Starting phenix.real_space_refine on Fri Aug 22 23:31:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c2h_45157/08_2025/9c2h_45157.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c2h_45157/08_2025/9c2h_45157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c2h_45157/08_2025/9c2h_45157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c2h_45157/08_2025/9c2h_45157.map" model { file = "/net/cci-nas-00/data/ceres_data/9c2h_45157/08_2025/9c2h_45157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c2h_45157/08_2025/9c2h_45157.cif" } resolution = 3.7 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= 0.001 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5450 2.51 5 N 1428 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8626 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 865 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "B" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 799 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 865 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 883 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "G" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "H" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 799 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 883 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "J" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 2.50, per 1000 atoms: 0.29 Number of scatterers: 8626 At special positions: 0 Unit cell: (135.96, 66, 128.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1704 8.00 N 1428 7.00 C 5450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 87 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 498.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 18 sheets defined 12.5% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 258 through 262 removed outlier: 4.098A pdb=" N ARG A 262 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 300 through 306 removed outlier: 3.900A pdb=" N ILE A 304 " --> pdb=" O HIS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.962A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 removed outlier: 3.645A pdb=" N VAL A 350 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.837A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.856A pdb=" N VAL C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 removed outlier: 4.033A pdb=" N ARG D 262 " --> pdb=" O ARG D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 274 Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 310 through 318 removed outlier: 4.005A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 355 removed outlier: 6.161A pdb=" N ILE D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.863A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.611A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'H' and resid 78 through 82 removed outlier: 4.062A pdb=" N VAL H 82 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.785A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.656A pdb=" N LEU J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 319 through 325 removed outlier: 4.845A pdb=" N THR A 329 " --> pdb=" O LEU D 339 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 334 " --> pdb=" O ARG D 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.759A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 83 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP B 75 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 62 removed outlier: 5.469A pdb=" N LEU B 45 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N SER B 40 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 100 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B 110 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 62 removed outlier: 5.469A pdb=" N LEU B 45 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N SER B 40 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.705A pdb=" N TRP C 34 " --> pdb=" O TRP C 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 19 through 23 removed outlier: 3.843A pdb=" N SER C 71 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 6 removed outlier: 4.039A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.645A pdb=" N TYR E 94 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TRP E 50 " --> pdb=" O LYS E 59 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS E 59 " --> pdb=" O TRP E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.533A pdb=" N LEU F 73 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.761A pdb=" N MET F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TYR F 49 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.767A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 11 removed outlier: 4.089A pdb=" N THR G 118 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS G 61 " --> pdb=" O GLU G 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.585A pdb=" N THR H 5 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER H 62 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 52 through 53 removed outlier: 5.331A pdb=" N LEU H 45 " --> pdb=" O GLN H 36 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN H 36 " --> pdb=" O LEU H 45 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 3 through 6 removed outlier: 4.152A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.512A pdb=" N ASP I 33 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TRP I 47 " --> pdb=" O LYS I 38 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TRP I 50 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS I 59 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 4 through 5 removed outlier: 3.589A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL J 21 " --> pdb=" O LEU J 73 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU J 73 " --> pdb=" O VAL J 21 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.796A pdb=" N MET J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASP J 100 " --> pdb=" O CYS J 88 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS J 88 " --> pdb=" O ASP J 100 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA J 34 " --> pdb=" O GLN J 89 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TYR J 49 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN J 37 " --> pdb=" O LYS J 45 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 666 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1484 1.32 - 1.45: 2521 1.45 - 1.57: 4753 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8830 Sorted by residual: bond pdb=" CA SER J 93 " pdb=" CB SER J 93 " ideal model delta sigma weight residual 1.528 1.488 0.040 1.50e-02 4.44e+03 7.24e+00 bond pdb=" N SER J 93 " pdb=" CA SER J 93 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.41e-02 5.03e+03 6.65e+00 bond pdb=" N PRO F 95 " pdb=" CA PRO F 95 " ideal model delta sigma weight residual 1.468 1.424 0.044 1.70e-02 3.46e+03 6.55e+00 bond pdb=" N LEU J 96 " pdb=" CA LEU J 96 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.45e+00 bond pdb=" N PHE J 98 " pdb=" CA PHE J 98 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.34e-02 5.57e+03 6.11e+00 ... (remaining 8825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 11796 2.56 - 5.11: 141 5.11 - 7.67: 12 7.67 - 10.22: 0 10.22 - 12.78: 1 Bond angle restraints: 11950 Sorted by residual: angle pdb=" N PRO J 95 " pdb=" CA PRO J 95 " pdb=" C PRO J 95 " ideal model delta sigma weight residual 112.47 99.69 12.78 2.06e+00 2.36e-01 3.85e+01 angle pdb=" N ASP D 348 " pdb=" CA ASP D 348 " pdb=" C ASP D 348 " ideal model delta sigma weight residual 114.75 107.94 6.81 1.26e+00 6.30e-01 2.92e+01 angle pdb=" N VAL J 29 " pdb=" CA VAL J 29 " pdb=" C VAL J 29 " ideal model delta sigma weight residual 111.88 106.79 5.09 1.06e+00 8.90e-01 2.31e+01 angle pdb=" N ASP A 348 " pdb=" CA ASP A 348 " pdb=" C ASP A 348 " ideal model delta sigma weight residual 114.75 109.07 5.68 1.26e+00 6.30e-01 2.03e+01 angle pdb=" N PHE J 98 " pdb=" CA PHE J 98 " pdb=" C PHE J 98 " ideal model delta sigma weight residual 110.53 105.30 5.23 1.32e+00 5.74e-01 1.57e+01 ... (remaining 11945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4957 16.94 - 33.89: 151 33.89 - 50.83: 59 50.83 - 67.77: 20 67.77 - 84.72: 3 Dihedral angle restraints: 5190 sinusoidal: 2016 harmonic: 3174 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 98 " pdb=" CB CYS B 98 " ideal model delta sinusoidal sigma weight residual 93.00 158.20 -65.20 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CA TYR F 94 " pdb=" C TYR F 94 " pdb=" N PRO F 95 " pdb=" CA PRO F 95 " ideal model delta harmonic sigma weight residual 0.00 26.06 -26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ALA G 107 " pdb=" C ALA G 107 " pdb=" N MET G 108 " pdb=" CA MET G 108 " ideal model delta harmonic sigma weight residual 180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 5187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1051 0.053 - 0.105: 190 0.105 - 0.158: 25 0.158 - 0.211: 2 0.211 - 0.263: 2 Chirality restraints: 1270 Sorted by residual: chirality pdb=" CA TYR F 94 " pdb=" N TYR F 94 " pdb=" C TYR F 94 " pdb=" CB TYR F 94 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA TYR J 94 " pdb=" N TYR J 94 " pdb=" C TYR J 94 " pdb=" CB TYR J 94 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA LEU F 96 " pdb=" N LEU F 96 " pdb=" C LEU F 96 " pdb=" CB LEU F 96 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1267 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 92 " -0.026 2.00e-02 2.50e+03 5.21e-02 2.71e+01 pdb=" C ASN F 92 " 0.090 2.00e-02 2.50e+03 pdb=" O ASN F 92 " -0.034 2.00e-02 2.50e+03 pdb=" N SER F 93 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 94 " 0.024 2.00e-02 2.50e+03 1.49e-02 4.46e+00 pdb=" CG TYR J 94 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR J 94 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR J 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR J 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR J 94 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR J 