Starting phenix.real_space_refine on Sat Jun 7 07:28:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c2h_45157/06_2025/9c2h_45157.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c2h_45157/06_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_45157/06_2025/9c2h_45157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c2h_45157/06_2025/9c2h_45157.map" model { file = "/net/cci-nas-00/data/ceres_data/9c2h_45157/06_2025/9c2h_45157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c2h_45157/06_2025/9c2h_45157.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.80, per 1000 atoms: 0.67 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: 2.19 Conformation dependent library (CDL) restraints added in 998.9 milliseconds 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: 1.18 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: 2.14 Time building geometry restraints manager: 2.49 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: 0.01 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: 2.290 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.540 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.720 ------------------------------------------------------------------------------- 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 : 7.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.001 TRP E 50 HIS 0.004 0.001 HIS B 61 PHE 0.013 0.001 PHE J 98 TYR 0.034 0.001 TYR J 94 ARG 0.003 0.000 ARG D 277 Details of bonding type rmsd hydrogen bonds : bond 0.21481 ( 262) hydrogen bonds : angle 9.21674 ( 666) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.60433 ( 8) covalent geometry : bond 0.00322 ( 8830) covalent geometry : angle 0.69746 (11950) *********************** 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 : 0.901 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: 0.7992 (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: 0.8663 (mttm) REVERT: A 362 THR cc_start: 0.8963 (p) cc_final: 0.8653 (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: 0.8375 (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: 0.7095 (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: 0.7988 (m-10) REVERT: E 38 LYS cc_start: 0.8473 (ptmt) cc_final: 0.7791 (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: 0.7926 (m-80) REVERT: E 107 TRP cc_start: 0.8431 (m100) cc_final: 0.7904 (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: 0.7967 (p90) REVERT: F 50 SER cc_start: 0.8214 (m) cc_final: 0.7936 (m) REVERT: F 54 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7575 (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: 0.7703 (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: 0.8141 (p) REVERT: G 28 THR cc_start: 0.8432 (m) cc_final: 0.8179 (m) REVERT: G 29 PHE cc_start: 0.8798 (t80) cc_final: 0.8559 (t80) REVERT: G 34 MET cc_start: 0.7339 (mtp) cc_final: 0.6985 (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: 0.6945 (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: 0.8288 (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: 0.6042 (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: 0.7808 (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: 0.2218 time to fit residues: 121.5538 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 : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 300 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 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 = 0.3673 r_free = 0.3673 target = 0.128006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115270 restraints weight = 14096.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119427 restraints weight = 6366.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122099 restraints weight = 3446.141| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8834 Z= 0.182 Angle : 0.626 10.060 11958 Z= 0.330 Chirality : 0.043 0.191 1270 Planarity : 0.005 0.060 1528 Dihedral : 4.693 19.833 1206 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.67 % Allowed : 13.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.26), residues: 1090 helix: -1.96 (0.66), residues: 62 sheet: -1.11 (0.26), residues: 444 loop : -1.76 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 50 HIS 0.005 0.001 HIS B 61 PHE 0.022 0.002 PHE E 29 TYR 0.026 0.002 TYR J 94 ARG 0.006 0.001 ARG D 276 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 262) hydrogen bonds : angle 6.85241 ( 666) SS BOND : bond 0.00061 ( 4) SS BOND : angle 1.41321 ( 8) covalent geometry : bond 0.00381 ( 8830) covalent geometry : angle 0.62534 (11950) *********************** 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 411 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 386 time to evaluate : 0.897 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: 0.7683 (m110) cc_final: 0.7370 (m110) REVERT: A 314 PHE cc_start: 0.8071 (t80) cc_final: 0.7815 (t80) REVERT: A 347 LYS cc_start: 0.8055 (mttp) cc_final: 0.7809 (mttp) REVERT: A 360 TYR cc_start: 0.8018 (p90) cc_final: 0.7696 (p90) REVERT: A 361 LYS cc_start: 0.9271 (mttt) cc_final: 0.8819 (mttm) REVERT: A 362 THR cc_start: 0.8897 (p) cc_final: 0.8577 (t) REVERT: B 19 LYS cc_start: 0.8621 (tttt) cc_final: 0.8200 (tttm) REVERT: B 27 PHE cc_start: 0.8661 (p90) cc_final: 0.7780 (p90) REVERT: B 28 THR cc_start: 0.8283 (m) cc_final: 0.8005 (m) REVERT: B 29 PHE cc_start: 0.9064 (t80) cc_final: 0.8718 (t80) REVERT: B 33 TYR cc_start: 0.8125 (m-10) cc_final: 0.7813 (m-10) REVERT: B 37 VAL cc_start: 0.8145 (t) cc_final: 0.7784 (m) REVERT: B 38 ARG cc_start: 0.8301 (ttm170) cc_final: 0.8099 (ttp-170) REVERT: B 54 GLU cc_start: 0.8100 (tt0) cc_final: 0.7773 (tt0) REVERT: B 71 THR cc_start: 0.8319 (m) cc_final: 0.7845 (p) REVERT: B 78 LYS cc_start: 0.8657 (mttt) cc_final: 0.8444 (mttt) REVERT: B 79 SER cc_start: 0.8515 (m) cc_final: 0.7878 (p) REVERT: B 85 MET cc_start: 0.7658 (mtt) cc_final: 0.7342 (mtt) REVERT: B 104 TYR cc_start: 0.7977 (m-80) cc_final: 0.7628 (m-80) REVERT: C 14 SER cc_start: 0.9107 (m) cc_final: 0.8862 (t) REVERT: C 18 LYS cc_start: 0.8745 (tttt) cc_final: 0.8407 (tttt) REVERT: C 19 VAL cc_start: 0.8742 (t) cc_final: 0.8493 (t) REVERT: C 21 MET cc_start: 0.6707 (mtm) cc_final: 0.6356 (mtm) REVERT: C 22 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.8044 (t) REVERT: C 32 MET cc_start: 0.6851 (ttm) cc_final: 0.6549 (ttm) REVERT: C 37 GLN cc_start: 0.8079 (tt0) cc_final: 0.7863 (tt0) REVERT: C 50 THR cc_start: 0.9109 (m) cc_final: 0.8527 (p) REVERT: C 51 SER cc_start: 0.8483 (p) cc_final: 0.8187 (m) REVERT: C 61 PHE cc_start: 0.8938 (m-10) cc_final: 0.8665 (m-80) REVERT: C 74 ILE cc_start: 0.8492 (mt) cc_final: 0.8228 (mt) REVERT: C 101 THR cc_start: 0.7500 (m) cc_final: 0.6895 (p) REVERT: D 276 ARG cc_start: 0.8139 (ptm-80) cc_final: 