1833 Dihedral : 29.546 176.126 3977 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.05 % Favored : 94.69 % Rotamer: Outliers : 3.17 % Allowed : 14.74 % Favored : 82.09 % 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: -1.02 (0.24), residues: 1129 helix: 0.55 (0.19), residues: 686 sheet: -2.97 (0.57), residues: 70 loop : -2.53 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 636 TYR 0.013 0.002 TYR K 663 PHE 0.022 0.003 PHE E 67 TRP 0.018 0.003 TRP K 217 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.31 (15075) covalent geometry : angle 0.86880 / 0.48 (21416) hydrogen bonds : bond 0.08449 / 5.74 ( 756) hydrogen bonds : angle 4.45163 / 3.13 ( 1990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8545 (mt0) cc_final: 0.8222 (mt0) REVERT: C 42 GLU cc_start: 0.8199 (tp30) cc_final: 0.7896 (mp0) REVERT: C 65 GLU cc_start: 0.7854 (tp30) cc_final: 0.7624 (tp30) REVERT: C 75 LYS cc_start: 0.8600 (mttp) cc_final: 0.8242 (tmtt) REVERT: C 78 ARG cc_start: 0.6325 (mtt-85) cc_final: 0.6106 (mtt-85) REVERT: D 67 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: E 54 TYR cc_start: 0.8298 (m-80) cc_final: 0.7820 (m-80) REVERT: H 84 MET cc_start: 0.8570 (mtm) cc_final: 0.8359 (mtm) REVERT: K 296 MET cc_start: 0.8048 (mtp) cc_final: 0.7394 (mmp) REVERT: K 328 LYS cc_start: 0.6228 (OUTLIER) cc_final: 0.6015 (mttt) REVERT: K 570 ILE cc_start: 0.9121 (pt) cc_final: 0.8663 (mp) REVERT: K 608 ASN cc_start: 0.7935 (t0) cc_final: 0.7388 (p0) REVERT: K 669 GLU cc_start: 0.8621 (tp30) cc_final: 0.8421 (tp30) outliers start: 31 outliers final: 18 residues processed: 197 average time/residue: 0.1274 time to fit residues: 35.9801 Evaluate side-chains 168 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain K residue 211 LYS Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 659 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 40.0000 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 85 GLN ** 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 = 0.3769 r_free = 0.3769 target = 0.106707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.071294 restraints weight = 40040.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.072173 restraints weight = 21669.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.073070 restraints weight = 14313.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.073143 restraints weight = 13182.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.073225 restraints weight = 12182.295| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15075 Z= 0.222 Angle : 0.718 9.729 21416 Z= 0.411 Chirality : 0.048 0.267 2428 Planarity : 0.005 0.043 1833 Dihedral : 29.407 177.577 3977 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 3.48 % Allowed : 17.81 % Favored : 78.71 % 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: 0.15 (0.25), residues: 1129 helix: 1.54 (0.20), residues: 689 sheet: -2.59 (0.58), residues: 68 loop : -2.19 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 69 TYR 0.014 0.002 TYR G 51 PHE 0.015 0.002 PHE E 67 TRP 0.013 0.002 TRP K 373 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (15075) covalent geometry : angle 0.71802 / 0.41 (21416) hydrogen bonds : bond 0.07294 / 4.97 ( 756) hydrogen bonds : angle 3.97565 / 2.81 ( 1990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8374 (mt0) cc_final: 0.8057 (mt0) REVERT: C 42 GLU cc_start: 0.8107 (tp30) cc_final: 0.7896 (mp0) REVERT: C 65 GLU cc_start: 0.8062 (tp30) cc_final: 0.7541 (tp30) REVERT: C 75 LYS cc_start: 0.8537 (mttp) cc_final: 0.8237 (tmtt) REVERT: C 82 ARG cc_start: 0.8690 (tpt170) cc_final: 0.8435 (tpt170) REVERT: C 91 ASP cc_start: 0.7943 (t0) cc_final: 0.7510 (t0) REVERT: D 67 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8548 (m-80) REVERT: E 54 TYR cc_start: 0.8206 (m-80) cc_final: 0.7845 (m-80) REVERT: H 86 ILE cc_start: 0.9527 (mm) cc_final: 0.9315 (mt) REVERT: K 212 TRP cc_start: 0.7940 (t-100) cc_final: 0.7613 (t-100) REVERT: K 296 MET cc_start: 0.8321 (mtp) cc_final: 0.7497 (mmp) REVERT: K 608 ASN cc_start: 0.7925 (t0) cc_final: 0.7352 (p0) REVERT: K 626 MET cc_start: 0.8684 (mmt) cc_final: 0.8474 (mmm) outliers start: 34 outliers final: 17 residues processed: 194 average time/residue: 0.1060 time to fit residues: 30.1801 Evaluate side-chains 173 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 576 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 61 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 10.