94 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 42 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO C 43 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.019 5.00e-02 4.00e+02 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2187 2.80 - 3.32: 7169 3.32 - 3.85: 13508 3.85 - 4.37: 15726 4.37 - 4.90: 27178 Nonbonded interactions: 65768 Sorted by model distance: nonbonded pdb=" OG1 THR A 271 " pdb=" O TYR G 104 " model vdw 2.274 3.040 nonbonded pdb=" O GLN I 3 " pdb=" NH2 ARG I 98 " model vdw 2.302 3.120 nonbonded pdb=" NH1 ARG G 38 " pdb=" OD1 ASP G 92 " model vdw 2.306 3.120 nonbonded pdb=" O TYR B 104 " pdb=" OG1 THR D 271 " model vdw 2.321 3.040 nonbonded pdb=" O GLY E 108 " pdb=" OG SER F 43 " model vdw 2.325 3.040 ... (remaining 65763 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } 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: 2.280 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.040 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 : 0.003 0.044 8834 Z= 0.191 Angle : 0.697 12.779 11958 Z= 0.423 Chirality : 0.042 0.263 1270 Planarity : 0.004 0.052 1528 Dihedral : 10.459 84.718 3174 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.26 % Favored : 91.65 % Rotamer: Outliers : 0.11 % Allowed : 0.00 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -2.73 (0.25), residues: 1090 helix: -2.69 (0.61), residues: 54 sheet: -1.66 (0.25), residues: 444 loop : -1.80 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 277 TYR 0.034 0.001 TYR J 94 PHE 0.013 0.001 PHE J 98 TRP 0.013 0.001 TRP E 50 HIS 0.004 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8830) covalent geometry : angle 0.69746 (11950) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.60433 ( 8) hydrogen bonds : bond 0.21481 ( 262) hydrogen bonds : angle 9.21674 ( 666) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 411 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7944 (m-40) cc_final: 0.7616 (m-40) REVERT: A 283 GLN cc_start: 0.7663 (mm110) cc_final: 0.7372 (mm110) REVERT: A 285 ASN cc_start: 0.8559 (t0) cc_final: 0.8297 (t0) REVERT: A 290 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7873 (mt-10) REVERT: A 291 LEU cc_start: 0.8685 (tp) cc_final: 0.8450 (tt) REVERT: A 314 PHE cc_start: 0.8286 (t80) cc_final: 0.7993 (t80) REVERT: A 347 LYS cc_start: 0.8374 (mttp) cc_final: 0.8121 (mttp) REVERT: A 360 TYR cc_start: 0.8226 (p90) cc_final: 0.7848 (p90) REVERT: A 361 LYS cc_start: 0.9222 (mttt) cc_final: 0.8662 (mttm) REVERT: A 362 THR cc_start: 0.8963 (p) cc_final: 0.8652 (t) REVERT: A 363 PHE cc_start: 0.8911 (m-80) cc_final: 0.8655 (m-80) REVERT: B 19 LYS cc_start: 0.8712 (tttt) cc_final: 0.8374 (tttm) REVERT: B 27 PHE cc_start: 0.8674 (p90) cc_final: 0.7948 (p90) REVERT: B 28 THR cc_start: 0.8479 (m) cc_final: 0.8142 (m) REVERT: B 29 PHE cc_start: 0.9082 (t80) cc_final: 0.8773 (t80) REVERT: B 33 TYR cc_start: 0.8288 (m-80) cc_final: 0.8074 (m-10) REVERT: B 37 VAL cc_start: 0.8413 (t) cc_final: 0.8025 (m) REVERT: B 50 GLU cc_start: 0.6389 (pt0) cc_final: 0.6005 (pt0) REVERT: B 55 SER cc_start: 0.8847 (m) cc_final: 0.8616 (p) REVERT: B 58 TYR cc_start: 0.8692 (m-80) cc_final: 0.7161 (m-80) REVERT: B 71 THR cc_start: 0.8403 (m) cc_final: 0.8070 (p) REVERT: B 104 TYR cc_start: 0.7762 (m-80) cc_final: 0.7173 (m-80) REVERT: C 14 SER cc_start: 0.9121 (m) cc_final: 0.8850 (p) REVERT: C 18 LYS cc_start: 0.8844 (tttt) cc_final: 0.8418 (tttt) REVERT: C 21 MET cc_start: 0.7718 (mtm) cc_final: 0.7494 (mtm) REVERT: C 29 VAL cc_start: 0.8192 (t) cc_final: 0.7897 (t) REVERT: C 36 GLN cc_start: 0.7329 (tt0) cc_final: 0.6833 (tt0) REVERT: C 37 GLN cc_start: 0.8143 (tt0) cc_final: 0.7940 (tt0) REVERT: C 38 LYS cc_start: 0.8755 (mttt) cc_final: 0.8475 (mttt) REVERT: C 50 THR cc_start: 0.9158 (m) cc_final: 0.8709 (p) REVERT: C 51 SER cc_start: 0.8520 (p) cc_final: 0.8244 (m) REVERT: C 55 SER cc_start: 0.8380 (t) cc_final: 0.8165 (p) REVERT: C 61 PHE cc_start: 0.8915 (m-10) cc_final: 0.8576 (m-80) REVERT: C 89 GLN cc_start: 0.8055 (mt0) cc_final: 0.7665 (mt0) REVERT: C 101 THR cc_start: 0.7899 (m) cc_final: 0.7406 (p) REVERT: D 269 ASN cc_start: 0.8095 (m-40) cc_final: 0.7854 (m-40) REVERT: D 290 GLU cc_start: 0.7305 (tt0) cc_final: 0.7096 (tt0) REVERT: D 298 TYR cc_start: 0.8069 (t80) cc_final: 0.7761 (t80) REVERT: D 329 THR cc_start: 0.9009 (p) cc_final: 0.8797 (t) REVERT: D 343 ASP cc_start: 0.8614 (t70) cc_final: 0.8270 (t0) REVERT: D 355 LYS cc_start: 0.5585 (mttm) cc_final: 0.4953 (mttm) REVERT: D 361 LYS cc_start: 0.9093 (mttt) cc_final: 0.8640 (mttm) REVERT: D 362 THR cc_start: 0.8788 (p) cc_final: 0.8553 (t) REVERT: E 36 TRP cc_start: 0.8331 (m100) cc_final: 0.7987 (m-10) REVERT: E 38 LYS cc_start: 0.8473 (ptmt) cc_final: 0.7793 (ttpp) REVERT: E 104 MET cc_start: 0.7922 (mtt) cc_final: 0.7452 (mmt) REVERT: E 106 TYR cc_start: 0.8316 (m-80) cc_final: 0.7925 (m-80) REVERT: E 107 TRP cc_start: 0.8431 (m100) cc_final: 0.7903 (m100) REVERT: F 9 LYS cc_start: 0.8724 (tttt) cc_final: 0.8486 (tttt) REVERT: F 10 PHE cc_start: 0.7993 (m-80) cc_final: 0.7339 (m-80) REVERT: F 20 SER cc_start: 0.8986 (t) cc_final: 0.8494 (p) REVERT: F 49 TYR cc_start: 0.8362 (p90) cc_final: 0.7968 (p90) REVERT: F 50 SER cc_start: 0.8214 (m) cc_final: 0.7937 (m) REVERT: F 54 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7574 (mtp180) REVERT: F 55 TYR cc_start: 0.8213 (m-80) cc_final: 0.7973 (m-10) REVERT: F 62 PHE cc_start: 0.8636 (m-80) cc_final: 0.8276 (m-10) REVERT: F 73 LEU cc_start: 0.8925 (tp) cc_final: 0.8661 (tt) REVERT: F 75 ILE cc_start: 0.8668 (mt) cc_final: 0.7702 (mt) REVERT: F 80 SER cc_start: 0.8937 (m) cc_final: 0.8493 (p) REVERT: F 81 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7622 (mm-30) REVERT: F 88 CYS cc_start: 0.8403 (t) cc_final: 0.8142 (p) REVERT: G 28 THR cc_start: 0.8432 (m) cc_final: 0.8182 (m) REVERT: G 29 PHE cc_start: 0.8798 (t80) cc_final: 0.8560 (t80) REVERT: G 34 MET cc_start: 0.7339 (mtp) cc_final: 0.6984 (mtp) REVERT: G 37 VAL cc_start: 0.8362 (t) cc_final: 0.8117 (m) REVERT: G 46 GLU cc_start: 0.7848 (tt0) cc_final: 0.7485 (tt0) REVERT: G 57 ASN cc_start: 0.8966 (t0) cc_final: 0.8567 (t0) REVERT: G 70 PHE cc_start: 0.8584 (m-80) cc_final: 0.8227 (m-80) REVERT: G 71 THR cc_start: 0.8326 (m) cc_final: 0.7872 (p) REVERT: G 79 SER cc_start: 0.8765 (m) cc_final: 0.8159 (p) REVERT: G 108 MET cc_start: 0.7578 (mpp) cc_final: 0.6946 (mpp) REVERT: H 10 ILE cc_start: 0.8910 (pt) cc_final: 0.8566 (mm) REVERT: H 21 MET cc_start: 0.7795 (mtm) cc_final: 0.7536 (mtm) REVERT: H 29 VAL cc_start: 0.8769 (t) cc_final: 0.8289 (m) REVERT: H 48 TYR cc_start: 0.7573 (p90) cc_final: 0.7033 (p90) REVERT: H 55 SER cc_start: 0.8310 (t) cc_final: 0.8074 (p) REVERT: H 60 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7716 (mtm-85) REVERT: H 85 TYR cc_start: 0.8422 (m-80) cc_final: 0.8170 (m-10) REVERT: H 88 PHE cc_start: 0.8445 (t80) cc_final: 0.8032 (t80) REVERT: H 89 GLN cc_start: 0.7729 (mt0) cc_final: 0.7468 (mt0) REVERT: H 101 THR cc_start: 0.8005 (m) cc_final: 0.7790 (p) REVERT: I 6 GLN cc_start: 0.6347 (mt0) cc_final: 0.6043 (mt0) REVERT: I 27 TYR cc_start: 0.5845 (t80) cc_final: 0.5085 (t80) REVERT: I 28 THR cc_start: 0.7970 (m) cc_final: 0.6885 (p) REVERT: I 30 THR cc_start: 0.8768 (p) cc_final: 0.8231 (t) REVERT: I 36 TRP cc_start: 0.8477 (m100) cc_final: 0.7904 (m-10) REVERT: I 57 SER cc_start: 0.9431 (m) cc_final: 0.8949 (p) REVERT: I 93 VAL cc_start: 0.7876 (t) cc_final: 0.7520 (p) REVERT: I 104 MET cc_start: 0.7941 (mtt) cc_final: 0.7727 (mtt) REVERT: I 113 VAL cc_start: 0.8411 (t) cc_final: 0.7974 (m) REVERT: J 20 SER cc_start: 0.8912 (t) cc_final: 0.8662 (m) REVERT: J 39 LYS cc_start: 0.8659 (mttt) cc_final: 0.8442 (mttt) REVERT: J 49 TYR cc_start: 0.8284 (p90) cc_final: 0.7932 (p90) REVERT: J 50 SER cc_start: 0.8367 (m) cc_final: 0.8113 (m) REVERT: J 55 TYR cc_start: 0.8531 (m-80) cc_final: 0.8312 (m-10) REVERT: J 77 ASN cc_start: 0.8013 (m110) cc_final: 0.7809 (m110) REVERT: J 90 GLN cc_start: 0.7360 (mt0) cc_final: 0.7145 (tm-30) REVERT: J 93 SER cc_start: 0.7822 (t) cc_final: 0.7422 (p) REVERT: J 103 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7954 (mtpt) outliers start: 1 outliers final: 0 residues processed: 411 average time/residue: 0.1035 time to fit residues: 57.1184 Evaluate side-chains 397 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 272 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN D 289 GLN D 300 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.115841 restraints weight = 14182.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120044 restraints weight = 6395.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.122717 restraints weight = 3451.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124410 restraints weight = 2074.