0.7854 (ptm160) REVERT: D 279 PRO cc_start: 0.8705 (Cg_exo) cc_final: 0.8362 (Cg_endo) REVERT: D 343 ASP cc_start: 0.8409 (t70) cc_final: 0.8024 (t0) REVERT: D 360 TYR cc_start: 0.7789 (p90) cc_final: 0.7359 (p90) REVERT: D 361 LYS cc_start: 0.9163 (mttt) cc_final: 0.8682 (mttm) REVERT: D 362 THR cc_start: 0.8628 (p) cc_final: 0.8372 (t) REVERT: E 22 CYS cc_start: 0.7536 (t) cc_final: 0.6594 (t) REVERT: E 36 TRP cc_start: 0.8249 (m100) cc_final: 0.7764 (m-10) REVERT: E 40 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7502 (mtt90) REVERT: E 76 SER cc_start: 0.8491 (p) cc_final: 0.8100 (t) REVERT: E 106 TYR cc_start: 0.7965 (m-80) cc_final: 0.7596 (m-80) REVERT: E 107 TRP cc_start: 0.8144 (m100) cc_final: 0.7890 (m100) REVERT: E 112 SER cc_start: 0.8555 (t) cc_final: 0.8186 (p) REVERT: F 9 LYS cc_start: 0.8603 (tttt) cc_final: 0.8350 (tttt) REVERT: F 10 PHE cc_start: 0.7937 (m-80) cc_final: 0.7332 (m-80) REVERT: F 20 SER cc_start: 0.8716 (t) cc_final: 0.8428 (p) REVERT: F 32 ASN cc_start: 0.6384 (t0) cc_final: 0.5990 (t0) REVERT: F 54 ARG cc_start: 0.7840 (mtm110) cc_final: 0.7277 (mtp180) REVERT: F 55 TYR cc_start: 0.8156 (m-80) cc_final: 0.7867 (m-10) REVERT: F 61 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7007 (ptt-90) REVERT: F 62 PHE cc_start: 0.8740 (m-80) cc_final: 0.8296 (m-10) REVERT: F 75 ILE cc_start: 0.8454 (mt) cc_final: 0.7656 (mt) REVERT: F 80 SER cc_start: 0.8982 (m) cc_final: 0.8733 (p) REVERT: F 88 CYS cc_start: 0.7971 (t) cc_final: 0.7585 (p) REVERT: F 90 GLN cc_start: 0.7579 (mt0) cc_final: 0.6190 (mt0) REVERT: F 93 SER cc_start: 0.8075 (t) cc_final: 0.7695 (p) REVERT: G 22 CYS cc_start: 0.8367 (t) cc_final: 0.7610 (t) REVERT: G 29 PHE cc_start: 0.8845 (t80) cc_final: 0.8623 (t80) REVERT: G 34 MET cc_start: 0.6827 (mtp) cc_final: 0.6610 (mtp) REVERT: G 57 ASN cc_start: 0.9104 (t0) cc_final: 0.8883 (t0) REVERT: G 58 TYR cc_start: 0.8734 (m-10) cc_final: 0.7843 (m-10) REVERT: G 70 PHE cc_start: 0.8601 (m-80) cc_final: 0.8364 (m-80) REVERT: G 71 THR cc_start: 0.8268 (m) cc_final: 0.7626 (p) REVERT: G 79 SER cc_start: 0.8657 (m) cc_final: 0.8076 (p) REVERT: G 108 MET cc_start: 0.7173 (mpp) cc_final: 0.6585 (mpp) REVERT: G 109 ASP cc_start: 0.7117 (t0) cc_final: 0.6902 (t0) REVERT: H 10 ILE cc_start: 0.8822 (pt) cc_final: 0.8431 (mm) REVERT: H 21 MET cc_start: 0.7106 (mtm) cc_final: 0.6854 (mtm) REVERT: H 29 VAL cc_start: 0.8694 (t) cc_final: 0.8209 (m) REVERT: H 37 GLN cc_start: 0.8298 (tt0) cc_final: 0.7920 (tt0) REVERT: H 44 LYS cc_start: 0.8239 (mttt) cc_final: 0.7561 (mtmm) REVERT: H 55 SER cc_start: 0.8432 (t) cc_final: 0.8190 (p) REVERT: H 61 PHE cc_start: 0.8999 (m-10) cc_final: 0.8762 (m-10) REVERT: H 65 ARG cc_start: 0.8364 (ttt180) cc_final: 0.8087 (ptm-80) REVERT: H 85 TYR cc_start: 0.8281 (m-80) cc_final: 0.7896 (m-10) REVERT: H 89 GLN cc_start: 0.7555 (mt0) cc_final: 0.6306 (mt0) REVERT: H 101 THR cc_start: 0.7760 (m) cc_final: 0.7349 (p) REVERT: I 11 LEU cc_start: 0.8383 (mt) cc_final: 0.7727 (mt) REVERT: I 27 TYR cc_start: 0.5691 (t80) cc_final: 0.4864 (t80) REVERT: I 28 THR cc_start: 0.7960 (m) cc_final: 0.6879 (p) REVERT: I 30 THR cc_start: 0.8708 (p) cc_final: 0.8301 (t) REVERT: I 36 TRP cc_start: 0.8366 (m100) cc_final: 0.7859 (m-10) REVERT: I 38 LYS cc_start: 0.8717 (tttp) cc_final: 0.7403 (tttp) REVERT: I 40 ARG cc_start: 0.7834 (mtt90) cc_final: 0.7371 (mtt90) REVERT: I 46 GLU cc_start: 0.7753 (pt0) cc_final: 0.7484 (pt0) REVERT: I 57 SER cc_start: 0.9392 (m) cc_final: 0.8934 (p) REVERT: I 93 VAL cc_start: 0.7420 (t) cc_final: 0.7172 (p) REVERT: I 113 VAL cc_start: 0.8488 (t) cc_final: 0.8072 (m) REVERT: J 49 TYR cc_start: 0.7797 (p90) cc_final: 0.7512 (p90) REVERT: J 50 SER cc_start: 0.7957 (m) cc_final: 0.7645 (m) REVERT: J 87 PHE cc_start: 0.8461 (m-10) cc_final: 0.8112 (m-10) REVERT: J 93 SER cc_start: 0.7459 (t) cc_final: 0.7131 (p) REVERT: J 96 LEU cc_start: 0.7908 (mp) cc_final: 0.7312 (mp) REVERT: J 103 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7997 (mtpt) outliers start: 25 outliers final: 17 residues processed: 391 average time/residue: 0.2158 time to fit residues: 112.3999 Evaluate side-chains 403 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 383 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain B residue 40 SER 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 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 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111919 restraints weight = 14362.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116126 restraints weight = 6581.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118791 restraints weight = 3612.446| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8834 Z= 0.248 Angle : 0.665 9.189 11958 Z= 0.353 Chirality : 0.044 0.204 1270 Planarity : 0.005 0.058 1528 Dihedral : 4.980 20.337 1206 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 5.44 % Allowed : 15.46 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.25), residues: 1090 helix: -1.76 (0.66), residues: 62 sheet: -1.04 (0.26), residues: 448 loop : -1.76 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 50 HIS 0.007 0.002 HIS B 61 PHE 0.017 0.002 PHE C 88 TYR 0.027 0.002 TYR J 94 ARG 0.006 0.001 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 262) hydrogen bonds : angle 6.62636 ( 666) SS BOND : bond 0.00094 ( 4) SS BOND : angle 1.36399 ( 8) covalent geometry : bond 0.00524 ( 8830) covalent geometry : angle 0.66408 (11950) *********************** 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 439 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 388 time to evaluate : 0.964 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: 0.7733 (m-40) cc_final: 0.7402 (m-40) REVERT: A 314 PHE cc_start: 0.8189 (t80) cc_final: 0.7912 (t80) REVERT: A 347 LYS cc_start: 0.8046 (mttp) cc_final: 0.7807 (mttp) REVERT: A 360 TYR cc_start: 0.7895 (p90) cc_final: 0.7544 (p90) REVERT: A 361 LYS cc_start: 0.9289 (mttt) cc_final: 0.8818 (mttm) REVERT: A 362 THR cc_start: 0.8890 (p) cc_final: 0.8627 (t) REVERT: B 19 LYS cc_start: 0.8639 (tttt) cc_final: 0.8238 (tttm) REVERT: B 27 PHE cc_start: 0.8637 (p90) cc_final: 0.8078 (p90) REVERT: B 28 THR cc_start: 0.8275 (m) cc_final: 0.8063 (m) REVERT: B 29 PHE cc_start: 0.8986 (t80) cc_final: 0.8672 (t80) REVERT: B 33 TYR cc_start: 0.8166 (m-10) cc_final: 0.7862 (m-10) REVERT: B 37 VAL cc_start: 0.8162 (t) cc_final: 0.7796 (m) REVERT: B 54 GLU cc_start: 0.8208 (tt0) cc_final: 0.7776 (tt0) REVERT: B 57 ASN cc_start: 0.9071 (t0) cc_final: 0.8812 (t0) REVERT: B 58 TYR cc_start: 0.8629 (m-80) cc_final: 0.8399 (m-10) REVERT: B 71 THR cc_start: 0.8301 (m) cc_final: 0.7798 (p) REVERT: B 79 SER cc_start: 0.8521 (m) cc_final: 0.7896 (p) REVERT: C 14 SER cc_start: 0.9136 (m) cc_final: 0.8863 (t) REVERT: C 18 LYS cc_start: 0.8745 (tttt) cc_final: 0.8437 (tttt) REVERT: C 21 MET cc_start: 0.6875 (mtm) cc_final: 0.6575 (mtm) REVERT: C 22 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8086 (t) REVERT: C 32 MET cc_start: 0.6880 (ttm) cc_final: 0.6663 (ttm) REVERT: C 51 SER cc_start: 0.8477 (p) cc_final: 0.8185 (m) REVERT: C 61 PHE cc_start: 0.8829 (m-10) cc_final: 0.8544 (m-80) REVERT: C 74 ILE cc_start: 0.8440 (mt) cc_final: 0.8112 (mt) REVERT: C 101 THR cc_start: 0.7413 (m) cc_final: 0.6895 (p) REVERT: D 279 PRO cc_start: 0.8793 (Cg_exo) cc_final: 0.8399 (Cg_endo) REVERT: D 343 ASP cc_start: 0.8442 (t70) cc_final: 0.8050 (t0) REVERT: D 360 TYR cc_start: 0.7790 (p90) cc_final: 0.7432 (p90) REVERT: D 361 LYS cc_start: 0.9187 (mttt) cc_final: 0.8714 (mttm) REVERT: D 362 THR cc_start: 0.8609 (p) cc_final: 0.8364 (t) REVERT: E 6 GLN cc_start: 0.6743 (mt0) cc_final: 0.6431 (mt0) REVERT: E 19 LYS cc_start: 0.8334 (tttt) cc_final: 0.8104 (tmtt) REVERT: E 22 CYS cc_start: 0.7611 (t) cc_final: 0.6689 (t) REVERT: E 36 TRP cc_start: 0.8323 (m100) cc_final: 0.7631 (m-10) REVERT: E 38 LYS cc_start: 0.8546 (ttpt) cc_final: 0.7979 (tttt) REVERT: E 76 SER cc_start: 0.8342 (p) cc_final: 0.8013 (t) REVERT: E 106 TYR cc_start: 0.8032 (m-80) cc_final: 0.7703 (m-80) REVERT: E 109 GLN cc_start: 0.8253 (pm20) cc_final: 0.7852 (pm20) REVERT: E 112 SER cc_start: 0.8623 (t) cc_final: 0.8168 (p) REVERT: F 9 LYS cc_start: 0.8607 (tttt) cc_final: 0.8371 (tttt) REVERT: F 10 PHE cc_start: 0.7979 (m-80) cc_final: 0.7399 (m-80) REVERT: F 20 SER cc_start: 0.8775 (t) cc_final: 0.8468 (p) REVERT: F 32 ASN cc_start: 0.6705 (t0) cc_final: 0.6183 (t0) REVERT: F 49 TYR cc_start: 0.7749 (p90) cc_final: 0.7522 (p90) REVERT: F 61 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8172 (ptt-90) REVERT: F 75 ILE cc_start: 0.8388 (mt) cc_final: 0.8165 (mt) REVERT: F 79 GLN cc_start: 0.7316 (mp10) cc_final: 0.7015 (pm20) REVERT: F 87 PHE cc_start: 0.8549 (m-10) cc_final: 0.8226 (m-10) REVERT: F 88 CYS cc_start: 0.7984 (t) cc_final: 0.7675 (p) REVERT: F 93 SER cc_start: 0.8082 (t) cc_final: 0.7756 (p) REVERT: G 22 CYS cc_start: 0.8327 (t) cc_final: 0.7460 (t) REVERT: G 27 PHE cc_start: 0.8509 (p90) cc_final: 0.7814 (p90) REVERT: G 29 PHE cc_start: 0.8859 (t80) cc_final: 0.8616 (t80) REVERT: G 34 MET cc_start: 0.7070 (mtp) cc_final: 0.6751 (mtp) REVERT: G 54 GLU cc_start: 0.8045 (tt0) cc_final: 0.7541 (tt0) REVERT: G 58 TYR cc_start: 0.8525 (m-10) cc_final: 0.8030 (m-80) REVERT: G 70 PHE cc_start: 0.8681 (m-80) cc_final: 0.8455 (m-80) REVERT: G 71 THR cc_start: 0.8265 (m) cc_final: 0.7587 (p) REVERT: G 79 SER cc_start: 0.8673 (m) cc_final: 0.8060 (p) REVERT: G 108 MET cc_start: 0.7136 (mpp) cc_final: 0.6562 (mpp) REVERT: H 10 ILE cc_start: 0.8851 (pt) cc_final: 0.8489 (mm) REVERT: H 29 VAL cc_start: 0.8651 (t) cc_final: 0.8238 (m) REVERT: H 34 TRP cc_start: 0.8190 (m100) cc_final: 0.7974 (m100) REVERT: H 37 GLN cc_start: 0.8355 (tt0) cc_final: 0.7937 (tt0) REVERT: H 42 SER cc_start: 0.8690 (m) cc_final: 0.8454 (p) REVERT: H 44 LYS cc_start: 0.8219 (mttt) cc_final: 0.7565 (mtmm) REVERT: H 48 TYR cc_start: 0.7297 (p90) cc_final: 0.6781 (p90) REVERT: H 55 SER cc_start: 0.8399 (t) cc_final: 0.8115 (p) REVERT: H 61 PHE cc_start: 0.8956 (m-10) cc_final: 0.8691 (m-10) REVERT: H 65 ARG cc_start: 0.8360 (ttt180) cc_final: 0.7969 (ptm-80) REVERT: H 82 VAL cc_start: 0.9220 (t) cc_final: 0.8873 (m) REVERT: H 89 GLN cc_start: 0.7360 (mt0) cc_final: 0.6912 (mt0) REVERT: H 101 THR cc_start: 0.7743 (m) cc_final: 0.7245 (p) REVERT: I 27 TYR cc_start: 0.5499 (t80) cc_final: 0.4556 (t80) REVERT: I 28 THR cc_start: 0.8029 (m) cc_final: 0.6935 (p) REVERT: I 30 THR cc_start: 0.8742 (p) cc_final: 0.8342 (t) REVERT: I 36 TRP cc_start: 0.8364 (m100) cc_final: 0.7772 (m-10) REVERT: I 38 LYS cc_start: 0.8735 (tttp) cc_final: 0.8227 (tttm) REVERT: I 57 SER cc_start: 0.9405 (m) cc_final: 0.8914 (p) REVERT: I 76 SER cc_start: 0.8649 (m) cc_final: 0.7979 (t) REVERT: I 93 VAL cc_start: 0.7513 (t) cc_final: 0.7227 (p) REVERT: I 104 MET cc_start: 0.7333 (mtt) cc_final: 0.6962 (mtt) REVERT: I 113 VAL cc_start: 0.8563 (t) cc_final: 0.8093 (m) REVERT: J 49 TYR cc_start: 0.7568 (p90) cc_final: 0.7268 (p90) REVERT: J 50 SER cc_start: 0.7782 (m) cc_final: 0.7485 (m) REVERT: J 87 PHE cc_start: 0.8456 (m-10) cc_final: 0.8171 (m-10) REVERT: J 93 SER cc_start: 0.7718 (t) cc_final: 0.7469 (p) REVERT: J 103 LYS cc_start: 0.8282 (mtpt) cc_final: 0.8032 (mtpt) outliers start: 51 outliers final: 37 residues processed: 400 average time/residue: 0.2311 time to fit residues: 123.6471 Evaluate side-chains 411 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 372 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 40 SER Chi-restraints excluded: chain B residue 60 THR 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 351 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 61 ASN 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 12 SER 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 60 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 5 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 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 69 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 77 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 0.9990 chunk 90 optimal weight: 0.0870 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN D 354 ASN E 61 ASN H 89 GLN ** I 6 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 = 0.3646 r_free = 0.3646 target = 0.126247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113108 restraints weight = 14299.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117299 restraints weight = 6570.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119906 restraints weight = 3610.376| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8834 Z= 0.174 Angle : 0.623 8.053 11958 Z= 0.325 Chirality : 0.043 0.175 1270 Planarity : 0.005 0.047 1528 Dihedral : 4.789 20.511 1206 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 5.65 % Allowed : 17.27 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.26), residues: 1090 helix: -1.57 (0.68), residues: 62 sheet: -0.84 (0.26), residues: 440 loop : -1.71 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 50 HIS 0.004 0.001 HIS B 61 PHE 0.024 0.002 PHE E 29 TYR 0.024 0.002 TYR J 94 ARG 0.008 0.001 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 262) hydrogen bonds : angle 6.32341 ( 666) SS BOND : bond 0.00274 ( 4) SS BOND : angle 1.26135 ( 8) covalent geometry : bond 0.00371 ( 8830) covalent geometry : angle 0.62218 (11950) *********************** 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 421 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 368 