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** 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 = 0.3774 r_free = 0.3774 target = 0.106817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.071486 restraints weight = 40130.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.072451 restraints weight = 21746.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.073240 restraints weight = 14374.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.073370 restraints weight = 13045.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.073466 restraints weight = 12104.883| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15075 Z= 0.178 Angle : 0.667 8.175 21416 Z= 0.383 Chirality : 0.045 0.264 2428 Planarity : 0.004 0.049 1833 Dihedral : 29.318 178.856 3973 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 2.76 % Allowed : 18.83 % Favored : 78.40 % 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: 0.70 (0.26), residues: 1129 helix: 1.95 (0.20), residues: 689 sheet: -2.09 (0.61), residues: 68 loop : -1.98 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 78 TYR 0.015 0.001 TYR K 253 PHE 0.017 0.001 PHE K 240 TRP 0.015 0.002 TRP K 265 HIS 0.008 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (15075) covalent geometry : angle 0.66681 / 0.38 (21416) hydrogen bonds : bond 0.06490 / 4.43 ( 756) hydrogen bonds : angle 3.77718 / 2.67 ( 1990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 GLU cc_start: 0.8079 (tp30) cc_final: 0.7853 (mp0) REVERT: C 65 GLU cc_start: 0.8310 (tp30) cc_final: 0.8063 (tp30) REVERT: C 75 LYS cc_start: 0.8568 (mttp) cc_final: 0.8278 (tmtt) REVERT: C 82 ARG cc_start: 0.8724 (tpt170) cc_final: 0.8327 (tpt170) REVERT: C 91 ASP cc_start: 0.7926 (t0) cc_final: 0.7449 (t0) REVERT: D 67 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: D 130 GLU cc_start: 0.6403 (tm-30) cc_final: 0.6083 (tm-30) REVERT: E 54 TYR cc_start: 0.8200 (m-80) cc_final: 0.7871 (m-80) REVERT: G 62 GLU cc_start: 0.8184 (tp30) cc_final: 0.7983 (tp30) REVERT: K 212 TRP cc_start: 0.7880 (t-100) cc_final: 0.7596 (t-100) REVERT: K 296 MET cc_start: 0.8394 (mtp) cc_final: 0.7510 (mmp) REVERT: K 608 ASN cc_start: 0.7923 (t0) cc_final: 0.7400 (p0) REVERT: K 626 MET cc_start: 0.8707 (mmt) cc_final: 0.8493 (mmm) outliers start: 27 outliers final: 18 residues processed: 188 average time/residue: 0.1050 time to fit residues: 29.1522 Evaluate side-chains 175 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 487 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 206 GLN ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.106814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.070743 restraints weight = 40113.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.072121 restraints weight = 21578.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.072989 restraints weight = 13816.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.073266 restraints weight = 11712.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.073328 restraints weight = 11622.423| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15075 Z= 0.176 Angle : 0.643 7.532 21416 Z= 0.368 Chirality : 0.044 0.263 2428 Planarity : 0.004 0.051 1833 Dihedral : 29.245 176.358 3973 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 2.66 % Allowed : 18.83 % Favored : 78.51 % 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: 0.92 (0.26), residues: 1129 helix: 2.14 (0.20), residues: 692 sheet: -2.14 (0.64), residues: 64 loop : -1.96 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 78 TYR 0.012 0.001 TYR G 51 PHE 0.016 0.001 PHE K 240 TRP 0.013 0.001 TRP K 217 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (15075) covalent geometry : angle 0.64338 / 0.37 (21416) hydrogen bonds : bond 0.06300 / 4.29 ( 756) hydrogen bonds : angle 3.61386 / 2.56 ( 1990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 42 GLU cc_start: 