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125585 restraints weight = 1356.511| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8834 Z= 0.163 Angle : 0.615 9.760 11958 Z= 0.323 Chirality : 0.043 0.185 1270 Planarity : 0.005 0.061 1528 Dihedral : 4.635 19.647 1206 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.88 % Allowed : 12.90 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -2.23 (0.26), residues: 1090 helix: -1.97 (0.66), residues: 62 sheet: -1.02 (0.26), residues: 438 loop : -1.77 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 277 TYR 0.026 0.002 TYR J 94 PHE 0.021 0.002 PHE E 29 TRP 0.025 0.002 TRP E 50 HIS 0.004 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8830) covalent geometry : angle 0.61464 (11950) SS BOND : bond 0.00092 ( 4) SS BOND : angle 1.38585 ( 8) hydrogen bonds : bond 0.04194 ( 262) hydrogen bonds : angle 6.79300 ( 666) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 388 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7660 (m110) cc_final: 0.7241 (m110) REVERT: A 285 ASN cc_start: 0.8338 (t0) cc_final: 0.8128 (t0) REVERT: A 314 PHE cc_start: 0.8061 (t80) cc_final: 0.7792 (t80) REVERT: A 347 LYS cc_start: 0.8036 (mttp) cc_final: 0.7788 (mttp) REVERT: A 360 TYR cc_start: 0.7976 (p90) cc_final: 0.7650 (p90) REVERT: A 361 LYS cc_start: 0.9276 (mttt) cc_final: 0.8829 (mttm) REVERT: A 362 THR cc_start: 0.8893 (p) cc_final: 0.8574 (t) REVERT: A 363 PHE cc_start: 0.8832 (m-80) cc_final: 0.8610 (m-80) REVERT: B 19 LYS cc_start: 0.8645 (tttt) cc_final: 0.8244 (tttm) REVERT: B 27 PHE cc_start: 0.8653 (p90) cc_final: 0.7773 (p90) REVERT: B 28 THR cc_start: 0.8268 (m) cc_final: 0.7983 (m) REVERT: B 29 PHE cc_start: 0.9059 (t80) cc_final: 0.8703 (t80) REVERT: B 33 TYR cc_start: 0.8121 (m-10) cc_final: 0.7789 (m-10) REVERT: B 37 VAL cc_start: 0.8107 (t) cc_final: 0.7756 (m) REVERT: B 38 ARG cc_start: 0.8271 (ttm170) cc_final: 0.8071 (ttp-170) REVERT: B 54 GLU cc_start: 0.8085 (tt0) cc_final: 0.7764 (tt0) REVERT: B 71 THR cc_start: 0.8308 (m) cc_final: 0.7835 (p) REVERT: B 79 SER cc_start: 0.8496 (m) cc_final: 0.7855 (p) REVERT: B 85 MET cc_start: 0.7613 (mtt) cc_final: 0.7317 (mtt) REVERT: B 104 TYR cc_start: 0.7859 (m-80) cc_final: 0.7499 (m-80) REVERT: C 14 SER cc_start: 0.9070 (m) cc_final: 0.8839 (t) REVERT: C 18 LYS cc_start: 0.8735 (tttt) cc_final: 0.8394 (tttt) REVERT: C 19 VAL cc_start: 0.8718 (t) cc_final: 0.8449 (t) REVERT: C 21 MET cc_start: 0.6670 (mtm) cc_final: 0.6322 (mtm) REVERT: C 22 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8033 (t) REVERT: C 32 MET cc_start: 0.6816 (ttm) cc_final: 0.6514 (ttm) REVERT: C 37 GLN cc_start: 0.8064 (tt0) cc_final: 0.7848 (tt0) REVERT: C 50 THR cc_start: 0.9098 (m) cc_final: 0.8531 (p) REVERT: C 51 SER cc_start: 0.8482 (p) cc_final: 0.8189 (m) REVERT: C 61 PHE cc_start: 0.8933 (m-10) cc_final: 0.8658 (m-80) REVERT: C 74 ILE cc_start: 0.8498 (mt) cc_final: 0.8250 (mt) REVERT: C 101 THR cc_start: 0.7501 (m) cc_final: 0.6889 (p) REVERT: D 276 ARG cc_start: 0.8120 (ptm-80) cc_final: 0.7845 (ptm160) REVERT: D 279 PRO cc_start: 0.8698 (Cg_exo) cc_final: 0.8361 (Cg_endo) REVERT: D 343 ASP cc_start: 0.8381 (t70) cc_final: 0.7978 (t70) REVERT: D 360 TYR cc_start: 0.7770 (p90) cc_final: 0.7301 (p90) REVERT: D 361 LYS cc_start: 0.9172 (mttt) cc_final: 0.8694 (mttm) REVERT: D 362 THR cc_start: 0.8611 (p) cc_final: 0.8355 (t) REVERT: E 22 CYS cc_start: 0.7431 (t) cc_final: 0.6535 (t) REVERT: E 36 TRP cc_start: 0.8245 (m100) cc_final: 0.7751 (m-10) REVERT: E 40 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7518 (mtt90) REVERT: E 76 SER cc_start: 0.8487 (p) cc_final: 0.8076 (t) REVERT: E 106 TYR cc_start: 0.7930 (m-80) cc_final: 0.7562 (m-80) REVERT: E 107 TRP cc_start: 0.8118 (m100) cc_final: 0.7871 (m100) REVERT: E 112 SER cc_start: 0.8553 (t) cc_final: 0.8183 (p) REVERT: F 9 LYS cc_start: 0.8572 (tttt) cc_final: 0.8342 (tttt) REVERT: F 10 PHE cc_start: 0.7875 (m-80) cc_final: 0.7263 (m-80) REVERT: F 20 SER cc_start: 0.8706 (t) cc_final: 0.8393 (p) REVERT: F 32 ASN cc_start: 0.6324 (t0) cc_final: 0.5916 (t0) REVERT: F 54 ARG cc_start: 0.7811 (mtm110) cc_final: 0.7244 (mtp180) REVERT: F 55 TYR cc_start: 0.8157 (m-80) cc_final: 0.7873 (m-10) REVERT: F 61 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7077 (ptt-90) REVERT: F 62 PHE cc_start: 0.8743 (m-80) cc_final: 0.8287 (m-10) REVERT: F 75 ILE cc_start: 0.8455 (mt) cc_final: 0.7657 (mt) REVERT: F 80 SER cc_start: 0.8974 (m) cc_final: 0.8744 (p) REVERT: F 88 CYS cc_start: 0.7912 (t) cc_final: 0.7546 (p) REVERT: F 93 SER cc_start: 0.7947 (t) cc_final: 0.7630 (p) REVERT: G 22 CYS cc_start: 0.8371 (t) cc_final: 0.7608 (t) REVERT: G 27 PHE cc_start: 0.8492 (p90) cc_final: 0.7763 (p90) REVERT: G 29 PHE cc_start: 0.8822 (t80) cc_final: 0.8590 (t80) REVERT: G 34 MET cc_start: 0.6820 (mtp) cc_final: 0.6576 (mtp) REVERT: G 57 ASN cc_start: 0.9100 (t0) cc_final: 0.8881 (t0) REVERT: G 70 PHE cc_start: 0.8582 (m-80) cc_final: 0.8357 (m-80) REVERT: G 71 THR cc_start: 0.8273 (m) cc_final: 0.7620 (p) REVERT: G 79 SER cc_start: 0.8655 (m) cc_final: 0.8089 (p) REVERT: G 108 MET cc_start: 0.7155 (mpp) cc_final: 0.6591 (mpp) REVERT: G 109 ASP cc_start: 0.7091 (t0) cc_final: 0.6881 (t0) REVERT: H 10 ILE cc_start: 0.8774 (pt) cc_final: 0.8398 (mm) REVERT: H 21 MET cc_start: 0.7060 (mtm) cc_final: 0.6816 (mtm) REVERT: H 29 VAL cc_start: 0.8674 (t) cc_final: 0.8197 (m) REVERT: H 37 GLN cc_start: 0.8316 (tt0) cc_final: 0.7941 (tt0) REVERT: H 44 LYS cc_start: 0.8213 (mttt) cc_final: 0.7763 (mttt) REVERT: H 55 SER cc_start: 0.8397 (t) cc_final: 0.8175 (p) REVERT: H 61 PHE cc_start: 0.9032 (m-10) cc_final: 0.8800 (m-10) REVERT: H 65 ARG cc_start: 0.8347 (ttt180) cc_final: 0.8081 (ptm-80) REVERT: H 85 TYR cc_start: 0.8253 (m-80) cc_final: 0.7880 (m-10) REVERT: H 89 GLN cc_start: 0.7508 (mt0) cc_final: 0.6264 (mt0) REVERT: H 101 THR cc_start: 0.7761 (m) cc_final: 0.7330 (p) REVERT: I 11 LEU cc_start: 0.8365 (mt) cc_final: 0.7735 (mt) REVERT: I 27 TYR cc_start: 0.5661 (t80) cc_final: 0.4875 (t80) REVERT: I 28 THR cc_start: 0.7987 (m) cc_final: 0.6905 (p) REVERT: I 30 THR cc_start: 0.8707 (p) cc_final: 0.8308 (t) REVERT: I 36 TRP cc_start: 0.8320 (m100) cc_final: 0.7843 (m-10) REVERT: I 38 LYS cc_start: 0.8707 (tttp) cc_final: 0.7432 (tttp) REVERT: I 40 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7389 (mtt90) REVERT: I 46 GLU cc_start: 0.7698 (pt0) cc_final: 0.7430 (pt0) REVERT: I 57 SER cc_start: 0.9390 (m) cc_final: 0.8941 (p) REVERT: I 93 VAL cc_start: 0.7356 (t) cc_final: 0.7105 (p) REVERT: I 113 VAL cc_start: 0.8517 (t) cc_final: 0.8091 (m) REVERT: J 49 TYR cc_start: 0.7740 (p90) cc_final: 0.7451 (p90) REVERT: J 50 SER cc_start: 0.7925 (m) cc_final: 0.7607 (m) REVERT: J 87 PHE cc_start: 0.8445 (m-10) cc_final: 0.8103 (m-10) REVERT: J 93 SER cc_start: 0.7399 (t) cc_final: 0.7077 (p) REVERT: J 96 LEU cc_start: 0.7875 (mp) cc_final: 0.7251 (mp) REVERT: J 103 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7967 (mtpt) outliers start: 27 outliers final: 19 residues processed: 395 average time/residue: 0.1015 time to fit residues: 54.2359 Evaluate side-chains 406 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 384 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 34 TRP Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 32 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 0.0050 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN F 79 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.114380 restraints weight = 14159.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118613 restraints weight = 6516.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121313 restraints weight = 3588.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123066 restraints weight = 2203.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124256 restraints weight = 1454.979| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8834 Z= 0.160 Angle : 0.605 8.571 11958 Z= 0.319 Chirality : 0.042 0.174 1270 Planarity : 0.004 0.050 1528 Dihedral : 4.632 20.386 1206 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.90 % Allowed : 16.10 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -2.05 (0.26), residues: 1090 helix: -1.72 (0.66), residues: 62 sheet: -0.89 (0.26), residues: 442 loop : -1.68 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 80 TYR 0.027 0.002 TYR J 94 PHE 0.016 0.002 PHE E 29 TRP 0.027 0.002 TRP E 50 HIS 0.004 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8830) covalent geometry : angle 0.60455 (11950) SS BOND : bond 0.00136 ( 4) SS BOND : angle 1.20978 ( 8) hydrogen bonds : bond 0.03837 ( 262) hydrogen bonds : angle 6.33777 ( 666) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 381 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7643 (m110) cc_final: 0.7292 (m110) REVERT: A 314 PHE cc_start: 0.8122 (t80) cc_final: 0.7850 (t80) REVERT: A 347 LYS cc_start: 0.8001 (mttp) cc_final: 0.7779 (mttp) REVERT: A 360 TYR cc_start: 0.8012 (p90) cc_final: 0.7569 (p90) REVERT: A 361 LYS cc_start: 0.9287 (mttt) cc_final: 0.8808 (mttm) REVERT: A 362 THR cc_start: 0.8881 (p) cc_final: 0.8573 (t) REVERT: A 363 PHE cc_start: 0.8832 (m-80) cc_final: 0.8629 (m-80) REVERT: B 27 PHE cc_start: 0.8687 (p90) cc_final: 0.7768 (p90) REVERT: B 28 THR cc_start: 0.8266 (m) cc_final: 0.7955 (m) REVERT: B 29 PHE cc_start: 0.8956 (t80) cc_final: 0.8678 (t80) REVERT: B 33 TYR cc_start: 0.8093 (m-10) cc_final: 0.7746 (m-10) REVERT: B 37 VAL cc_start: 0.8090 (t) cc_final: 0.7745 (m) REVERT: B 54 GLU cc_start: 0.8236 (tt0) cc_final: 0.7811 (tt0) REVERT: B 58 TYR cc_start: 0.8643 (m-80) cc_final: 0.8406 (m-10) REVERT: B 71 THR cc_start: 0.8264 (m) cc_final: 0.7746 (p) REVERT: B 79 SER cc_start: 0.8537 (m) cc_final: 0.7875 (p) REVERT: B 85 MET cc_start: 0.7506 (mtt) cc_final: 0.7298 (mtt) REVERT: C 14 SER cc_start: 0.9062 (m) cc_final: 0.8821 (t) REVERT: C 18 LYS cc_start: 0.8731 (tttt) cc_final: 0.8406 (tttt) REVERT: C 32 MET cc_start: 0.6796 (ttm) cc_final: 0.6576 (ttm) REVERT: C 37 GLN cc_start: 0.8187 (tt0) cc_final: 0.7965 (tt0) REVERT: C 51 SER cc_start: 0.8471 (p) cc_final: 0.8142 (m) REVERT: C 61 PHE cc_start: 0.8824 (m-10) cc_final: 0.8534 (m-80) REVERT: C 74 ILE cc_start: 0.8433 (mt) cc_final: 0.8128 (mt) REVERT: C 101 THR cc_start: 0.7365 (m) cc_final: 0.6738 (p) REVERT: D 343 ASP cc_start: 0.8366 (t70) cc_final: 0.7974 (t70) REVERT: D 361 LYS cc_start: 0.9165 (mttt) cc_final: 0.8660 (mttm) REVERT: D 362 THR cc_start: 0.8575 (p) cc_final: 0.8347 (t) REVERT: E 6 GLN cc_start: 0.6755 (mt0) cc_final: 0.6361 (mt0) REVERT: E 19 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8109 (tmtt) REVERT: E 22 CYS cc_start: 0.7442 (t) cc_final: 0.6595 (t) REVERT: E 36 TRP cc_start: 0.8260 (m100) cc_final: 0.7731 (m-10) REVERT: E 38 LYS cc_start: 0.8431 (ttpt) cc_final: 0.8065 (tttt) REVERT: E 76 SER cc_start: 0.8308 (p) cc_final: 0.7968 (t) REVERT: E 106 TYR cc_start: 0.7994 (m-80) cc_final: 0.7652 (m-80) REVERT: E 107 TRP cc_start: 0.8132 (m100) cc_final: 0.7763 (m-10) REVERT: E 109 GLN cc_start: 0.8203 (pm20) cc_final: 0.7601 (pm20) REVERT: E 112 SER cc_start: 0.8589 (t) cc_final: 0.8152 (p) REVERT: F 20 SER cc_start: 0.8728 (t) cc_final: 0.8371 (p) REVERT: F 32 ASN cc_start: 0.6622 (t0) cc_final: 