time to evaluate : 0.915 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: 0.7692 (m-40) cc_final: 0.7411 (m-40) REVERT: A 314 PHE cc_start: 0.8190 (t80) cc_final: 0.7902 (t80) REVERT: A 361 LYS cc_start: 0.9246 (mttt) cc_final: 0.8778 (mttm) REVERT: A 362 THR cc_start: 0.8869 (p) cc_final: 0.8631 (t) REVERT: B 19 LYS cc_start: 0.8609 (tttt) cc_final: 0.7988 (ttmm) REVERT: B 27 PHE cc_start: 0.8660 (p90) cc_final: 0.7752 (p90) REVERT: B 28 THR cc_start: 0.8251 (m) cc_final: 0.7932 (m) REVERT: B 29 PHE cc_start: 0.8944 (t80) cc_final: 0.8622 (t80) REVERT: B 33 TYR cc_start: 0.8090 (m-10) cc_final: 0.7776 (m-10) REVERT: B 38 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.7952 (ttp-110) REVERT: B 54 GLU cc_start: 0.8191 (tt0) cc_final: 0.7696 (tt0) REVERT: B 57 ASN cc_start: 0.8921 (t0) cc_final: 0.8720 (t0) REVERT: B 58 TYR cc_start: 0.8656 (m-80) cc_final: 0.8355 (m-10) REVERT: B 71 THR cc_start: 0.8293 (m) cc_final: 0.7710 (p) REVERT: B 79 SER cc_start: 0.8552 (m) cc_final: 0.7942 (p) REVERT: B 101 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6463 (p0) REVERT: B 104 TYR cc_start: 0.7887 (m-10) cc_final: 0.7673 (m-10) REVERT: C 14 SER cc_start: 0.9096 (m) cc_final: 0.8798 (t) REVERT: C 18 LYS cc_start: 0.8746 (tttt) cc_final: 0.8469 (tttt) REVERT: C 32 MET cc_start: 0.6767 (ttm) cc_final: 0.6564 (ttm) REVERT: C 51 SER cc_start: 0.8409 (p) cc_final: 0.8144 (m) REVERT: C 61 PHE cc_start: 0.8787 (m-10) cc_final: 0.8477 (m-80) REVERT: C 74 ILE cc_start: 0.8459 (mt) cc_final: 0.8146 (mt) REVERT: C 101 THR cc_start: 0.7381 (m) cc_final: 0.6881 (p) REVERT: D 343 ASP cc_start: 0.8503 (t70) cc_final: 0.8121 (t70) REVERT: D 361 LYS cc_start: 0.9185 (mttt) cc_final: 0.8670 (mttm) REVERT: D 362 THR cc_start: 0.8610 (p) cc_final: 0.8344 (t) REVERT: E 19 LYS cc_start: 0.8367 (tttt) cc_final: 0.7977 (tmtt) REVERT: E 36 TRP cc_start: 0.8411 (m100) cc_final: 0.7965 (m-10) REVERT: E 38 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8074 (tttt) REVERT: E 46 GLU cc_start: 0.7445 (pt0) cc_final: 0.7213 (pt0) REVERT: E 63 LYS cc_start: 0.8828 (tttp) cc_final: 0.8613 (tttp) REVERT: E 104 MET cc_start: 0.7323 (mtt) cc_final: 0.7041 (mmt) REVERT: E 106 TYR cc_start: 0.7970 (m-80) cc_final: 0.7597 (m-80) REVERT: E 107 TRP cc_start: 0.8131 (m100) cc_final: 0.7679 (m-10) REVERT: E 109 GLN cc_start: 0.8218 (pm20) cc_final: 0.7746 (pm20) REVERT: E 112 SER cc_start: 0.8568 (t) cc_final: 0.8108 (p) REVERT: F 4 MET cc_start: 0.7840 (mmm) cc_final: 0.7358 (mmm) REVERT: F 20 SER cc_start: 0.8835 (t) cc_final: 0.8411 (p) REVERT: F 32 ASN cc_start: 0.6480 (t0) cc_final: 0.6053 (t0) REVERT: F 61 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8086 (ptt-90) REVERT: F 79 GLN cc_start: 0.7239 (mp10) cc_final: 0.6731 (pm20) REVERT: F 87 PHE cc_start: 0.8469 (m-10) cc_final: 0.8242 (m-10) REVERT: F 90 GLN cc_start: 0.7253 (mt0) cc_final: 0.6492 (mt0) REVERT: F 93 SER cc_start: 0.7929 (t) cc_final: 0.7599 (p) REVERT: G 22 CYS cc_start: 0.8170 (t) cc_final: 0.7542 (t) REVERT: G 27 PHE cc_start: 0.8507 (p90) cc_final: 0.7823 (p90) REVERT: G 29 PHE cc_start: 0.8855 (t80) cc_final: 0.8618 (t80) REVERT: G 34 MET cc_start: 0.7018 (mtp) cc_final: 0.6671 (mtp) REVERT: G 54 GLU cc_start: 0.8098 (tt0) cc_final: 0.7653 (tt0) REVERT: G 58 TYR cc_start: 0.8533 (m-10) cc_final: 0.7941 (m-80) REVERT: G 71 THR cc_start: 0.8190 (m) cc_final: 0.7549 (p) REVERT: G 79 SER cc_start: 0.8657 (m) cc_final: 0.8033 (p) REVERT: G 108 MET cc_start: 0.7197 (mpp) cc_final: 0.6481 (mpp) REVERT: G 109 ASP cc_start: 0.7144 (t0) cc_final: 0.6907 (t70) REVERT: H 10 ILE cc_start: 0.8828 (pt) cc_final: 0.8435 (mm) REVERT: H 29 VAL cc_start: 0.8629 (t) cc_final: 0.8244 (m) REVERT: H 34 TRP cc_start: 0.8167 (m100) cc_final: 0.7903 (m100) REVERT: H 37 GLN cc_start: 0.8290 (tt0) cc_final: 0.7912 (tt0) REVERT: H 48 TYR cc_start: 0.7246 (p90) cc_final: 0.6676 (p90) REVERT: H 55 SER cc_start: 0.8401 (t) cc_final: 0.8145 (p) REVERT: H 61 PHE cc_start: 0.8992 (m-10) cc_final: 0.8761 (m-10) REVERT: H 65 ARG cc_start: 0.8280 (ttt180) cc_final: 0.7883 (ptm-80) REVERT: H 82 VAL cc_start: 0.9195 (t) cc_final: 0.8854 (m) REVERT: H 85 TYR cc_start: 0.8227 (m-80) cc_final: 0.7870 (m-10) REVERT: H 101 THR cc_start: 0.7759 (m) cc_final: 0.7272 (p) REVERT: I 3 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7567 (tp40) REVERT: I 27 TYR cc_start: 0.5457 (t80) cc_final: 0.4427 (t80) REVERT: I 28 THR cc_start: 0.7983 (m) cc_final: 0.6846 (p) REVERT: I 30 THR cc_start: 0.8829 (p) cc_final: 0.8351 (t) REVERT: I 36 TRP cc_start: 0.8356 (m100) cc_final: 0.7855 (m-10) REVERT: I 38 LYS cc_start: 0.8677 (tttp) cc_final: 0.8224 (tttm) REVERT: I 57 SER cc_start: 0.9401 (m) cc_final: 0.8925 (p) REVERT: I 76 SER cc_start: 0.8632 (m) cc_final: 0.7986 (t) REVERT: I 113 VAL cc_start: 0.8574 (t) cc_final: 0.8123 (m) REVERT: J 49 TYR cc_start: 0.7444 (p90) cc_final: 0.7161 (p90) REVERT: J 50 SER cc_start: 0.7614 (m) cc_final: 0.7356 (m) REVERT: J 87 PHE cc_start: 0.8404 (m-10) cc_final: 0.8147 (m-10) REVERT: J 92 ASN cc_start: 0.8740 (t0) cc_final: 0.8197 (t0) REVERT: J 103 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7955 (mtpt) outliers start: 53 outliers final: 41 residues processed: 386 average time/residue: 0.2099 time to fit residues: 109.0206 Evaluate side-chains 399 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 355 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 57 VAL 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 D residue 354 ASN Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 61 ASN 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 7 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 26 SER 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN G 57 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 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 = 0.3634 r_free = 0.3634 target = 0.125425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112344 restraints weight = 14377.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116453 restraints weight = 6674.