0.8068 (tp30) cc_final: 0.7843 (mp0) REVERT: C 75 LYS cc_start: 0.8587 (mttp) cc_final: 0.8282 (tmtt) REVERT: C 82 ARG cc_start: 0.8721 (tpt170) cc_final: 0.8332 (tpt170) REVERT: C 91 ASP cc_start: 0.7807 (t0) cc_final: 0.7299 (t0) REVERT: D 67 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8518 (m-80) REVERT: D 130 GLU cc_start: 0.6249 (tm-30) cc_final: 0.5949 (tm-30) REVERT: E 54 TYR cc_start: 0.8199 (m-80) cc_final: 0.7818 (m-80) REVERT: G 57 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8383 (tm-30) REVERT: K 212 TRP cc_start: 0.7912 (t-100) cc_final: 0.7492 (t-100) REVERT: K 296 MET cc_start: 0.8261 (mtp) cc_final: 0.7466 (mmp) REVERT: K 575 LYS cc_start: 0.7931 (tmmt) cc_final: 0.7706 (ttpp) REVERT: K 608 ASN cc_start: 0.8049 (t0) cc_final: 0.7471 (p0) REVERT: K 626 MET cc_start: 0.8717 (mmt) cc_final: 0.8213 (mmm) outliers start: 26 outliers final: 21 residues processed: 181 average time/residue: 0.1180 time to fit residues: 31.3815 Evaluate side-chains 170 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 448 MET Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 112 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 625 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.105646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069379 restraints weight = 39909.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.071128 restraints weight = 21254.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.071855 restraints weight = 13821.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.072167 restraints weight = 11854.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.072146 restraints weight = 11733.058| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15075 Z= 0.202 Angle : 0.657 7.527 21416 Z= 0.374 Chirality : 0.044 0.269 2428 Planarity : 0.004 0.050 1833 Dihedral : 29.253 171.329 3973 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 3.17 % Allowed : 18.53 % Favored : 78.30 % 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: 0.84 (0.26), residues: 1129 helix: 2.10 (0.20), residues: 693 sheet: -2.02 (0.59), residues: 70 loop : -2.06 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 TYR 0.011 0.001 TYR K 325 PHE 0.013 0.001 PHE K 240 TRP 0.022 0.002 TRP K 217 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (15075) covalent geometry : angle 0.65748 / 0.37 (21416) hydrogen bonds : bond 0.06429 / 4.37 ( 756) hydrogen bonds : angle 3.69459 / 2.62 ( 1990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: C 42 GLU cc_start: 0.7983 (tp30) cc_final: 0.7711 (mp0) REVERT: C 65 GLU cc_start: 0.8436 (tp30) cc_final: 0.7740 (tp30) REVERT: C 75 LYS cc_start: 0.8535 (mttp) cc_final: 0.8282 (tmtt) REVERT: C 82 ARG cc_start: 0.8750 (tpt170) cc_final: 0.8409 (tpt170) REVERT: C 91 ASP cc_start: 0.7917 (t0) cc_final: 0.7376 (t0) REVERT: D 67 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8578 (m-80) REVERT: D 118 GLU cc_start: 0.8500 (mp0) cc_final: 0.8225 (mm-30) REVERT: D 130 GLU cc_start: 0.6375 (tm-30) cc_final: 0.6062 (tm-30) REVERT: E 54 TYR cc_start: 0.8245 (m-80) cc_final: 0.7839 (m-80) REVERT: G 57 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8434 (tm-30) REVERT: H 138 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8218 (mm-30) REVERT: K 212 TRP cc_start: 0.7731 (t-100) cc_final: 0.7459 (t-100) REVERT: K 296 MET cc_start: 0.8202 (mtp) cc_final: 0.7470 (mmp) REVERT: K 575 LYS cc_start: 0.7884 (tmmt) cc_final: 0.7660 (ttpp) REVERT: K 608 ASN cc_start: 0.8107 (t0) cc_final: 0.7417 (p0) REVERT: K 622 TRP cc_start: 0.8562 (OUTLIER) cc_final: 0.8124 (m-10) REVERT: K 626 MET cc_start: 0.8363 (mmt) cc_final: 0.8096 (mmm) outliers start: 31 outliers final: 25 residues processed: 176 average time/residue: 0.1092 time to fit residues: 28.7195 Evaluate side-chains 178 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 260 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 622 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 71 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 104 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.105477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.069789 restraints weight = 39799.