0.6167 (t0) REVERT: F 61 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8173 (ptt-90) REVERT: F 87 PHE cc_start: 0.8543 (m-10) cc_final: 0.8237 (m-10) REVERT: F 93 SER cc_start: 0.8046 (t) cc_final: 0.7715 (p) REVERT: G 22 CYS cc_start: 0.8348 (t) cc_final: 0.7483 (t) REVERT: G 29 PHE cc_start: 0.8850 (t80) cc_final: 0.8614 (t80) REVERT: G 34 MET cc_start: 0.6933 (mtp) cc_final: 0.6620 (mtp) REVERT: G 54 GLU cc_start: 0.8021 (tt0) cc_final: 0.7666 (tt0) REVERT: G 70 PHE cc_start: 0.8618 (m-80) cc_final: 0.8386 (m-80) REVERT: G 71 THR cc_start: 0.8178 (m) cc_final: 0.7516 (p) REVERT: G 79 SER cc_start: 0.8647 (m) cc_final: 0.8061 (p) REVERT: G 108 MET cc_start: 0.7117 (mpp) cc_final: 0.6543 (mpp) REVERT: H 10 ILE cc_start: 0.8765 (pt) cc_final: 0.8392 (mm) REVERT: H 29 VAL cc_start: 0.8648 (t) cc_final: 0.8192 (m) REVERT: H 32 MET cc_start: 0.6680 (ttm) cc_final: 0.6470 (ttm) REVERT: H 37 GLN cc_start: 0.8372 (tt0) cc_final: 0.7973 (tt0) REVERT: H 44 LYS cc_start: 0.8203 (mttt) cc_final: 0.7578 (mtmm) REVERT: H 55 SER cc_start: 0.8389 (t) cc_final: 0.8166 (p) REVERT: H 61 PHE cc_start: 0.9006 (m-10) cc_final: 0.8759 (m-10) REVERT: H 65 ARG cc_start: 0.8270 (ttt180) cc_final: 0.8049 (ptm-80) REVERT: H 82 VAL cc_start: 0.9269 (t) cc_final: 0.8899 (m) REVERT: H 85 TYR cc_start: 0.8183 (m-80) cc_final: 0.7816 (m-10) REVERT: H 89 GLN cc_start: 0.7276 (mt0) cc_final: 0.6887 (mt0) REVERT: H 101 THR cc_start: 0.7892 (m) cc_final: 0.7303 (p) REVERT: I 27 TYR cc_start: 0.5453 (t80) cc_final: 0.4676 (t80) REVERT: I 28 THR cc_start: 0.8005 (m) cc_final: 0.6888 (p) REVERT: I 30 THR cc_start: 0.8688 (p) cc_final: 0.8291 (t) REVERT: I 36 TRP cc_start: 0.8337 (m100) cc_final: 0.7798 (m-10) REVERT: I 38 LYS cc_start: 0.8690 (tttp) cc_final: 0.8417 (tttm) REVERT: I 46 GLU cc_start: 0.7661 (pt0) cc_final: 0.7190 (pt0) REVERT: I 57 SER cc_start: 0.9378 (m) cc_final: 0.8947 (p) REVERT: I 76 SER cc_start: 0.8619 (m) cc_final: 0.7998 (t) REVERT: I 93 VAL cc_start: 0.7388 (t) cc_final: 0.7110 (p) REVERT: I 104 MET cc_start: 0.7164 (mtt) cc_final: 0.6864 (mtt) REVERT: I 113 VAL cc_start: 0.8550 (t) cc_final: 0.8105 (m) REVERT: J 49 TYR cc_start: 0.7433 (p90) cc_final: 0.7150 (p90) REVERT: J 50 SER cc_start: 0.7689 (m) cc_final: 0.7376 (m) REVERT: J 61 ARG cc_start: 0.8424 (mtm110) cc_final: 0.8114 (ptp90) REVERT: J 87 PHE cc_start: 0.8509 (m-10) cc_final: 0.8261 (m-10) REVERT: J 103 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7996 (mtpt) outliers start: 46 outliers final: 30 residues processed: 387 average time/residue: 0.1012 time to fit residues: 52.9652 Evaluate side-chains 400 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 368 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 34 TRP Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 102 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN H 89 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.128122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114961 restraints weight = 14303.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119137 restraints weight = 6547.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121817 restraints weight = 3598.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123596 restraints weight = 2201.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124750 restraints weight = 1448.421| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8834 Z= 0.133 Angle : 0.593 8.248 11958 Z= 0.307 Chirality : 0.042 0.154 1270 Planarity : 0.004 0.044 1528 Dihedral : 4.477 20.408 1206 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.22 % Allowed : 17.06 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -1.88 (0.26), residues: 1090 helix: -1.54 (0.68), residues: 62 sheet: -0.78 (0.26), residues: 440 loop : -1.57 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 80 TYR 0.024 0.002 TYR J 94 PHE 0.024 0.002 PHE E 29 TRP 0.024 0.002 TRP E 50 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8830) covalent geometry : angle 0.59200 (11950) SS BOND : bond 0.00264 ( 4) SS BOND : angle 1.17401 ( 8) hydrogen bonds : bond 0.03435 ( 262) hydrogen bonds : angle 6.13320 ( 666) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 363 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7624 (m110) cc_final: 0.7277 (m110) REVERT: A 314 PHE cc_start: 0.8164 (t80) cc_final: 0.7855 (t80) REVERT: A 360 TYR cc_start: 0.8016 (p90) cc_final: 0.7704 (p90) REVERT: A 361 LYS cc_start: 0.9237 (mttt) cc_final: 0.8713 (mttm) REVERT: A 362 THR cc_start: 0.8862 (p) cc_final: 0.8583 (t) REVERT: A 363 PHE cc_start: 0.8838 (m-80) cc_final: 0.8631 (m-80) REVERT: B 19 LYS cc_start: 0.8542 (tttt) cc_final: 0.7935 (ttmm) REVERT: B 27 PHE cc_start: 0.8697 (p90) cc_final: 0.7759 (p90) REVERT: B 28 THR cc_start: 0.8273 (m) cc_final: 0.7955 (m) REVERT: B 29 PHE cc_start: 0.8884 (t80) cc_final: 0.8608 (t80) REVERT: B 33 TYR cc_start: 0.8108 (m-10) cc_final: 0.7731 (m-10) REVERT: B 37 VAL cc_start: 0.8052 (t) cc_final: 0.7748 (m) REVERT: B 54 GLU cc_start: 0.8215 (tt0) cc_final: 0.7732 (tt0) REVERT: B 57 ASN cc_start: 0.8849 (t0) cc_final: 0.8499 (t0) REVERT: B 58 TYR cc_start: 0.8659 (m-80) cc_final: 0.8337 (m-10) REVERT: B 71 THR cc_start: 0.8203 (m) cc_final: 0.7724 (p) REVERT: B 78 LYS cc_start: 0.8590 (mttp) cc_final: 0.8376 (mttp) REVERT: B 79 SER cc_start: 0.8541 (m) cc_final: 0.7898 (p) REVERT: B 101 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6194 (p0) REVERT: B 104 TYR cc_start: 0.7888 (m-80) cc_final: 0.7594 (m-10) REVERT: C 14 SER cc_start: 0.9017 (m) cc_final: 0.8750 (t) REVERT: C 18 LYS cc_start: 0.8728 (tttt) cc_final: 0.8402 (tttt) REVERT: C 32 MET cc_start: 0.6699 (ttm) cc_final: 0.6489 (ttm) REVERT: C 51 SER cc_start: 0.8448 (p) cc_final: 0.8122 (m) REVERT: C 61 PHE cc_start: 0.8793 (m-10) cc_final: 0.8499 (m-80) REVERT: C 66 SER cc_start: 0.8535 (t) cc_final: 0.8280 (p) REVERT: C 74 ILE cc_start: 0.8448 (mt) cc_final: 0.8234 (mt) REVERT: C 101 THR cc_start: 0.7416 (m) cc_final: 0.6885 (p) REVERT: D 343 ASP cc_start: 0.8365 (t70) cc_final: 0.7959 (t70) REVERT: D 361 LYS cc_start: 0.9173 (mttt) cc_final: 0.8651 (mttm) REVERT: D 362 THR cc_start: 0.8601 (p) cc_final: 0.8333 (t) REVERT: E 19 LYS cc_start: 0.8392 (tttt) cc_final: 0.7963 (tmtt) REVERT: E 36 TRP cc_start: 0.8301 (m100) cc_final: 0.8034 (m-10) REVERT: E 38 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8004 (tttt) REVERT: E 104 MET cc_start: 0.7194 (mtt) cc_final: 0.6980 (mtt) REVERT: E 106 TYR cc_start: 0.7984 (m-80) cc_final: 0.7672 (m-80) REVERT: E 107 TRP cc_start: 0.8117 (m100) cc_final: 0.7757 (m-10) REVERT: E 109 GLN cc_start: 0.8196 (pm20) cc_final: 0.7770 (pm20) REVERT: E 112 SER cc_start: 0.8557 (t) cc_final: 0.8147 (p) REVERT: F 3 VAL cc_start: 0.8895 (p) cc_final: 0.8693 (m) REVERT: F 4 MET cc_start: 0.7811 (mmm) cc_final: 0.7276 (mmm) REVERT: F 20 SER cc_start: 0.8737 (t) cc_final: 0.8282 (p) REVERT: F 32 ASN cc_start: 0.6549 (t0) cc_final: 0.6070 (t0) REVERT: F 50 SER cc_start: 0.7845 (m) cc_final: 0.7445 (t) REVERT: F 90 GLN cc_start: 0.7233 (mt0) cc_final: 0.6518 (mt0) REVERT: F 93 SER cc_start: 0.7902 (t) cc_final: 0.7573 (p) REVERT: G 22 CYS cc_start: 0.8239 (t) cc_final: 0.7622 (t) REVERT: G 27 PHE cc_start: 0.8536 (p90) cc_final: 0.7840 (p90) REVERT: G 29 PHE cc_start: 0.8800 (t80) cc_final: 0.8580 (t80) REVERT: G 34 MET cc_start: 0.6944 (mtp) cc_final: 0.6588 (mtp) REVERT: G 54 GLU cc_start: 0.8021 (tt0) cc_final: 0.7614 (tt0) REVERT: G 71 THR cc_start: 0.8116 (m) cc_final: 0.7429 (p) REVERT: G 79 SER cc_start: 0.8669 (m) cc_final: 0.8071 (p) REVERT: G 108 MET cc_start: 0.7103 (mpp) cc_final: 0.6445 (mpp) REVERT: H 4 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7612 (mtm) REVERT: H 10 ILE cc_start: 0.8756 (pt) cc_final: 0.8368 (mm) REVERT: H 29 VAL cc_start: 0.8622 (t) cc_final: 0.8160 (m) REVERT: H 32 MET cc_start: 0.6648 (ttm) cc_final: 0.6442 (ttm) REVERT: H 37 GLN cc_start: 0.8331 (tt0) cc_final: 0.7964 (tt0) REVERT: H 55 SER cc_start: 0.8386 (t) cc_final: 0.8167 (p) REVERT: H 61 PHE cc_start: 0.9027 (m-10) cc_final: 0.8793 (m-10) REVERT: H 65 ARG cc_start: 0.8268 (ttt180) cc_final: 0.7981 (ptm-80) REVERT: H 82 VAL cc_start: 0.9245 (t) cc_final: 0.8912 (m) REVERT: H 85 TYR cc_start: 0.8130 (m-80) cc_final: 0.7758 (m-10) REVERT: H 101 THR cc_start: 0.7706 (m) cc_final: 0.7158 (p) REVERT: I 3 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7570 (tp40) REVERT: I 27 TYR cc_start: 0.5429 (t80) cc_final: 0.4589 (t80) REVERT: I 28 THR cc_start: 0.7974 (m) cc_final: 0.6844 (p) REVERT: I 30 THR cc_start: 0.8698 (p) cc_final: 0.8257 (t) REVERT: I 36 TRP cc_start: 0.8285 (m100) cc_final: 0.7782 (m-10) REVERT: I 38 LYS cc_start: 0.8700 (tttp) cc_final: 0.8257 (tttm) REVERT: I 57 SER cc_start: 0.9384 (m) cc_final: 0.8919 (p) REVERT: I 76 SER cc_start: 0.8585 (m) cc_final: 0.7962 (t) REVERT: I 82 GLN cc_start: 0.8032 (tp40) cc_final: 0.7575 (tp40) REVERT: I 93 VAL cc_start: 0.7411 (t) cc_final: 0.7090 (p) REVERT: I 104 MET cc_start: 0.7199 (mtt) cc_final: 0.6915 (mtt) REVERT: I 113 VAL cc_start: 0.8566 (t) cc_final: 0.8077 (m) REVERT: J 4 MET cc_start: 0.8147 (mmm) cc_final: 0.7845 (mmm) REVERT: J 92 ASN cc_start: 0.8635 (t0) cc_final: 0.8112 (t0) REVERT: J 103 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7918 (mtpt) outliers start: 49 outliers final: 38 residues processed: 375 average time/residue: 0.0997 time to fit residues: 50.7694 Evaluate side-chains 400 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 359 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 34 TRP Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 83 optimal weight: 0.7980 chunk 73 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 98 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 272 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113746 restraints weight = 14308.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117864 restraints weight = 6543.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120485 restraints weight = 3585.