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119116 restraints weight = 3690.141| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3545 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= 0.190 Angle : 0.629 7.638 11958 Z= 0.331 Chirality : 0.044 0.182 1270 Planarity : 0.005 0.065 1528 Dihedral : 4.839 23.901 1206 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 5.97 % Allowed : 18.02 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.26), residues: 1090 helix: -1.69 (0.67), residues: 62 sheet: -0.87 (0.26), residues: 436 loop : -1.55 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 50 HIS 0.004 0.002 HIS B 61 PHE 0.023 0.002 PHE I 29 TYR 0.024 0.002 TYR J 94 ARG 0.011 0.001 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 262) hydrogen bonds : angle 6.14677 ( 666) SS BOND : bond 0.00092 ( 4) SS BOND : angle 1.16678 ( 8) covalent geometry : bond 0.00404 ( 8830) covalent geometry : angle 0.62817 (11950) *********************** 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 404 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 348 time to evaluate : 0.881 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: 0.7702 (m110) cc_final: 0.7477 (m110) REVERT: A 314 PHE cc_start: 0.8189 (t80) cc_final: 0.7911 (t80) REVERT: A 361 LYS cc_start: 0.9216 (mttt) cc_final: 0.8679 (mttm) REVERT: A 362 THR cc_start: 0.8870 (p) cc_final: 0.8640 (t) REVERT: B 27 PHE cc_start: 0.8667 (p90) cc_final: 0.7767 (p90) REVERT: B 28 THR cc_start: 0.8284 (m) cc_final: 0.7951 (m) REVERT: B 29 PHE cc_start: 0.8845 (t80) cc_final: 0.8563 (t80) REVERT: B 33 TYR cc_start: 0.8116 (m-10) cc_final: 0.7859 (m-10) REVERT: B 38 ARG cc_start: 0.8285 (ttp-110) cc_final: 0.7930 (ttp-110) REVERT: B 54 GLU cc_start: 0.8242 (tt0) cc_final: 0.7745 (tt0) REVERT: B 57 ASN cc_start: 0.8929 (t0) cc_final: 0.8726 (t0) REVERT: B 58 TYR cc_start: 0.8684 (m-80) cc_final: 0.8351 (m-10) REVERT: B 71 THR cc_start: 0.8284 (m) cc_final: 0.7698 (p) REVERT: B 79 SER cc_start: 0.8560 (m) cc_final: 0.7944 (p) REVERT: B 101 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6479 (p0) REVERT: B 104 TYR cc_start: 0.7896 (m-10) cc_final: 0.7690 (m-10) REVERT: C 14 SER cc_start: 0.9108 (m) cc_final: 0.8810 (t) REVERT: C 18 LYS cc_start: 0.8734 (tttt) cc_final: 0.8470 (tttt) REVERT: C 51 SER cc_start: 0.8392 (p) cc_final: 0.8181 (m) REVERT: C 61 PHE cc_start: 0.8788 (m-10) cc_final: 0.8488 (m-80) REVERT: C 74 ILE cc_start: 0.8475 (mt) cc_final: 0.8167 (mt) REVERT: C 101 THR cc_start: 0.7484 (m) cc_final: 0.7165 (p) REVERT: D 343 ASP cc_start: 0.8484 (t70) cc_final: 0.8118 (t70) REVERT: D 361 LYS cc_start: 0.9178 (mttt) cc_final: 0.8745 (mttm) REVERT: D 362 THR cc_start: 0.8592 (p) cc_final: 0.8327 (t) REVERT: E 19 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7983 (tmtt) REVERT: E 36 TRP cc_start: 0.8394 (m100) cc_final: 0.8037 (m-10) REVERT: E 38 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8095 (tttt) REVERT: E 46 GLU cc_start: 0.7452 (pt0) cc_final: 0.7217 (pt0) REVERT: E 63 LYS cc_start: 0.8800 (tttp) cc_final: 0.8542 (tttp) REVERT: E 104 MET cc_start: 0.7261 (mtt) cc_final: 0.6998 (mtt) REVERT: E 106 TYR cc_start: 0.8066 (m-80) cc_final: 0.7707 (m-80) REVERT: E 107 TRP cc_start: 0.8112 (m100) cc_final: 0.7730 (m-10) REVERT: E 109 GLN cc_start: 0.8245 (pm20) cc_final: 0.7869 (pm20) REVERT: E 112 SER cc_start: 0.8561 (t) cc_final: 0.8111 (p) REVERT: F 20 SER cc_start: 0.8839 (t) cc_final: 0.8375 (p) REVERT: F 32 ASN cc_start: 0.6506 (t0) cc_final: 0.6081 (t0) REVERT: F 50 SER cc_start: 0.7890 (m) cc_final: 0.7449 (t) REVERT: F 90 GLN cc_start: 0.7287 (mt0) cc_final: 0.7009 (mt0) REVERT: F 93 SER cc_start: 0.7873 (t) cc_final: 0.7550 (p) REVERT: G 22 CYS cc_start: 0.8104 (t) cc_final: 0.7517 (t) REVERT: G 27 PHE cc_start: 0.8525 (p90) cc_final: 0.7795 (p90) REVERT: G 29 PHE cc_start: 0.8846 (t80) cc_final: 0.8559 (t80) REVERT: G 34 MET cc_start: 0.7082 (mtp) cc_final: 0.6672 (mtp) REVERT: G 54 GLU cc_start: 0.8245 (tt0) cc_final: 0.7886 (tt0) REVERT: G 71 THR cc_start: 0.8150 (m) cc_final: 0.7500 (p) REVERT: G 79 SER cc_start: 0.8695 (m) cc_final: 0.8053 (p) REVERT: G 108 MET cc_start: 0.7163 (mpp) cc_final: 0.6463 (mpp) REVERT: H 10 ILE cc_start: 0.8830 (pt) cc_final: 0.8431 (mm) REVERT: H 29 VAL cc_start: 0.8619 (t) cc_final: 0.8213 (m) REVERT: H 34 TRP cc_start: 0.8213 (m100) cc_final: 0.7816 (m100) REVERT: H 37 GLN cc_start: 0.8288 (tt0) cc_final: 0.7869 (tt0) REVERT: H 48 TYR cc_start: 0.7202 (p90) cc_final: 0.6681 (p90) REVERT: H 55 SER cc_start: 0.8415 (t) cc_final: 0.8141 (p) REVERT: H 61 PHE cc_start: 0.8980 (m-10) cc_final: 0.8734 (m-10) REVERT: H 65 ARG cc_start: 0.8235 (ttt180) cc_final: 0.7853 (ptm-80) REVERT: H 82 VAL cc_start: 0.9180 (t) cc_final: 0.8890 (m) REVERT: H 85 TYR cc_start: 0.8248 (m-80) cc_final: 0.7905 (m-10) REVERT: H 89 GLN cc_start: 0.7263 (mt0) cc_final: 0.6804 (mt0) REVERT: H 101 THR cc_start: 0.7911 (m) cc_final: 0.7398 (p) REVERT: I 3 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7555 (tp40) REVERT: I 27 TYR cc_start: 0.5345 (t80) cc_final: 0.4264 (t80) REVERT: I 28 THR cc_start: 0.7971 (m) cc_final: 0.6832 (p) REVERT: I 30 THR cc_start: 0.8836 (p) cc_final: 0.8349 (t) REVERT: I 36 TRP cc_start: 0.8362 (m100) cc_final: 0.7760 (m-10) REVERT: I 38 LYS cc_start: 0.8671 (tttp) cc_final: 0.8180 (tttm) REVERT: I 57 SER cc_start: 0.9399 (m) cc_final: 0.8908 (p) REVERT: I 76 SER cc_start: 0.8626 (m) cc_final: 0.8035 (t) REVERT: I 109 GLN cc_start: 0.8125 (pm20) cc_final: 0.7882 (pm20) REVERT: I 113 VAL cc_start: 0.8557 (t) cc_final: 0.8075 (m) REVERT: J 44 PRO cc_start: 0.7148 (Cg_endo) cc_final: 0.6874 (Cg_exo) REVERT: J 50 SER cc_start: 0.7623 (m) cc_final: 0.7015 (t) REVERT: J 87 PHE cc_start: 0.8389 (m-10) cc_final: 0.8177 (m-10) REVERT: J 92 ASN cc_start: 0.8700 (t0) cc_final: 0.8174 (t0) REVERT: J 103 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7971 (mtpt) outliers start: 56 outliers final: 44 residues processed: 364 average time/residue: 0.2189 time to fit residues: 106.8513 Evaluate side-chains 394 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 347 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 34 TRP Chi-restraints excluded: chain C residue 57 VAL 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 40 ARG Chi-restraints excluded: chain E residue 61 ASN 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 26 SER 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.0370 chunk 17 optimal weight: 0.0980 chunk 60 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 chunk 3 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 81 optimal weight: 0.8980 overall best weight: 0.1556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN A 300 HIS E 61 ASN G 57 ASN ** H 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 = 0.3691 r_free = 0.3691 target = 0.129472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116551 restraints weight = 14178.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120667 restraints weight = 6553.