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.070731 restraints weight = 22219.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.071578 restraints weight = 14812.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.071648 restraints weight = 13739.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.071720 restraints weight = 12735.581| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15075 Z= 0.195 Angle : 0.659 8.854 21416 Z= 0.373 Chirality : 0.044 0.266 2428 Planarity : 0.004 0.049 1833 Dihedral : 29.209 168.768 3973 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 3.07 % Allowed : 19.55 % Favored : 77.38 % 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: 0.96 (0.26), residues: 1129 helix: 2.20 (0.20), residues: 692 sheet: -1.68 (0.62), residues: 58 loop : -2.10 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 636 TYR 0.010 0.001 TYR B 72 PHE 0.009 0.001 PHE E 67 TRP 0.016 0.001 TRP K 217 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (15075) covalent geometry : angle 0.65873 / 0.37 (21416) hydrogen bonds : bond 0.06299 / 4.28 ( 756) hydrogen bonds : angle 3.64235 / 2.58 ( 1990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: C 42 GLU cc_start: 0.7976 (tp30) cc_final: 0.7580 (mp0) REVERT: C 75 LYS cc_start: 0.8599 (mttp) cc_final: 0.8380 (tmtt) REVERT: C 82 ARG cc_start: 0.8731 (tpt170) cc_final: 0.8398 (tpt170) REVERT: D 67 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8586 (m-80) REVERT: D 118 GLU cc_start: 0.8520 (mp0) cc_final: 0.8218 (mm-30) REVERT: D 130 GLU cc_start: 0.6357 (tm-30) cc_final: 0.6045 (tm-30) REVERT: E 54 TYR cc_start: 0.8211 (m-80) cc_final: 0.7794 (m-80) REVERT: G 57 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8441 (tm-30) REVERT: H 138 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8131 (mm-30) REVERT: K 212 TRP cc_start: 0.7686 (t-100) cc_final: 0.7408 (t-100) REVERT: K 296 MET cc_start: 0.8218 (mtp) cc_final: 0.7501 (mmp) REVERT: K 575 LYS cc_start: 0.7895 (tmmt) cc_final: 0.7668 (ttpp) REVERT: K 608 ASN cc_start: 0.8204 (t0) cc_final: 0.7493 (p0) REVERT: K 622 TRP cc_start: 0.8505 (OUTLIER) cc_final: 0.8112 (m-10) outliers start: 30 outliers final: 23 residues processed: 175 average time/residue: 0.1089 time to fit residues: 28.5925 Evaluate side-chains 175 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 260 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 622 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 75 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 50.0000 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 0.0050 chunk 48 optimal weight: 4.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.105822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.070219 restraints weight = 40043.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.071148 restraints weight = 22238.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.071772 restraints weight = 14925.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.072042 restraints weight = 13940.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.072061 restraints weight = 12913.524| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15075 Z= 0.173 Angle : 0.641 8.083 21416 Z= 0.364 Chirality : 0.044 0.319 2428 Planarity : 0.004 0.049 1833 Dihedral : 29.145 166.813 3973 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 2.97 % Allowed : 20.06 % Favored : 76.97 % 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: 1.06 (0.26), residues: 1129 helix: 2.26 (0.20), residues: 692 sheet: -1.52 (0.64), residues: 58 loop : -2.03 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 30 TYR 0.010 0.001 TYR G 51 PHE 0.021 0.001 PHE K 240 TRP 0.014 0.001 TRP K 217 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (15075) covalent geometry : angle 0.64117 / 0.36 (21416) hydrogen bonds : bond 0.06104 / 4.14 ( 756) hydrogen bonds : angle 3.58520 / 2.54 ( 1990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8309 (tp30) cc_final: 0.7820 (tp30) REVERT: C 75 LYS cc_start: 0.8601 (mttp) cc_final: 0.8382 (tmtt) REVERT: C 82 ARG cc_start: 0.8713 (tpt170) cc_final: 0.8377 (tpt170) REVERT: C 91 ASP cc_start: 0.7814 (t0) cc_final: 0.7356 (t0) REVERT: D 67 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: D 118 GLU cc_start: 0.8518 (mp0) cc_final: 0.8221 (mm-30) REVERT: D 130 GLU cc_start: 0.6338 (tm-30) cc_final: 0.6008 (tm-30) REVERT: E 54 TYR cc_start: 0.8234 (m-80) cc_final: 0.7780 (m-80) REVERT: E 118 THR cc_start: 0.9313 (m) cc_final: 0.8904 (p) REVERT: G 57 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8428 (tm-30) REVERT: G 85 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8086 (tp-100) REVERT: H 60 GLU cc_start: 0.8252 (tp30) cc_final: 0.7972 (tp30) REVERT: H 138 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8169 (mm-30) REVERT: K 212 TRP cc_start: 0.7717 (t-100) cc_final: 0.7423 (t-100) REVERT: K 296 MET cc_start: 0.8226 (mtp) cc_final: 0.7512 (mmp) REVERT: K 575 LYS cc_start: 0.7912 (tmmt) cc_final: 0.7665 (ttpp) REVERT: K 608 ASN cc_start: 0.8218 (t0) cc_final: 0.7490 (p0) REVERT: K 622 TRP cc_start: 0.8536 (OUTLIER) cc_final: 0.8221 (m-10) outliers start: 29 outliers final: 25 residues processed: 173 average time/residue: 0.1088 time to fit residues: 28.1680 Evaluate side-chains 176 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 260 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 325 TYR Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 622 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 24 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 67 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 77 optimal weight: 40.0000 chunk 130 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 ASN ** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.103335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.065752 restraints weight = 40090.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.067704 restraints weight = 21251.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.068960 restraints weight = 14771.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.069474 restraints weight = 12088.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.070025 restraints weight = 11007.013| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15075 Z= 0.285 Angle : 0.756 10.140 21416 Z= 0.416 Chirality : 0.049 0.334 2428 Planarity : 0.005 0.047 1833 Dihedral : 29.307 163.007 3973 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 3.38 % Allowed : 20.16 % Favored : 76.46 % 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: 0.51 (0.25), residues: 1129 helix: 1.82 (0.19), residues: 692 sheet: -1.49 (0.63), residues: 58 loop : -2.30 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 431 TYR 0.016 0.002 TYR B 72 PHE 0.018 0.002 PHE E 67 TRP 0.017 0.002 TRP K 265 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.29 (15075) covalent geometry : angle 0.75583 / 0.42 (21416) hydrogen bonds : bond 0.07506 / 5.10 ( 756) hydrogen bonds : angle 3.99291 / 2.81 ( 1990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8880 (m-30) cc_final: 0.8652 (m-30) REVERT: C 65 GLU cc_start: 0.8405 (tp30) cc_final: 0.7888 (tp30) REVERT: C 75 LYS cc_start: 0.8574 (mttp) cc_final: 0.8333 (tptp) REVERT: C 82 ARG cc_start: 0.8787 (tpt170) cc_final: 0.8468 (tpt170) REVERT: D 67 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: D 118 GLU cc_start: 0.8621 (mp0) cc_final: 0.8362 (mm-30) REVERT: D 130 GLU cc_start: 0.6687 (tm-30) cc_final: 0.6359 (tm-30) REVERT: E 54 TYR cc_start: 0.8319 (m-80) cc_final: 0.7861 (m-80) REVERT: G 57 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8488 (tm-30) REVERT: H 138 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8197 (mm-30) REVERT: K 212 TRP cc_start: 0.7751 (t-100) cc_final: 0.7479 (t-100) REVERT: K 296 MET cc_start: 0.8257 (mtp) cc_final: 0.7513 (mmp) REVERT: K 354 MET cc_start: 0.7234 (mtm) cc_final: 0.7003 (mtm) REVERT: K 608 ASN cc_start: 0.8187 (t0) cc_final: 0.7616 (p0) REVERT: K 622 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.8357 (m-10) outliers start: 33 outliers final: 28 residues processed: 169 average time/residue: 0.1216 time to fit residues: 30.4822 Evaluate side-chains 170 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 260 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 448 MET Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 622 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 48 optimal weight: 0.0030 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.106157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.070327 restraints weight = 39681.