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122265 restraints weight = 2185.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123429 restraints weight = 1430.127| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8834 Z= 0.175 Angle : 0.607 8.773 11958 Z= 0.319 Chirality : 0.043 0.167 1270 Planarity : 0.004 0.059 1528 Dihedral : 4.632 20.575 1206 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 5.54 % Allowed : 17.80 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -1.83 (0.25), residues: 1090 helix: -1.57 (0.67), residues: 62 sheet: -0.74 (0.26), residues: 432 loop : -1.53 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 80 TYR 0.026 0.002 TYR J 94 PHE 0.024 0.002 PHE I 29 TRP 0.028 0.002 TRP E 50 HIS 0.005 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8830) covalent geometry : angle 0.60666 (11950) SS BOND : bond 0.00149 ( 4) SS BOND : angle 1.11330 ( 8) hydrogen bonds : bond 0.03687 ( 262) hydrogen bonds : angle 6.09147 ( 666) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 353 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7644 (m-40) cc_final: 0.7332 (m-40) REVERT: A 314 PHE cc_start: 0.8146 (t80) cc_final: 0.7849 (t80) REVERT: A 320 ILE cc_start: 0.8063 (mp) cc_final: 0.7835 (mm) REVERT: A 361 LYS cc_start: 0.9235 (mttt) cc_final: 0.8657 (mttm) REVERT: A 362 THR cc_start: 0.8879 (p) cc_final: 0.8594 (t) REVERT: A 363 PHE cc_start: 0.8840 (m-80) cc_final: 0.8637 (m-80) REVERT: B 27 PHE cc_start: 0.8686 (p90) cc_final: 0.7756 (p90) REVERT: B 28 THR cc_start: 0.8263 (m) cc_final: 0.7922 (m) REVERT: B 29 PHE cc_start: 0.8767 (t80) cc_final: 0.8545 (t80) REVERT: B 33 TYR cc_start: 0.8098 (m-10) cc_final: 0.7737 (m-10) REVERT: B 54 GLU cc_start: 0.8220 (tt0) cc_final: 0.7706 (tt0) REVERT: B 57 ASN cc_start: 0.8909 (t0) cc_final: 0.8617 (t0) REVERT: B 58 TYR cc_start: 0.8679 (m-80) cc_final: 0.8325 (m-10) REVERT: B 71 THR cc_start: 0.8197 (m) cc_final: 0.7722 (p) REVERT: B 78 LYS cc_start: 0.8563 (mttp) cc_final: 0.8356 (mttp) REVERT: B 79 SER cc_start: 0.8537 (m) cc_final: 0.7900 (p) REVERT: B 101 ASP cc_start: 0.6824 (OUTLIER) cc_final: 0.6335 (p0) REVERT: B 104 TYR cc_start: 0.7869 (m-80) cc_final: 0.7561 (m-10) REVERT: C 14 SER cc_start: 0.9014 (m) cc_final: 0.8778 (t) REVERT: C 18 LYS cc_start: 0.8712 (tttt) cc_final: 0.8445 (tttt) REVERT: C 34 TRP cc_start: 0.8230 (OUTLIER) cc_final: 0.7850 (m-10) REVERT: C 51 SER cc_start: 0.8406 (p) cc_final: 0.8179 (m) REVERT: C 61 PHE cc_start: 0.8796 (m-10) cc_final: 0.8491 (m-80) REVERT: C 101 THR cc_start: 0.7375 (m) cc_final: 0.6876 (p) REVERT: D 343 ASP cc_start: 0.8450 (t70) cc_final: 0.8055 (t70) REVERT: D 361 LYS cc_start: 0.9194 (mttt) cc_final: 0.8713 (mttm) REVERT: D 362 THR cc_start: 0.8580 (p) cc_final: 0.8315 (t) REVERT: E 10 GLU cc_start: 0.7339 (tt0) cc_final: 0.7081 (tt0) REVERT: E 19 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7951 (tmtt) REVERT: E 36 TRP cc_start: 0.8356 (m100) cc_final: 0.8004 (m-10) REVERT: E 38 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8004 (tttt) REVERT: E 46 GLU cc_start: 0.7333 (pt0) cc_final: 0.7086 (pt0) REVERT: E 104 MET cc_start: 0.7222 (mtt) cc_final: 0.7008 (mtt) REVERT: E 106 TYR cc_start: 0.8021 (m-80) cc_final: 0.7714 (m-80) REVERT: E 107 TRP cc_start: 0.8140 (m100) cc_final: 0.7718 (m-10) REVERT: E 109 GLN cc_start: 0.8250 (pm20) cc_final: 0.7950 (pm20) REVERT: E 112 SER cc_start: 0.8590 (t) cc_final: 0.8093 (p) REVERT: F 3 VAL cc_start: 0.8879 (p) cc_final: 0.8629 (m) REVERT: F 4 MET cc_start: 0.7790 (mmm) cc_final: 0.7439 (mmm) REVERT: F 20 SER cc_start: 0.8733 (t) cc_final: 0.8275 (p) REVERT: F 32 ASN cc_start: 0.6570 (t0) cc_final: 0.6121 (t0) REVERT: F 50 SER cc_start: 0.7746 (m) cc_final: 0.7367 (t) REVERT: F 87 PHE cc_start: 0.8474 (m-10) cc_final: 0.8268 (m-10) REVERT: F 90 GLN cc_start: 0.7267 (mt0) cc_final: 0.6796 (mt0) REVERT: F 93 SER cc_start: 0.7835 (t) cc_final: 0.7484 (p) REVERT: G 22 CYS cc_start: 0.8175 (t) cc_final: 0.7580 (t) REVERT: G 27 PHE cc_start: 0.8540 (p90) cc_final: 0.7798 (p90) REVERT: G 29 PHE cc_start: 0.8833 (t80) cc_final: 0.8629 (t80) REVERT: G 34 MET cc_start: 0.6978 (mtp) cc_final: 0.6615 (mtp) REVERT: G 54 GLU cc_start: 0.8043 (tt0) cc_final: 0.7679 (tt0) REVERT: G 71 THR cc_start: 0.8104 (m) cc_final: 0.7414 (p) REVERT: G 79 SER cc_start: 0.8652 (m) cc_final: 0.8011 (p) REVERT: G 108 MET cc_start: 0.7060 (mpp) cc_final: 0.6398 (mpp) REVERT: H 4 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7261 (mtm) REVERT: H 10 ILE cc_start: 0.8809 (pt) cc_final: 0.8433 (mm) REVERT: H 29 VAL cc_start: 0.8564 (t) cc_final: 0.8171 (m) REVERT: H 37 GLN cc_start: 0.8387 (tt0) cc_final: 0.7961 (tt0) REVERT: H 48 TYR cc_start: 0.7244 (p90) cc_final: 0.6778 (p90) REVERT: H 55 SER cc_start: 0.8374 (t) cc_final: 0.8122 (p) REVERT: H 61 PHE cc_start: 0.8995 (m-10) cc_final: 0.8751 (m-10) REVERT: H 65 ARG cc_start: 0.8327 (ttt180) cc_final: 0.8001 (ptm-80) REVERT: H 82 VAL cc_start: 0.9261 (t) cc_final: 0.8954 (m) REVERT: H 89 GLN cc_start: 0.7352 (mt0) cc_final: 0.7107 (mt0) REVERT: H 96 THR cc_start: 0.8136 (m) cc_final: 0.7911 (m) REVERT: H 101 THR cc_start: 0.7911 (m) cc_final: 0.7463 (p) REVERT: I 3 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7555 (tp40) REVERT: I 27 TYR cc_start: 0.5623 (t80) cc_final: 0.4687 (t80) REVERT: I 28 THR cc_start: 0.8007 (m) cc_final: 0.6870 (p) REVERT: I 30 THR cc_start: 0.8701 (p) cc_final: 0.8226 (t) REVERT: I 36 TRP cc_start: 0.8348 (m100) cc_final: 0.7720 (m-10) REVERT: I 38 LYS cc_start: 0.8665 (tttp) cc_final: 0.8343 (tttm) REVERT: I 46 GLU cc_start: 0.7619 (pt0) cc_final: 0.7187 (pt0) REVERT: I 57 SER cc_start: 0.9386 (m) cc_final: 0.8948 (p) REVERT: I 82 GLN cc_start: 0.8111 (tp40) cc_final: 0.7610 (tp40) REVERT: I 104 MET cc_start: 0.7204 (mtt) cc_final: 0.6960 (mtt) REVERT: I 109 GLN cc_start: 0.8207 (pm20) cc_final: 0.8001 (pm20) REVERT: I 113 VAL cc_start: 0.8558 (t) cc_final: 0.8078 (m) REVERT: J 61 ARG cc_start: 0.8397 (mtm110) cc_final: 0.8197 (mtm180) REVERT: J 87 PHE cc_start: 0.8328 (m-10) cc_final: 0.7913 (m-10) REVERT: J 103 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7941 (mtpt) outliers start: 52 outliers final: 41 residues processed: 364 average time/residue: 0.1014 time to fit residues: 49.8118 Evaluate side-chains 396 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 350 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 34 TRP Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 12 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN F 89 GLN G 57 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 ASN J 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112031 restraints weight = 14540.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116118 restraints weight = 6652.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118707 restraints weight = 3642.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120451 restraints weight = 2224.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121578 restraints weight = 1457.747| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8834 Z= 0.224 Angle : 0.643 9.446 11958 Z= 0.336 Chirality : 0.044 0.199 1270 Planarity : 0.005 0.041 1528 Dihedral : 4.804 20.935 1206 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 6.29 % Allowed : 18.55 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -1.85 (0.25), residues: 1090 helix: -1.56 (0.67), residues: 62 sheet: -0.76 (0.26), residues: 436 loop : -1.53 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 80 TYR 0.025 0.002 TYR J 94 PHE 0.027 0.002 PHE I 29 TRP 0.031 0.003 TRP E 50 HIS 0.006 0.002 HIS C 33 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8830) covalent geometry : angle 0.64259 (11950) SS BOND : bond 0.00265 ( 4) SS BOND : angle 1.31266 ( 8) hydrogen bonds : bond 0.03957 ( 262) hydrogen bonds : angle 6.11401 ( 666) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 350 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8321 (ttmm) REVERT: A 269 ASN cc_start: 0.7671 (m110) cc_final: 0.7432 (m110) REVERT: A 314 PHE cc_start: 0.8184 (t80) cc_final: 0.7861 (t80) REVERT: A 320 ILE cc_start: 0.8086 (mp) cc_final: 0.7885 (mm) REVERT: A 361 LYS cc_start: 0.9226 (mttt) cc_final: 0.8695 (mttm) REVERT: A 362 THR cc_start: 0.8892 (p) cc_final: 0.8600 (t) REVERT: A 363 PHE cc_start: 0.8861 (m-80) cc_final: 0.8639 (m-80) REVERT: B 27 PHE cc_start: 0.8661 (p90) cc_final: 0.7769 (p90) REVERT: B 28 THR cc_start: 0.8269 (m) cc_final: 0.7927 (m) REVERT: B 29 PHE cc_start: 0.8735 (t80) cc_final: 0.8528 (t80) REVERT: B 33 TYR cc_start: 0.8151 (m-10) cc_final: 0.7876 (m-10) REVERT: B 54 GLU cc_start: 0.8223 (tt0) cc_final: 0.7683 (tt0) REVERT: B 57 ASN cc_start: 0.8939 (t0) cc_final: 0.8661 (t0) REVERT: B 58 TYR cc_start: 0.8724 (m-80) cc_final: 0.8338 (m-10) REVERT: B 71 THR cc_start: 0.8183 (m) cc_final: 0.7724 (p) REVERT: B 78 LYS cc_start: 0.8563 (mttp) cc_final: 0.8346 (mttp) REVERT: B 79 SER cc_start: 0.8572 (m) cc_final: 0.7945 (p) REVERT: B 101 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6383 (p0) REVERT: B 104 TYR cc_start: 0.7860 (m-80) cc_final: 0.7563 (m-10) REVERT: C 14 SER cc_start: 0.9070 (m) cc_final: 0.8817 (t) REVERT: C 18 LYS cc_start: 0.8711 (tttt) cc_final: 0.8447 (tttt) REVERT: C 21 MET cc_start: 0.6864 (mtm) cc_final: 0.6567 (mtm) REVERT: C 34 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.7866 (m-10) REVERT: C 101 THR cc_start: 0.7506 (m) cc_final: 0.7299 (p) REVERT: D 343 ASP cc_start: 0.8485 (t70) cc_final: 0.8107 (t70) REVERT: D 361 LYS cc_start: 0.9230 (mttt) cc_final: 0.8801 (mttm) REVERT: D 362 THR cc_start: 0.8569 (p) cc_final: 0.8308 (t) REVERT: E 10 GLU cc_start: 0.7343 (tt0) cc_final: 0.7072 (tt0) REVERT: E 19 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7927 (tmtt) REVERT: E 22 CYS cc_start: 0.7524 (t) cc_final: 0.6338 (t) REVERT: E 36 TRP cc_start: 0.8357 (m100) cc_final: 0.7897 (m-10) REVERT: E 38 LYS cc_start: 0.8482 (ttpt) cc_final: 0.7819 (tttt) REVERT: E 46 GLU cc_start: 0.7332 (pt0) cc_final: 0.7025 (pt0) REVERT: E 63 LYS cc_start: 