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123312 restraints weight = 3612.040| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8834 Z= 0.104 Angle : 0.578 6.437 11958 Z= 0.302 Chirality : 0.042 0.138 1270 Planarity : 0.004 0.041 1528 Dihedral : 4.516 24.315 1206 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.58 % Allowed : 19.51 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.26), residues: 1090 helix: -1.64 (0.65), residues: 62 sheet: -0.72 (0.26), residues: 436 loop : -1.37 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 50 HIS 0.002 0.000 HIS G 61 PHE 0.027 0.002 PHE I 29 TYR 0.021 0.002 TYR J 94 ARG 0.008 0.001 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 262) hydrogen bonds : angle 5.77653 ( 666) SS BOND : bond 0.00268 ( 4) SS BOND : angle 1.07443 ( 8) covalent geometry : bond 0.00223 ( 8830) covalent geometry : angle 0.57733 (11950) *********************** 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 384 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 341 time to evaluate : 0.933 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: 0.7485 (m110) cc_final: 0.7114 (m110) REVERT: A 314 PHE cc_start: 0.8173 (t80) cc_final: 0.7887 (t80) REVERT: A 361 LYS cc_start: 0.9134 (mttt) cc_final: 0.8698 (mttm) REVERT: B 27 PHE cc_start: 0.8707 (p90) cc_final: 0.7817 (p90) REVERT: B 28 THR cc_start: 0.8266 (m) cc_final: 0.7935 (m) REVERT: B 33 TYR cc_start: 0.8042 (m-10) cc_final: 0.7798 (m-10) REVERT: B 37 VAL cc_start: 0.7955 (t) cc_final: 0.7513 (m) REVERT: B 54 GLU cc_start: 0.8222 (tt0) cc_final: 0.7667 (tt0) REVERT: B 58 TYR cc_start: 0.8634 (m-80) cc_final: 0.8315 (m-10) REVERT: B 71 THR cc_start: 0.8203 (m) cc_final: 0.7711 (p) REVERT: B 79 SER cc_start: 0.8529 (m) cc_final: 0.7931 (p) REVERT: B 100 PHE cc_start: 0.8381 (p90) cc_final: 0.8000 (p90) REVERT: B 101 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6119 (p0) REVERT: B 104 TYR cc_start: 0.7842 (m-10) cc_final: 0.7549 (m-10) REVERT: C 14 SER cc_start: 0.9029 (m) cc_final: 0.8743 (t) REVERT: C 18 LYS cc_start: 0.8736 (tttt) cc_final: 0.8449 (tttt) REVERT: C 61 PHE cc_start: 0.8734 (m-10) cc_final: 0.8419 (m-80) REVERT: C 74 ILE cc_start: 0.8353 (mt) cc_final: 0.8064 (mt) REVERT: C 101 THR cc_start: 0.7594 (m) cc_final: 0.7101 (p) REVERT: D 343 ASP cc_start: 0.8453 (t70) cc_final: 0.8116 (t70) REVERT: D 361 LYS cc_start: 0.9183 (mttt) cc_final: 0.8651 (mttm) REVERT: D 362 THR cc_start: 0.8566 (p) cc_final: 0.8312 (t) REVERT: E 10 GLU cc_start: 0.7181 (tt0) cc_final: 0.6919 (tt0) REVERT: E 19 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7943 (tmtt) REVERT: E 22 CYS cc_start: 0.7527 (t) cc_final: 0.6344 (t) REVERT: E 36 TRP cc_start: 0.8340 (m100) cc_final: 0.8001 (m-10) REVERT: E 40 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7535 (mtt90) REVERT: E 46 GLU cc_start: 0.7334 (pt0) cc_final: 0.7046 (pt0) REVERT: E 104 MET cc_start: 0.7158 (mtt) cc_final: 0.6904 (mtt) REVERT: E 106 TYR cc_start: 0.8088 (m-80) cc_final: 0.7766 (m-80) REVERT: E 107 TRP cc_start: 0.8105 (m100) cc_final: 0.7741 (m-10) REVERT: E 112 SER cc_start: 0.8350 (t) cc_final: 0.7902 (p) REVERT: F 4 MET cc_start: 0.7861 (mmm) cc_final: 0.7589 (mmm) REVERT: F 20 SER cc_start: 0.8736 (t) cc_final: 0.8268 (p) REVERT: F 32 ASN cc_start: 0.6553 (t0) cc_final: 0.6166 (t0) REVERT: F 50 SER cc_start: 0.7669 (m) cc_final: 0.7307 (t) REVERT: F 79 GLN cc_start: 0.7424 (pm20) cc_final: 0.7007 (pm20) REVERT: F 90 GLN cc_start: 0.6991 (mt0) cc_final: 0.6442 (mt0) REVERT: F 93 SER cc_start: 0.7787 (t) cc_final: 0.7481 (p) REVERT: G 22 CYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7522 (t) REVERT: G 29 PHE cc_start: 0.8801 (t80) cc_final: 0.8585 (t80) REVERT: G 34 MET cc_start: 0.6913 (mtp) cc_final: 0.6521 (mtp) REVERT: G 54 GLU cc_start: 0.8241 (tt0) cc_final: 0.7916 (tt0) REVERT: G 71 THR cc_start: 0.8053 (m) cc_final: 0.7322 (p) REVERT: G 79 SER cc_start: 0.8692 (m) cc_final: 0.8021 (p) REVERT: G 80 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7724 (mtp85) REVERT: G 108 MET cc_start: 0.7191 (mpp) cc_final: 0.6447 (mpp) REVERT: G 109 ASP cc_start: 0.7003 (t0) cc_final: 0.6773 (t0) REVERT: H 10 ILE cc_start: 0.8746 (pt) cc_final: 0.8338 (mm) REVERT: H 29 VAL cc_start: 0.8554 (t) cc_final: 0.8131 (m) REVERT: H 34 TRP cc_start: 0.8154 (m100) cc_final: 0.7786 (m100) REVERT: H 37 GLN cc_start: 0.8262 (tt0) cc_final: 0.7894 (tt0) REVERT: H 55 SER cc_start: 0.8376 (t) cc_final: 0.8149 (p) REVERT: H 61 PHE cc_start: 0.8972 (m-10) cc_final: 0.8654 (m-10) REVERT: H 65 ARG cc_start: 0.8150 (ttt180) cc_final: 0.7829 (ptm-80) REVERT: H 82 VAL cc_start: 0.9154 (t) cc_final: 0.8840 (m) REVERT: H 85 TYR cc_start: 0.8173 (m-80) cc_final: 0.7852 (m-10) REVERT: H 89 GLN cc_start: 0.7239 (mt0) cc_final: 0.6770 (mt0) REVERT: H 101 THR cc_start: 0.7802 (m) cc_final: 0.7298 (p) REVERT: I 3 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7493 (tp40) REVERT: I 27 TYR cc_start: 0.5449 (t80) cc_final: 0.4520 (t80) REVERT: I 28 THR cc_start: 0.7941 (m) cc_final: 0.6820 (p) REVERT: I 30 THR cc_start: 0.8775 (p) cc_final: 0.8254 (t) REVERT: I 36 TRP cc_start: 0.8308 (m100) cc_final: 0.7900 (m-10) REVERT: I 38 LYS cc_start: 0.8570 (tttp) cc_final: 0.8155 (tttm) REVERT: I 57 SER cc_start: 0.9386 (m) cc_final: 0.8927 (p) REVERT: I 104 MET cc_start: 0.7226 (mtt) cc_final: 0.6936 (mmt) REVERT: I 109 GLN cc_start: 0.8270 (pm20) cc_final: 0.8052 (pm20) REVERT: I 113 VAL cc_start: 0.8528 (t) cc_final: 0.8046 (m) REVERT: J 44 PRO cc_start: 0.6758 (Cg_endo) cc_final: 0.6521 (Cg_exo) REVERT: J 50 SER cc_start: 0.7312 (m) cc_final: 0.6805 (t) REVERT: J 79 GLN cc_start: 0.7513 (pp30) cc_final: 0.7155 (pm20) REVERT: J 92 ASN cc_start: 0.8583 (t0) cc_final: 0.8174 (t0) REVERT: J 103 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7957 (mtpt) outliers start: 43 outliers final: 29 residues processed: 353 average time/residue: 0.2249 time to fit residues: 105.8965 Evaluate side-chains 372 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 339 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 347 LYS 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 101 ASP 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 347 LYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 VAL 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 F residue 2 ILE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 22 CYS 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 32 ASN Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 F 89 GLN G 57 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.126973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113866 restraints weight = 14405.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117997 restraints weight = 6649.