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.072120 restraints weight = 21312.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.072747 restraints weight = 13628.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.072951 restraints weight = 11985.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.073037 restraints weight = 11886.782| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15075 Z= 0.143 Angle : 0.649 15.286 21416 Z= 0.367 Chirality : 0.043 0.263 2428 Planarity : 0.004 0.049 1833 Dihedral : 29.024 162.373 3973 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 1.74 % Allowed : 21.90 % Favored : 76.36 % 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: 1129 helix: 2.28 (0.20), residues: 692 sheet: -1.18 (0.66), residues: 56 loop : -1.96 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 431 TYR 0.013 0.001 TYR G 51 PHE 0.024 0.001 PHE K 240 TRP 0.015 0.001 TRP K 217 HIS 0.007 0.001 HIS K 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (15075) covalent geometry : angle 0.64939 / 0.37 (21416) hydrogen bonds : bond 0.05742 / 3.88 ( 756) hydrogen bonds : angle 3.56424 / 2.54 ( 1990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 65 GLU cc_start: 0.8396 (tp30) cc_final: 0.7904 (tp30) REVERT: C 75 LYS cc_start: 0.8595 (mttp) cc_final: 0.8333 (tptp) REVERT: C 82 ARG cc_start: 0.8668 (tpt170) cc_final: 0.8349 (tpt170) REVERT: C 91 ASP cc_start: 0.8150 (t0) cc_final: 0.7889 (t0) REVERT: D 67 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8513 (m-80) REVERT: D 118 GLU cc_start: 0.8475 (mp0) cc_final: 0.8181 (mm-30) REVERT: D 130 GLU cc_start: 0.6200 (tm-30) cc_final: 0.5880 (tm-30) REVERT: E 54 TYR cc_start: 0.8301 (m-80) cc_final: 0.7838 (m-80) REVERT: E 118 THR cc_start: 0.9317 (m) cc_final: 0.8967 (p) REVERT: G 57 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8481 (tm-30) REVERT: H 138 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8125 (mm-30) REVERT: K 212 TRP cc_start: 0.7875 (t-100) cc_final: 0.7564 (t-100) REVERT: K 296 MET cc_start: 0.8166 (mtp) cc_final: 0.7513 (mmp) REVERT: K 608 ASN cc_start: 0.8347 (t0) cc_final: 0.7662 (p0) outliers start: 17 outliers final: 11 residues processed: 162 average time/residue: 0.1200 time to fit residues: 28.9670 Evaluate side-chains 153 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 487 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 122 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.106320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.070341 restraints weight = 39951.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.071985 restraints weight = 21260.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.072704 restraints weight = 13836.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072905 restraints weight = 12196.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072975 restraints weight = 11882.177| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.159 15075 Z= 0.181 Angle : 0.821 59.200 21416 Z= 0.486 Chirality : 0.047 1.022 2428 Planarity : 0.004 0.048 1833 Dihedral : 29.025 162.350 3973 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.07 % Favored : 95.75 % Rotamer: Outliers : 1.33 % Allowed : 22.21 % Favored : 76.46 % Cbeta Deviations : 0.09 % 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: 1129 helix: 2.28 (0.20), residues: 692 sheet: -1.18 (0.67), residues: 56 loop : -1.95 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 30 TYR 0.012 0.001 TYR K 618 PHE 0.022 0.001 PHE K 240 TRP 0.013 0.002 TRP K 217 HIS 0.004 0.001 HIS K 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.18 (15075) covalent geometry : angle 0.82134 / 0.49 (21416) hydrogen bonds : bond 0.05742 / 3.87 ( 756) hydrogen bonds : angle 3.55673 / 2.53 ( 1990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2304.66 seconds wall clock time: 40 minutes 33.93 seconds (2433.93 seconds total)