0.8849 (tttp) cc_final: 0.8634 (tttp) REVERT: E 104 MET cc_start: 0.7278 (mtt) cc_final: 0.7027 (mtt) REVERT: E 106 TYR cc_start: 0.8061 (m-80) cc_final: 0.7768 (m-80) REVERT: E 112 SER cc_start: 0.8557 (t) cc_final: 0.8099 (p) REVERT: F 3 VAL cc_start: 0.8806 (p) cc_final: 0.8422 (m) REVERT: F 4 MET cc_start: 0.7811 (mmm) cc_final: 0.7607 (mmm) REVERT: F 20 SER cc_start: 0.8754 (t) cc_final: 0.8256 (p) REVERT: F 32 ASN cc_start: 0.6506 (t0) cc_final: 0.6077 (t0) REVERT: F 42 GLN cc_start: 0.8618 (mm110) cc_final: 0.8406 (mm110) REVERT: F 50 SER cc_start: 0.7882 (m) cc_final: 0.7464 (t) REVERT: F 87 PHE cc_start: 0.8477 (m-10) cc_final: 0.8204 (m-10) REVERT: F 90 GLN cc_start: 0.7301 (mt0) cc_final: 0.6967 (mt0) REVERT: F 93 SER cc_start: 0.7855 (t) cc_final: 0.7480 (p) REVERT: G 22 CYS cc_start: 0.8074 (t) cc_final: 0.7548 (t) REVERT: G 27 PHE cc_start: 0.8508 (p90) cc_final: 0.7696 (p90) REVERT: G 29 PHE cc_start: 0.8871 (t80) cc_final: 0.8647 (t80) REVERT: G 34 MET cc_start: 0.7047 (mtp) cc_final: 0.6682 (mtp) REVERT: G 54 GLU cc_start: 0.7965 (tt0) cc_final: 0.7594 (tt0) REVERT: G 71 THR cc_start: 0.8106 (m) cc_final: 0.7426 (p) REVERT: G 79 SER cc_start: 0.8723 (m) cc_final: 0.8036 (p) REVERT: G 80 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.8102 (mtp85) REVERT: G 108 MET cc_start: 0.7010 (mpp) cc_final: 0.6387 (mpp) REVERT: H 10 ILE cc_start: 0.8834 (pt) cc_final: 0.8456 (mm) REVERT: H 29 VAL cc_start: 0.8565 (t) cc_final: 0.8214 (m) REVERT: H 37 GLN cc_start: 0.8372 (tt0) cc_final: 0.7945 (tt0) REVERT: H 48 TYR cc_start: 0.7280 (p90) cc_final: 0.6749 (p90) REVERT: H 55 SER cc_start: 0.8394 (t) cc_final: 0.8134 (p) REVERT: H 61 PHE cc_start: 0.8895 (m-10) cc_final: 0.8606 (m-10) REVERT: H 65 ARG cc_start: 0.8269 (ttt180) cc_final: 0.7903 (ptm-80) REVERT: H 82 VAL cc_start: 0.9259 (t) cc_final: 0.8970 (m) REVERT: H 101 THR cc_start: 0.7779 (m) cc_final: 0.7316 (p) REVERT: I 3 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7563 (tp40) REVERT: I 27 TYR cc_start: 0.5546 (t80) cc_final: 0.4439 (t80) REVERT: I 28 THR cc_start: 0.7991 (m) cc_final: 0.6853 (p) REVERT: I 30 THR cc_start: 0.8783 (p) cc_final: 0.8226 (t) REVERT: I 36 TRP cc_start: 0.8313 (m100) cc_final: 0.7764 (m-10) REVERT: I 38 LYS cc_start: 0.8680 (tttp) cc_final: 0.8338 (tttm) REVERT: I 46 GLU cc_start: 0.7653 (pt0) cc_final: 0.7108 (pt0) REVERT: I 57 SER cc_start: 0.9397 (m) cc_final: 0.8951 (p) REVERT: I 82 GLN cc_start: 0.8144 (tp40) cc_final: 0.7824 (tp40) REVERT: I 104 MET cc_start: 0.7200 (mtt) cc_final: 0.6999 (mmt) REVERT: I 109 GLN cc_start: 0.8210 (pm20) cc_final: 0.7986 (pm20) REVERT: I 113 VAL cc_start: 0.8592 (t) cc_final: 0.8121 (m) REVERT: J 61 ARG cc_start: 0.8447 (mtm110) cc_final: 0.8135 (ptp90) REVERT: J 87 PHE cc_start: 0.8307 (m-10) cc_final: 0.7966 (m-10) REVERT: J 103 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7959 (mtpt) outliers start: 59 outliers final: 44 residues processed: 365 average time/residue: 0.1005 time to fit residues: 49.7175 Evaluate side-chains 398 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 350 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 34 TRP Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN C 37 GLN G 57 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113204 restraints weight = 14434.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117256 restraints weight = 6622.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119872 restraints weight = 3648.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121637 restraints weight = 2243.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.122848 restraints weight = 1488.608| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8834 Z= 0.178 Angle : 0.617 8.597 11958 Z= 0.323 Chirality : 0.043 0.163 1270 Planarity : 0.005 0.062 1528 Dihedral : 4.747 20.853 1206 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 5.65 % Allowed : 19.51 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -1.75 (0.26), residues: 1090 helix: -1.57 (0.66), residues: 62 sheet: -0.69 (0.26), residues: 436 loop : -1.45 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 80 TYR 0.025 0.002 TYR J 94 PHE 0.028 0.002 PHE I 29 TRP 0.030 0.003 TRP E 50 HIS 0.004 0.002 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8830) covalent geometry : angle 0.61613 (11950) SS BOND : bond 0.00253 ( 4) SS BOND : angle 1.24512 ( 8) hydrogen bonds : bond 0.03597 ( 262) hydrogen bonds : angle 5.94834 ( 666) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 340 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7643 (m-40) cc_final: 0.7277 (m-40) REVERT: A 314 PHE cc_start: 0.8197 (t80) cc_final: 0.7886 (t80) REVERT: A 361 LYS cc_start: 0.9184 (mttt) cc_final: 0.8664 (mttm) REVERT: A 362 THR cc_start: 0.8884 (p) cc_final: 0.8589 (t) REVERT: A 363 PHE cc_start: 0.8815 (m-80) cc_final: 0.8604 (m-80) REVERT: B 27 PHE cc_start: 0.8675 (p90) cc_final: 0.7774 (p90) REVERT: B 28 THR cc_start: 0.8260 (m) cc_final: 0.7915 (m) REVERT: B 29 PHE cc_start: 0.8728 (t80) cc_final: 0.8515 (t80) REVERT: B 33 TYR cc_start: 0.8133 (m-10) cc_final: 0.7852 (m-10) REVERT: B 54 GLU cc_start: 0.8188 (tt0) cc_final: 0.7610 (tt0) REVERT: B 57 ASN cc_start: 0.8954 (t0) cc_final: 0.8682 (t0) REVERT: B 58 TYR cc_start: 0.8733 (m-10) cc_final: 0.8295 (m-10) REVERT: B 71 THR cc_start: 0.8191 (m) cc_final: 0.7692 (p) REVERT: B 79 SER cc_start: 0.8590 (m) cc_final: 0.7972 (p) REVERT: B 101 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6335 (p0) REVERT: B 104 TYR cc_start: 0.7850 (m-10) cc_final: 0.7559 (m-10) REVERT: C 5 THR cc_start: 0.8703 (t) cc_final: 0.8270 (p) REVERT: C 14 SER cc_start: 0.9059 (m) cc_final: 0.8776 (t) REVERT: C 18 LYS cc_start: 0.8720 (tttt) cc_final: 0.8442 (tttt) REVERT: C 21 MET cc_start: 0.6833 (mtm) cc_final: 0.6490 (mtm) REVERT: D 343 ASP cc_start: 0.8423 (t70) cc_final: 0.8134 (t70) REVERT: D 361 LYS cc_start: 0.9231 (mttt) cc_final: 0.8874 (mttm) REVERT: D 362 THR cc_start: 0.8575 (p) cc_final: 0.8337 (t) REVERT: E 10 GLU cc_start: 0.7362 (tt0) cc_final: 0.7068 (tt0) REVERT: E 19 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7923 (tmtt) REVERT: E 36 TRP cc_start: 0.8310 (m100) cc_final: 0.7957 (m-10) REVERT: E 38 LYS cc_start: 0.8492 (ttpt) cc_final: 0.7997 (tttt) REVERT: E 46 GLU cc_start: 0.7305 (pt0) cc_final: 0.7012 (pt0) REVERT: E 63 LYS cc_start: 0.8828 (tttp) cc_final: 0.8611 (tttp) REVERT: E 104 MET cc_start: 0.7349 (mtt) cc_final: 0.7047 (mtt) REVERT: E 106 TYR cc_start: 0.8084 (m-80) cc_final: 0.7750 (m-80) REVERT: E 107 TRP cc_start: 0.8088 (m100) cc_final: 0.7680 (m-10) REVERT: E 112 SER cc_start: 0.8378 (t) cc_final: 0.7908 (p) REVERT: F 3 VAL cc_start: 0.8769 (p) cc_final: 0.8372 (m) REVERT: F 20 SER cc_start: 0.8750 (t) cc_final: 0.8228 (p) REVERT: F 32 ASN cc_start: 0.6622 (t0) cc_final: 0.6180 (t0) REVERT: F 50 SER cc_start: 0.7774 (m) cc_final: 0.7373 (t) REVERT: F 79 GLN cc_start: 0.7974 (pp30) cc_final: 0.7475 (pp30) REVERT: F 87 PHE cc_start: 0.8450 (m-10) cc_final: 0.8217 (m-10) REVERT: F 90 GLN cc_start: 0.7273 (mt0) cc_final: 0.6983 (mt0) REVERT: F 93 SER cc_start: 0.7805 (t) cc_final: 0.7486 (p) REVERT: G 22 CYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7335 (t) REVERT: G 27 PHE cc_start: 0.8509 (p90) cc_final: 0.7685 (p90) REVERT: G 29 PHE cc_start: 0.8848 (t80) cc_final: 0.8632 (t80) REVERT: G 34 MET cc_start: 0.6978 (mtp) cc_final: 0.6634 (mtp) REVERT: G 54 GLU cc_start: 0.8104 (tt0) cc_final: 0.7721 (tt0) REVERT: G 79 SER cc_start: 0.8680 (m) cc_final: 0.7958 (p) REVERT: G 80 ARG cc_start: 0.8339 (mtt-85) cc_final: 0.8127 (mtt-85) REVERT: G 108 MET cc_start: 0.7055 (mpp) cc_final: 0.6408 (mpp) REVERT: G 111 TRP cc_start: 0.8519 (m-10) cc_final: 0.8291 (m-10) REVERT: H 10 ILE cc_start: 0.8807 (pt) cc_final: 0.8404 (mm) REVERT: H 29 VAL cc_start: 0.8532 (t) cc_final: 0.8178 (m) REVERT: H 37 GLN cc_start: 0.8307 (tt0) cc_final: 0.7880 (tt0) REVERT: H 55 SER cc_start: 0.8378 (t) cc_final: 0.8135 (p) REVERT: H 61 PHE cc_start: 0.8899 (m-10) cc_final: 0.8589 (m-10) REVERT: H 65 ARG cc_start: 0.8219 (ttt180) cc_final: 0.7828 (ptm-80) REVERT: H 82 VAL cc_start: 0.9197 (t) cc_final: 0.8929 (m) REVERT: H 85 TYR cc_start: 0.8219 (m-80) cc_final: 0.7818 (m-10) REVERT: H 101 THR cc_start: 0.7767 (m) cc_final: 0.7271 (p) REVERT: I 3 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7564 (tp40) REVERT: I 27 TYR cc_start: 0.5634 (t80) cc_final: 0.4552 (t80) REVERT: I 28 THR cc_start: 0.7969 (m) cc_final: 0.6833 (p) REVERT: I 30 THR cc_start: 0.8765 (p) cc_final: 0.8195 (t) REVERT: I 36 TRP cc_start: 0.8350 (m100) cc_final: 0.7734 (m-10) REVERT: I 38 LYS cc_start: 0.8682 (tttp) cc_final: 0.8315 (tttm) REVERT: I 46 GLU cc_start: 0.7666 (pt0) cc_final: 0.7057 (pt0) REVERT: I 57 SER cc_start: 0.9371 (m) cc_final: 0.8920 (p) REVERT: I 82 GLN cc_start: 0.8061 (tp40) cc_final: 0.7816 (tp40) REVERT: I 113 VAL cc_start: 0.8583 (t) cc_final: 0.8096 (m) REVERT: J 44 PRO cc_start: 0.7266 (Cg_endo) cc_final: 0.6925 (Cg_exo) REVERT: J 61 ARG cc_start: 0.8261 (mtm110) cc_final: 0.7841 (ptp90) REVERT: J 87 PHE cc_start: 0.8175 (m-10) cc_final: 0.7879 (m-10) REVERT: J 103 LYS cc_start: 0.8265 (mtpt) cc_final: 0.8003 (mtpt) outliers start: 53 outliers final: 42 residues processed: 355 average time/residue: 0.1016 time to fit residues: 48.7608 Evaluate side-chains 384 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 338 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 34 TRP Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 93 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN G 57 ASN H 6 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112472 restraints weight = 14261.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116521 restraints weight = 6579.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119080 restraints weight = 3643.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120842 restraints weight = 2269.