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120616 restraints weight = 3677.903| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8834 Z= 0.174 Angle : 0.612 6.286 11958 Z= 0.325 Chirality : 0.043 0.178 1270 Planarity : 0.005 0.057 1528 Dihedral : 4.696 24.082 1206 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 4.90 % Allowed : 20.58 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.26), residues: 1090 helix: -1.49 (0.67), residues: 62 sheet: -0.56 (0.26), residues: 428 loop : -1.42 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 50 HIS 0.005 0.001 HIS C 33 PHE 0.029 0.002 PHE I 29 TYR 0.022 0.002 TYR J 94 ARG 0.007 0.001 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 262) hydrogen bonds : angle 5.85205 ( 666) SS BOND : bond 0.00272 ( 4) SS BOND : angle 1.26579 ( 8) covalent geometry : bond 0.00375 ( 8830) covalent geometry : angle 0.61146 (11950) *********************** 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 387 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 341 time to evaluate : 1.070 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: 0.7657 (m-40) cc_final: 0.7270 (m-40) REVERT: A 314 PHE cc_start: 0.8231 (t80) cc_final: 0.7941 (t80) REVERT: A 361 LYS cc_start: 0.9057 (mttt) cc_final: 0.8509 (mttm) REVERT: B 27 PHE cc_start: 0.8685 (p90) cc_final: 0.7827 (p90) REVERT: B 28 THR cc_start: 0.8238 (m) cc_final: 0.7899 (m) REVERT: B 29 PHE cc_start: 0.8788 (t80) cc_final: 0.8547 (t80) REVERT: B 33 TYR cc_start: 0.8075 (m-10) cc_final: 0.7798 (m-10) REVERT: B 54 GLU cc_start: 0.8246 (tt0) cc_final: 0.7661 (tt0) REVERT: B 58 TYR cc_start: 0.8745 (m-80) cc_final: 0.8349 (m-10) REVERT: B 71 THR cc_start: 0.8195 (m) cc_final: 0.7712 (p) REVERT: B 79 SER cc_start: 0.8550 (m) cc_final: 0.7958 (p) REVERT: B 101 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6271 (p0) REVERT: B 104 TYR cc_start: 0.7832 (m-10) cc_final: 0.7525 (m-10) REVERT: C 5 THR cc_start: 0.8633 (t) cc_final: 0.8193 (p) REVERT: C 14 SER cc_start: 0.9062 (m) cc_final: 0.8770 (t) REVERT: C 18 LYS cc_start: 0.8735 (tttt) cc_final: 0.8460 (tttt) REVERT: C 61 PHE cc_start: 0.8755 (m-10) cc_final: 0.8441 (m-80) REVERT: C 74 ILE cc_start: 0.8485 (mt) cc_final: 0.8260 (mt) REVERT: C 101 THR cc_start: 0.7610 (m) cc_final: 0.7041 (p) REVERT: D 343 ASP cc_start: 0.8516 (t70) cc_final: 0.8205 (t70) REVERT: D 361 LYS cc_start: 0.9181 (mttt) cc_final: 0.8725 (mttm) REVERT: D 362 THR cc_start: 0.8562 (p) cc_final: 0.8295 (t) REVERT: E 10 GLU cc_start: 0.7257 (tt0) cc_final: 0.6950 (tt0) REVERT: E 19 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7942 (tmtt) REVERT: E 36 TRP cc_start: 0.8310 (m100) cc_final: 0.8000 (m-10) REVERT: E 38 LYS cc_start: 0.8487 (ttpt) cc_final: 0.7853 (tttt) REVERT: E 46 GLU cc_start: 0.7314 (pt0) cc_final: 0.6991 (pt0) REVERT: E 106 TYR cc_start: 0.8020 (m-80) cc_final: 0.7696 (m-80) REVERT: E 107 TRP cc_start: 0.8089 (m100) cc_final: 0.7711 (m-10) REVERT: E 112 SER cc_start: 0.8413 (t) cc_final: 0.7917 (p) REVERT: F 4 MET cc_start: 0.7792 (mmm) cc_final: 0.7589 (mmm) REVERT: F 20 SER cc_start: 0.8756 (t) cc_final: 0.8252 (p) REVERT: F 32 ASN cc_start: 0.6686 (t0) cc_final: 0.6208 (t0) REVERT: F 50 SER cc_start: 0.7721 (m) cc_final: 0.7313 (t) REVERT: F 87 PHE cc_start: 0.8480 (m-10) cc_final: 0.8188 (m-10) REVERT: F 93 SER cc_start: 0.7870 (t) cc_final: 0.7509 (p) REVERT: G 22 CYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7411 (t) REVERT: G 27 PHE cc_start: 0.8429 (p90) cc_final: 0.7802 (p90) REVERT: G 29 PHE cc_start: 0.8853 (t80) cc_final: 0.8648 (t80) REVERT: G 34 MET cc_start: 0.7030 (mtp) cc_final: 0.6643 (mtp) REVERT: G 54 GLU cc_start: 0.8247 (tt0) cc_final: 0.7831 (tt0) REVERT: G 79 SER cc_start: 0.8706 (m) cc_final: 0.7991 (p) REVERT: G 80 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.7821 (mtp85) REVERT: G 108 MET cc_start: 0.7150 (mpp) cc_final: 0.6454 (mpp) REVERT: G 109 ASP cc_start: 0.7077 (t0) cc_final: 0.6869 (t70) REVERT: H 10 ILE cc_start: 0.8814 (pt) cc_final: 0.8399 (mm) REVERT: H 29 VAL cc_start: 0.8544 (t) cc_final: 0.8159 (m) REVERT: H 34 TRP cc_start: 0.8235 (m100) cc_final: 0.7992 (m100) REVERT: H 37 GLN cc_start: 0.8242 (tt0) cc_final: 0.7858 (tt0) REVERT: H 48 TYR cc_start: 0.7224 (p90) cc_final: 0.6702 (p90) REVERT: H 55 SER cc_start: 0.8386 (t) cc_final: 0.8121 (p) REVERT: H 61 PHE cc_start: 0.8911 (m-10) cc_final: 0.8590 (m-10) REVERT: H 65 ARG cc_start: 0.8206 (ttt180) cc_final: 0.7822 (ptm-80) REVERT: H 82 VAL cc_start: 0.9175 (t) cc_final: 0.8906 (m) REVERT: H 85 TYR cc_start: 0.8209 (m-80) cc_final: 0.7866 (m-10) REVERT: H 89 GLN cc_start: 0.7291 (mt0) cc_final: 0.6825 (mt0) REVERT: H 101 THR cc_start: 0.7884 (m) cc_final: 0.7427 (p) REVERT: I 3 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7504 (tp40) REVERT: I 27 TYR cc_start: 0.5541 (t80) cc_final: 0.4457 (t80) REVERT: I 28 THR cc_start: 0.7948 (m) cc_final: 0.6806 (p) REVERT: I 30 THR cc_start: 0.8820 (p) cc_final: 0.8270 (t) REVERT: I 36 TRP cc_start: 0.8400 (m100) cc_final: 0.7840 (m-10) REVERT: I 38 LYS cc_start: 0.8668 (tttp) cc_final: 0.8344 (tttm) REVERT: I 46 GLU cc_start: 0.7610 (pt0) cc_final: 0.7176 (pt0) REVERT: I 57 SER cc_start: 0.9369 (m) cc_final: 0.8904 (p) REVERT: I 104 MET cc_start: 0.7292 (mtt) cc_final: 0.7077 (mmt) REVERT: I 113 VAL cc_start: 0.8561 (t) cc_final: 0.8076 (m) REVERT: J 50 SER cc_start: 0.7522 (m) cc_final: 0.7004 (t) REVERT: J 87 PHE cc_start: 0.8382 (m-10) cc_final: 0.7851 (m-10) REVERT: J 92 ASN cc_start: 0.8712 (t0) cc_final: 0.8178 (t0) REVERT: J 103 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7985 (mtpt) outliers start: 46 outliers final: 38 residues processed: 355 average time/residue: 0.2143 time to fit residues: 101.9124 Evaluate side-chains 381 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 339 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 12 VAL Chi-restraints excluded: chain B residue 13 GLN 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 22 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 18 VAL 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 26 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 93 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN C 36 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN H 6 GLN ** 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 = 0.3667 r_free = 0.3667 target = 0.127725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114576 restraints weight = 14600.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118634 restraints weight = 6745.