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122028 restraints weight = 1509.010| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8834 Z= 0.194 Angle : 0.637 9.024 11958 Z= 0.335 Chirality : 0.044 0.163 1270 Planarity : 0.005 0.042 1528 Dihedral : 4.848 27.256 1206 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 5.65 % Allowed : 20.15 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -1.74 (0.26), residues: 1090 helix: -1.51 (0.66), residues: 62 sheet: -0.71 (0.26), residues: 434 loop : -1.43 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 80 TYR 0.024 0.002 TYR J 94 PHE 0.033 0.002 PHE I 29 TRP 0.033 0.003 TRP E 50 HIS 0.005 0.002 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8830) covalent geometry : angle 0.63692 (11950) SS BOND : bond 0.00248 ( 4) SS BOND : angle 1.22972 ( 8) hydrogen bonds : bond 0.03700 ( 262) hydrogen bonds : angle 5.95197 ( 666) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 340 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7662 (m110) cc_final: 0.7417 (m110) REVERT: A 314 PHE cc_start: 0.8260 (t80) cc_final: 0.7927 (t80) REVERT: A 361 LYS cc_start: 0.9172 (mttt) cc_final: 0.8656 (mttm) REVERT: A 362 THR cc_start: 0.8897 (p) cc_final: 0.8598 (t) REVERT: A 363 PHE cc_start: 0.8826 (m-80) cc_final: 0.8541 (m-80) REVERT: B 27 PHE cc_start: 0.8674 (p90) cc_final: 0.7763 (p90) REVERT: B 28 THR cc_start: 0.8271 (m) cc_final: 0.7936 (m) REVERT: B 33 TYR cc_start: 0.8108 (m-10) cc_final: 0.7830 (m-10) REVERT: B 54 GLU cc_start: 0.8201 (tt0) cc_final: 0.7597 (tt0) REVERT: B 57 ASN cc_start: 0.8971 (t0) cc_final: 0.8713 (t0) REVERT: B 58 TYR cc_start: 0.8749 (m-10) cc_final: 0.8284 (m-10) REVERT: B 71 THR cc_start: 0.8177 (m) cc_final: 0.7670 (p) REVERT: B 79 SER cc_start: 0.8602 (m) cc_final: 0.7985 (p) REVERT: B 101 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6429 (p0) REVERT: B 104 TYR cc_start: 0.7854 (m-10) cc_final: 0.7559 (m-10) REVERT: C 5 THR cc_start: 0.8670 (t) cc_final: 0.8194 (p) REVERT: C 14 SER cc_start: 0.9061 (m) cc_final: 0.8784 (t) REVERT: C 18 LYS cc_start: 0.8700 (tttt) cc_final: 0.8429 (tttt) REVERT: C 32 MET cc_start: 0.6566 (ttm) cc_final: 0.6283 (ttp) REVERT: D 343 ASP cc_start: 0.8429 (t70) cc_final: 0.8153 (t70) REVERT: D 361 LYS cc_start: 0.9222 (mttt) cc_final: 0.8866 (mttm) REVERT: D 362 THR cc_start: 0.8578 (p) cc_final: 0.8337 (t) REVERT: E 10 GLU cc_start: 0.7350 (tt0) cc_final: 0.7057 (tt0) REVERT: E 19 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7927 (tmtt) REVERT: E 36 TRP cc_start: 0.8240 (m100) cc_final: 0.7965 (m-10) REVERT: E 38 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8026 (tttt) REVERT: E 46 GLU cc_start: 0.7303 (pt0) cc_final: 0.7035 (pt0) REVERT: E 63 LYS cc_start: 0.8829 (tttp) cc_final: 0.8609 (tttp) REVERT: E 82 GLN cc_start: 0.7776 (mm110) cc_final: 0.7532 (mm110) REVERT: E 104 MET cc_start: 0.7373 (mtt) cc_final: 0.7046 (mtt) REVERT: E 106 TYR cc_start: 0.8009 (m-80) cc_final: 0.7700 (m-80) REVERT: E 107 TRP cc_start: 0.8083 (m100) cc_final: 0.7576 (m-10) REVERT: E 112 SER cc_start: 0.8515 (t) cc_final: 0.8064 (p) REVERT: F 3 VAL cc_start: 0.8754 (p) cc_final: 0.8542 (m) REVERT: F 20 SER cc_start: 0.8742 (t) cc_final: 0.8220 (p) REVERT: F 32 ASN cc_start: 0.6658 (t0) cc_final: 0.6189 (t0) REVERT: F 50 SER cc_start: 0.7760 (m) cc_final: 0.7325 (t) REVERT: F 87 PHE cc_start: 0.8426 (m-10) cc_final: 0.8218 (m-10) REVERT: F 93 SER cc_start: 0.7812 (t) cc_final: 0.7476 (p) REVERT: G 22 CYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7317 (t) REVERT: G 27 PHE cc_start: 0.8505 (p90) cc_final: 0.7686 (p90) REVERT: G 29 PHE cc_start: 0.8860 (t80) cc_final: 0.8635 (t80) REVERT: G 34 MET cc_start: 0.6975 (mtp) cc_final: 0.6634 (mtp) REVERT: G 54 GLU cc_start: 0.8107 (tt0) cc_final: 0.7710 (tt0) REVERT: G 79 SER cc_start: 0.8690 (m) cc_final: 0.7971 (p) REVERT: G 80 ARG cc_start: 0.8428 (mtt-85) cc_final: 0.8168 (mtt-85) REVERT: G 108 MET cc_start: 0.7079 (mpp) cc_final: 0.6428 (mpp) REVERT: G 111 TRP cc_start: 0.8523 (m-10) cc_final: 0.8311 (m-10) REVERT: H 10 ILE cc_start: 0.8815 (pt) cc_final: 0.8402 (mm) REVERT: H 18 LYS cc_start: 0.8832 (pttt) cc_final: 0.8594 (ptmt) REVERT: H 29 VAL cc_start: 0.8499 (t) cc_final: 0.8153 (m) REVERT: H 37 GLN cc_start: 0.8316 (tt0) cc_final: 0.7881 (tt0) REVERT: H 55 SER cc_start: 0.8381 (t) cc_final: 0.8151 (p) REVERT: H 61 PHE cc_start: 0.8892 (m-10) cc_final: 0.8576 (m-10) REVERT: H 65 ARG cc_start: 0.8250 (ttt180) cc_final: 0.7855 (ptm-80) REVERT: H 82 VAL cc_start: 0.9201 (t) cc_final: 0.8948 (m) REVERT: H 85 TYR cc_start: 0.8227 (m-80) cc_final: 0.7840 (m-10) REVERT: H 101 THR cc_start: 0.7903 (m) cc_final: 0.7398 (p) REVERT: I 3 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7562 (tp40) REVERT: I 27 TYR cc_start: 0.5618 (t80) cc_final: 0.4508 (t80) REVERT: I 28 THR cc_start: 0.7921 (m) cc_final: 0.6790 (p) REVERT: I 30 THR cc_start: 0.8728 (p) cc_final: 0.8194 (t) REVERT: I 36 TRP cc_start: 0.8301 (m100) cc_final: 0.7789 (m-10) REVERT: I 38 LYS cc_start: 0.8680 (tttp) cc_final: 0.8304 (tttm) REVERT: I 46 GLU cc_start: 0.7698 (pt0) cc_final: 0.7065 (pt0) REVERT: I 57 SER cc_start: 0.9367 (m) cc_final: 0.8897 (p) REVERT: I 82 GLN cc_start: 0.8084 (tp40) cc_final: 0.7865 (tp40) REVERT: I 104 MET cc_start: 0.7381 (mtt) cc_final: 0.7132 (mmt) REVERT: I 113 VAL cc_start: 0.8581 (t) cc_final: 0.8100 (m) REVERT: J 44 PRO cc_start: 0.7382 (Cg_endo) cc_final: 0.7117 (Cg_exo) REVERT: J 87 PHE cc_start: 0.8154 (m-10) cc_final: 0.7866 (m-10) REVERT: J 103 LYS cc_start: 0.8266 (mtpt) cc_final: 0.8005 (mtpt) outliers start: 53 outliers final: 44 residues processed: 355 average time/residue: 0.1016 time to fit residues: 48.8819 Evaluate side-chains 386 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 338 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 34 TRP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 0.0980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 289 GLN D 283 GLN G 57 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.113243 restraints weight = 14395.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117308 restraints weight = 6640.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119915 restraints weight = 3678.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121709 restraints weight = 2273.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122900 restraints weight = 1504.795| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8834 Z= 0.161 Angle : 0.637 8.312 11958 Z= 0.333 Chirality : 0.043 0.153 1270 Planarity : 0.004 0.040 1528 Dihedral : 4.786 28.715 1206 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 5.65 % Allowed : 21.22 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -1.63 (0.26), residues: 1090 helix: -1.36 (0.68), residues: 62 sheet: -0.65 (0.26), residues: 434 loop : -1.36 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 80 TYR 0.023 0.002 TYR J 94 PHE 0.037 0.002 PHE I 29 TRP 0.034 0.003 TRP E 50 HIS 0.004 0.001 HIS G 61 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8830) covalent geometry : angle 0.63657 (11950) SS BOND : bond 0.00240 ( 4) SS BOND : angle 1.23102 ( 8) hydrogen bonds : bond 0.03436 ( 262) hydrogen bonds : angle 5.80409 ( 666) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 341 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7625 (m-40) cc_final: 0.7273 (m-40) REVERT: A 314 PHE cc_start: 0.8244 (t80) cc_final: 0.7917 (t80) REVERT: A 361 LYS cc_start: 0.9151 (mttt) cc_final: 0.8642 (mttm) REVERT: A 362 THR cc_start: 0.8883 (p) cc_final: 0.8585 (t) REVERT: B 27 PHE cc_start: 0.8688 (p90) cc_final: 0.7790 (p90) REVERT: B 28 THR cc_start: 0.8248 (m) cc_final: 0.7925 (m) REVERT: B 29 PHE cc_start: 0.8783 (t80) cc_final: 0.8528 (t80) REVERT: B 33 TYR cc_start: 0.8130 (m-10) cc_final: 0.7855 (m-10) REVERT: B 54 GLU cc_start: 0.8209 (tt0) cc_final: 0.7581 (tt0) REVERT: B 57 ASN cc_start: 0.8972 (t0) cc_final: 0.8723 (t0) REVERT: B 58 TYR cc_start: 0.8734 (m-10) cc_final: 0.8254 (m-10) REVERT: B 71 THR cc_start: 0.8164 (m) cc_final: 0.7642 (p) REVERT: B 79 SER cc_start: 0.8567 (m) cc_final: 0.7993 (p) REVERT: B 101 ASP cc_start: 0.6840 (OUTLIER) cc_final: 0.6315 (p0) REVERT: B 104 TYR cc_start: 0.7840 (m-10) cc_final: 0.7527 (m-10) REVERT: C 5 THR cc_start: 0.8627 (t) cc_final: 0.8191 (p) REVERT: C 6 GLN cc_start: 0.7274 (mt0) cc_final: 0.7029 (mt0) REVERT: C 14 SER cc_start: 0.9031 (m) cc_final: 0.8764 (t) REVERT: C 18 LYS cc_start: 0.8696 (tttt) cc_final: 0.8419 (tttt) REVERT: C 32 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.6281 (ttp) REVERT: D 343 ASP cc_start: 0.8416 (t70) cc_final: 0.8148 (t70) REVERT: D 361 LYS cc_start: 0.9217 (mttt) cc_final: 0.8823 (mttm) REVERT: D 362 THR cc_start: 0.8567 (p) cc_final: 0.8319 (t) REVERT: E 10 GLU cc_start: 0.7341 (tt0) cc_final: 0.7056 (tt0) REVERT: E 19 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7952 (tmtt) REVERT: E 36 TRP cc_start: 0.8203 (m100) cc_final: 0.7953 (m-10) REVERT: E 38 LYS cc_start: 0.8480 (ttpt) cc_final: 0.8029 (tttt) REVERT: E 43 GLN cc_start: 0.8292 (mp10) cc_final: 0.8044 (mm110) REVERT: E 46 GLU cc_start: 0.7240 (pt0) cc_final: 0.6880 (pt0) REVERT: E 63 LYS cc_start: 0.8825 (tttp) cc_final: 0.8604 (tttp) REVERT: E 82 GLN cc_start: 0.7759 (mm110) cc_final: 0.7509 (mm110) REVERT: E 104 MET cc_start: 0.7361 (mtt) cc_final: 0.7018 (mtt) REVERT: E 106 TYR cc_start: 0.7998 (m-80) cc_final: 0.7687 (m-80) REVERT: E 107 TRP cc_start: 0.8074 (m100) cc_final: 0.7623 (m-10) REVERT: E 112 SER cc_start: 0.8511 (t) cc_final: 0.8060 (p) REVERT: F 17 ASP cc_start: 0.7364 (p0) cc_final: 0.6755 (p0) REVERT: F 20 SER cc_start: 0.8646 (t) cc_final: 0.8157 (p) REVERT: F 32 ASN cc_start: 0.6678 (t0) cc_final: 0.6216 (t0) REVERT: F 50 SER cc_start: 0.7668 (m) cc_final: 0.7244 (t) REVERT: F 93 SER cc_start: 0.7790 (t) cc_final: 0.7444 (p) REVERT: G 22 CYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7333 (t) REVERT: G 27 PHE cc_start: 0.8488 (p90) cc_final: 0.7647 (p90) REVERT: G 29 PHE cc_start: 0.8841 (t80) cc_final: 0.8624 (t80) REVERT: G 34 MET cc_start: 0.6973 (mtp) cc_final: 0.6633 (mtp) REVERT: G 54 GLU cc_start: 0.8103 (tt0) cc_final: 0.7728 (tt0) REVERT: G 79 SER cc_start: 0.8695 (m) cc_final: 0.8024 (p) REVERT: G 80 ARG cc_start: 0.8374 (mtt-85) cc_final: 0.7942 (mtp85) REVERT: G 108 MET cc_start: 0.7084 (mpp) cc_final: 0.6431 (mpp) REVERT: G 111 TRP cc_start: 0.8498 (m-10) cc_final: 0.8266 (m-10) REVERT: H 10 ILE cc_start: 0.8806 (pt) cc_final: 0.8401 (mm) REVERT: H 18 LYS cc_start: 0.8831 (pttt) cc_final: 0.8607 (ptmt) REVERT: H 29 VAL cc_start: 0.8516 (t) cc_final: 0.8192 (m) REVERT: H 37 GLN cc_start: 0.8302 (tt0) cc_final: 0.7859 (tt0) REVERT: H 48 TYR cc_start: 0.7230 (p90) cc_final: 0.6685 (p90) REVERT: H 55 SER cc_start: 0.8368 (t) cc_final: 0.8111 (p) REVERT: H 61 PHE cc_start: 0.8904 (m-10) cc_final: 0.8577 (m-10) REVERT: H 65 ARG cc_start: 0.8198 (ttt180) cc_final: 0.7794 (ptm-80) REVERT: H 82 VAL cc_start: 0.9193 (t) cc_final: 0.8938 (m) REVERT: H 85 TYR cc_start: 0.8224 (m-80) cc_final: 0.7822 (m-10) REVERT: H 101 THR cc_start: 0.7831 (m) cc_final: 0.7282 (p) REVERT: I 3 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7550 (tp40) REVERT: I 27 TYR cc_start: 0.5657 (t80) cc_final: 0.4584 (t80) REVERT: I 28 THR cc_start: 0.7916 (m) cc_final: 0.6794 (p) REVERT: I 30 THR cc_start: 0.8721 (p) cc_final: 0.8190 (t) REVERT: I 36 TRP cc_start: 0.8352 (m100) cc_final: 0.7757 (m-10) REVERT: I 38 LYS cc_start: 0.8659 (tttp) cc_final: 0.8299 (tttm) REVERT: I 46 GLU cc_start: 0.7561 (pt0) cc_final: 0.6981 (pt0) REVERT: I 57 SER cc_start: 0.9359 (m) cc_final: 0.8929 (p) REVERT: I 82 GLN cc_start: 0.8048 (tp40) cc_final: 0.7826 (tp40) REVERT: I 104 MET cc_start: 0.7335 (mtt) cc_final: 0.7105 (mmt) REVERT: I 113 VAL cc_start: 0.8571 (t) cc_final: 0.8087 (m) REVERT: J 44 PRO cc_start: 0.7292 (Cg_endo) cc_final: 0.7016 (Cg_exo) REVERT: J 87 PHE cc_start: 0.8143 (m-10) cc_final: 0.7820 (m-10) REVERT: J 103 LYS cc_start: 0.8264 (mtpt) cc_final: 0.8000 (mtpt) outliers start: 53 outliers final: 43 residues processed: 356 average time/residue: 0.0968 time to fit residues: 47.1266 Evaluate side-chains 387 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 339 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 34 TRP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 76 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 39 optimal weight: 0.0170 chunk 44 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 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 = 0.3666 r_free = 0.3666 target = 0.127378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114354 restraints weight = 14388.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118426 restraints weight = 6643.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121077 restraints weight = 3680.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122840 restraints weight = 2273.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124023 restraints weight = 1502.748| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8834 Z= 0.145 Angle : 0.634 7.977 11958 Z= 0.330 Chirality : 0.043 0.152 1270 Planarity : 0.004 0.037 1528 Dihedral : 4.722 26.654 1206 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 5.22 % Allowed : 21.75 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -1.56 (0.26), residues: 1090 helix: -1.27 (0.69), residues: 62 sheet: -0.53 (0.26), residues: 428 loop : -1.37 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 80 TYR 0.023 0.002 TYR J 94 PHE 0.037 0.002 PHE I 29 TRP 0.036 0.002 TRP E 50 HIS 0.004 0.001 HIS G 61 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8830) covalent geometry : angle 0.63363 (11950) SS BOND : bond 0.00269 ( 4) SS BOND : angle 1.19765 ( 8) hydrogen bonds : bond 0.03324 ( 262) hydrogen bonds : angle 5.73917 ( 666) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 335 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7635 (m110) cc_final: 0.7410 (m110) REVERT: A 314 PHE cc_start: 0.8208 (t80) cc_final: 0.7899 (t80) REVERT: A 361 LYS cc_start: 0.9205 (mttt) cc_final: 0.8694 (mttm) REVERT: A 362 THR cc_start: 0.8848 (p) cc_final: 0.8639 (t) REVERT: B 27 PHE cc_start: 0.8698 (p90) cc_final: 0.7806 (p90) REVERT: B 28 THR cc_start: 0.8222 (m) cc_final: 0.7890 (m) REVERT: B 33 TYR cc_start: 0.8087 (m-10) cc_final: 0.7856 (m-10) REVERT: B 54 GLU cc_start: 0.8186 (tt0) cc_final: 0.7590 (tt0) REVERT: B 57 ASN cc_start: 0.8976 (t0) cc_final: 0.8716 (t0) REVERT: B 58 TYR cc_start: 0.8716 (m-10) cc_final: 0.8249 (m-10) REVERT: B 71 THR cc_start: 0.8151 (m) cc_final: 0.7674 (p) REVERT: B 79 SER cc_start: 0.8556 (m) cc_final: 0.7975 (p) REVERT: B 101 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6233 (p0) REVERT: B 104 TYR cc_start: 0.7853 (m-10) cc_final: 0.7531 (m-10) REVERT: C 5 THR cc_start: 0.8701 (t) cc_final: 0.8263 (p) REVERT: C 14 SER cc_start: 0.8996 (m) cc_final: 0.8726 (t) REVERT: C 18 LYS cc_start: 0.8679 (tttt) cc_final: 0.8407 (tttt) REVERT: C 32 MET cc_start: 0.6516 (ttm) cc_final: 0.6217 (ttp) REVERT: D 285 ASN cc_start: 0.8505 (p0) cc_final: 0.7880 (p0) REVERT: D 343 ASP cc_start: 0.8408 (t70) cc_final: 0.8167 (t70) REVERT: D 361 LYS cc_start: 0.9214 (mttt) cc_final: 0.8822 (mttm) REVERT: D 362 THR cc_start: 0.8552 (p) cc_final: 0.8298 (t) REVERT: E 10 GLU cc_start: 0.7326 (tt0) cc_final: 0.7036 (tt0) REVERT: E 19 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7989 (tmtt) REVERT: E 36 TRP cc_start: 0.8213 (m100) cc_final: 0.7977 (m-10) REVERT: E 38 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8002 (tttt) REVERT: E 46 GLU cc_start: 0.7186 (pt0) cc_final: 0.6766 (pt0) REVERT: E 63 LYS cc_start: 0.8809 (tttp) cc_final: 0.8575 (tttp) REVERT: E 82 GLN cc_start: 0.7746 (mm110) cc_final: 0.7536 (mm110) REVERT: E 104 MET cc_start: 0.7322 (mtt) cc_final: 0.7071 (mtt) REVERT: E 106 TYR cc_start: 0.8102 (m-80) cc_final: 0.7708 (m-80) REVERT: E 107 TRP cc_start: 0.8086 (m100) cc_final: 0.7646 (m-10) REVERT: E 112 SER cc_start: 0.8344 (t) cc_final: 0.7871 (p) REVERT: F 20 SER cc_start: 0.8668 (t) cc_final: 0.8177 (p) REVERT: F 32 ASN cc_start: 0.6632 (t0) cc_final: 0.6217 (t0) REVERT: F 50 SER cc_start: 0.7648 (m) cc_final: 0.7226 (t) REVERT: F 87 PHE cc_start: 0.8519 (m-10) cc_final: 0.8207 (m-10) REVERT: F 93 SER cc_start: 0.7779 (t) cc_final: 0.7451 (p) REVERT: G 22 CYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7306 (t) REVERT: G 27 PHE cc_start: 0.8455 (p90) cc_final: 0.7638 (p90) REVERT: G 29 PHE cc_start: 0.8840 (t80) cc_final: 0.8627 (t80) REVERT: G 34 MET cc_start: 0.6945 (mtp) cc_final: 0.6615 (mtp) REVERT: G 54 GLU cc_start: 0.8074 (tt0) cc_final: 0.7712 (tt0) REVERT: G 79 SER cc_start: 0.8665 (m) cc_final: 0.7984 (p) REVERT: G 108 MET cc_start: 0.7105 (mpp) cc_final: 0.6454 (mpp) REVERT: G 111 TRP cc_start: 0.8491 (m-10) cc_final: 0.8229 (m-10) REVERT: H 10 ILE cc_start: 0.8756 (pt) cc_final: 0.8355 (mm) REVERT: H 18 LYS cc_start: 0.8801 (pttt) cc_final: 0.8552 (ptmt) REVERT: H 29 VAL cc_start: 0.8488 (t) cc_final: 0.8168 (m) REVERT: H 37 GLN cc_start: 0.8315 (tt0) cc_final: 0.7884 (tt0) REVERT: H 55 SER cc_start: 0.8363 (t) cc_final: 0.8109 (p) REVERT: H 61 PHE cc_start: 0.8968 (m-10) cc_final: 0.8645 (m-10) REVERT: H 65 ARG cc_start: 0.8201 (ttt180) cc_final: 0.7813 (ptm-80) REVERT: H 82 VAL cc_start: 0.9187 (t) cc_final: 0.8942 (m) REVERT: H 85 TYR cc_start: 0.8200 (m-80) cc_final: 0.7802 (m-10) REVERT: H 101 THR cc_start: 0.7843 (m) cc_final: 0.7370 (p) REVERT: I 3 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7534 (tp40) REVERT: I 27 TYR cc_start: 0.5696 (t80) cc_final: 0.4644 (t80) REVERT: I 28 THR cc_start: 0.7923 (m) cc_final: 0.6800 (p) REVERT: I 30 THR cc_start: 0.8792 (p) cc_final: 0.8210 (t) REVERT: I 36 TRP cc_start: 0.8263 (m100) cc_final: 0.7848 (m-10) REVERT: I 38 LYS cc_start: 0.8648 (tttp) cc_final: 0.8310 (tttm) REVERT: I 46 GLU cc_start: 0.7525 (pt0) cc_final: 0.6929 (pt0) REVERT: I 57 SER cc_start: 0.9372 (m) cc_final: 0.8959 (p) REVERT: I 104 MET cc_start: 0.7314 (mtt) cc_final: 0.7092 (mmt) REVERT: I 113 VAL cc_start: 0.8567 (t) cc_final: 0.8077 (m) REVERT: J 44 PRO cc_start: 0.7193 (Cg_endo) cc_final: 0.6910 (Cg_exo) REVERT: J 87 PHE cc_start: 0.8200 (m-10) cc_final: 0.7895 (m-10) REVERT: J 103 LYS cc_start: 0.8264 (mtpt) cc_final: 0.8000 (mtpt) outliers start: 49 outliers final: 40 residues processed: 350 average time/residue: 0.0984 time to fit residues: 46.8928 Evaluate side-chains 378 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 334 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 34 TRP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 93 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 289 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.126731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113684 restraints weight = 14296.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117746 restraints weight = 6624.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120333 restraints weight = 3671.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122132 restraints weight = 2286.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123283 restraints weight = 1507.567| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8834 Z= 0.168 Angle : 0.651 8.428 11958 Z= 0.339 Chirality : 0.044 0.154 1270 Planarity : 0.004 0.039 1528 Dihedral : 4.781 24.966 1206 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 5.01 % Allowed : 21.64 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -1.58 (0.26), residues: 1090 helix: -1.26 (0.68), residues: 62 sheet: -0.53 (0.27), residues: 428 loop : -1.40 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 80 TYR 0.023 0.002 TYR J 94 PHE 0.038 0.002 PHE I 29 TRP 0.035 0.003 TRP E 50 HIS 0.005 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8830) covalent geometry : angle 0.65040 (11950) SS BOND : bond 0.00248 ( 4) SS BOND : angle 1.00751 ( 8) hydrogen bonds : bond 0.03435 ( 262) hydrogen bonds : angle 5.76384 ( 666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.83 seconds wall clock time: 30 minutes 26.44 seconds (1826.44 seconds total)