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121341 restraints weight = 3761.737| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3995 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= 0.155 Angle : 0.629 7.680 11958 Z= 0.331 Chirality : 0.043 0.174 1270 Planarity : 0.004 0.040 1528 Dihedral : 4.711 22.523 1206 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 5.44 % Allowed : 21.75 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.26), residues: 1090 helix: -1.45 (0.67), residues: 62 sheet: -0.50 (0.26), residues: 428 loop : -1.42 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 50 HIS 0.004 0.001 HIS G 61 PHE 0.032 0.002 PHE I 29 TYR 0.021 0.002 TYR C 86 ARG 0.006 0.001 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 262) hydrogen bonds : angle 5.75628 ( 666) SS BOND : bond 0.00214 ( 4) SS BOND : angle 1.17606 ( 8) covalent geometry : bond 0.00339 ( 8830) covalent geometry : angle 0.62826 (11950) *********************** 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 389 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 338 time to evaluate : 0.906 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: 0.7647 (m110) cc_final: 0.7424 (m110) REVERT: A 314 PHE cc_start: 0.8230 (t80) cc_final: 0.7938 (t80) REVERT: A 361 LYS cc_start: 0.9083 (mttt) cc_final: 0.8506 (mttm) REVERT: B 27 PHE cc_start: 0.8674 (p90) cc_final: 0.7842 (p90) REVERT: B 28 THR cc_start: 0.8245 (m) cc_final: 0.7913 (m) REVERT: B 29 PHE cc_start: 0.8784 (t80) cc_final: 0.8576 (t80) REVERT: B 33 TYR cc_start: 0.8080 (m-10) cc_final: 0.7822 (m-10) REVERT: B 54 GLU cc_start: 0.8194 (tt0) cc_final: 0.7588 (tt0) REVERT: B 58 TYR cc_start: 0.8756 (m-10) cc_final: 0.8344 (m-10) REVERT: B 71 THR cc_start: 0.8177 (m) cc_final: 0.7713 (p) REVERT: B 79 SER cc_start: 0.8571 (m) cc_final: 0.7967 (p) REVERT: B 101 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6256 (p0) REVERT: B 104 TYR cc_start: 0.7820 (m-10) cc_final: 0.7497 (m-10) REVERT: C 5 THR cc_start: 0.8597 (t) cc_final: 0.8199 (p) REVERT: C 14 SER cc_start: 0.9065 (m) cc_final: 0.8774 (t) REVERT: C 18 LYS cc_start: 0.8734 (tttt) cc_final: 0.8449 (tttt) REVERT: C 32 MET cc_start: 0.6492 (ttm) cc_final: 0.6268 (ttp) REVERT: C 61 PHE cc_start: 0.8729 (m-10) cc_final: 0.8407 (m-80) REVERT: C 74 ILE cc_start: 0.8373 (mt) cc_final: 0.8157 (mt) REVERT: C 101 THR cc_start: 0.7530 (m) cc_final: 0.7117 (p) REVERT: D 343 ASP cc_start: 0.8464 (t70) cc_final: 0.8180 (t70) REVERT: D 361 LYS cc_start: 0.9214 (mttt) cc_final: 0.8792 (mttm) REVERT: D 362 THR cc_start: 0.8560 (p) cc_final: 0.8301 (t) REVERT: E 10 GLU cc_start: 0.7244 (tt0) cc_final: 0.6926 (tt0) REVERT: E 19 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7975 (tmtt) REVERT: E 36 TRP cc_start: 0.8291 (m100) cc_final: 0.7990 (m-10) REVERT: E 38 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8089 (tttt) REVERT: E 46 GLU cc_start: 0.7258 (pt0) cc_final: 0.6952 (pt0) REVERT: E 106 TYR cc_start: 0.8028 (m-80) cc_final: 0.7748 (m-80) REVERT: E 107 TRP cc_start: 0.8068 (m100) cc_final: 0.7692 (m-10) REVERT: E 112 SER cc_start: 0.8377 (t) cc_final: 0.7871 (p) REVERT: F 4 MET cc_start: 0.7738 (mmm) cc_final: 0.7514 (mmm) REVERT: F 20 SER cc_start: 0.8740 (t) cc_final: 0.8206 (p) REVERT: F 32 ASN cc_start: 0.6671 (t0) cc_final: 0.6228 (t0) REVERT: F 50 SER cc_start: 0.7685 (m) cc_final: 0.7289 (t) REVERT: F 87 PHE cc_start: 0.8512 (m-10) cc_final: 0.8209 (m-10) REVERT: F 93 SER cc_start: 0.7851 (t) cc_final: 0.7494 (p) REVERT: G 22 CYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7352 (t) REVERT: G 27 PHE cc_start: 0.8364 (p90) cc_final: 0.7713 (p90) REVERT: G 29 PHE cc_start: 0.8818 (t80) cc_final: 0.8597 (t80) REVERT: G 34 MET cc_start: 0.7000 (mtp) cc_final: 0.6578 (mtp) REVERT: G 54 GLU cc_start: 0.8279 (tt0) cc_final: 0.7885 (tt0) REVERT: G 79 SER cc_start: 0.8702 (m) cc_final: 0.7956 (p) REVERT: G 108 MET cc_start: 0.7178 (mpp) cc_final: 0.6451 (mpp) REVERT: G 109 ASP cc_start: 0.7037 (t0) cc_final: 0.6828 (t70) REVERT: H 10 ILE cc_start: 0.8796 (pt) cc_final: 0.8379 (mm) REVERT: H 29 VAL cc_start: 0.8568 (t) cc_final: 0.8207 (m) REVERT: H 34 TRP cc_start: 0.8180 (m100) cc_final: 0.7951 (m100) REVERT: H 37 GLN cc_start: 0.8230 (tt0) cc_final: 0.7850 (tt0) REVERT: H 48 TYR cc_start: 0.7207 (p90) cc_final: 0.6686 (p90) REVERT: H 55 SER cc_start: 0.8366 (t) cc_final: 0.8112 (p) REVERT: H 61 PHE cc_start: 0.8950 (m-10) cc_final: 0.8620 (m-10) REVERT: H 65 ARG cc_start: 0.8188 (ttt180) cc_final: 0.7809 (ptm-80) REVERT: H 82 VAL cc_start: 0.9173 (t) cc_final: 0.8922 (m) REVERT: H 85 TYR cc_start: 0.8181 (m-80) cc_final: 0.7834 (m-10) REVERT: H 89 GLN cc_start: 0.7262 (mt0) cc_final: 0.6861 (mt0) REVERT: H 101 THR cc_start: 0.7871 (m) cc_final: 0.7428 (p) REVERT: I 3 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7513 (tp40) REVERT: I 27 TYR cc_start: 0.5547 (t80) cc_final: 0.4505 (t80) REVERT: I 28 THR cc_start: 0.7940 (m) cc_final: 0.6816 (p) REVERT: I 30 THR cc_start: 0.8722 (p) cc_final: 0.8212 (t) REVERT: I 36 TRP cc_start: 0.8349 (m100) cc_final: 0.7919 (m-10) REVERT: I 38 LYS cc_start: 0.8638 (tttp) cc_final: 0.8331 (tttm) REVERT: I 46 GLU cc_start: 0.7607 (pt0) cc_final: 0.6993 (pt0) REVERT: I 57 SER cc_start: 0.9369 (m) cc_final: 0.8923 (p) REVERT: I 104 MET cc_start: 0.7299 (mtt) cc_final: 0.7069 (mmt) REVERT: I 113 VAL cc_start: 0.8577 (t) cc_final: 0.8116 (m) REVERT: J 50 SER cc_start: 0.7478 (m) cc_final: 0.6979 (t) REVERT: J 61 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8070 (ptm160) REVERT: J 92 ASN cc_start: 0.8705 (t0) cc_final: 0.8175 (t0) REVERT: J 103 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7945 (mtpt) outliers start: 51 outliers final: 38 residues processed: 354 average time/residue: 0.2112 time to fit residues: 100.7833 Evaluate side-chains 383 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 340 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 347 LYS 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 22 THR Chi-restraints excluded: chain C residue 34 TRP Chi-restraints excluded: chain C residue 36 GLN 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 18 VAL 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 26 SER Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 6 GLN 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 82 GLN 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 61 ARG Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 77 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 0.0040 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN C 36 GLN F 6 GLN ** F 89 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114168 restraints weight = 14262.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118318 restraints weight = 6635.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120950 restraints weight = 3676.995| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8834 Z= 0.148 Angle : 0.620 6.592 11958 Z= 0.328 Chirality : 0.043 0.163 1270 Planarity : 0.004 0.036 1528 Dihedral : 4.673 21.228 1206 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 5.01 % Allowed : 22.39 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.26), residues: 1090 helix: -1.35 (0.68), residues: 62 sheet: -0.52 (0.26), residues: 428 loop : -1.38 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 50 HIS 0.004 0.001 HIS G 61 PHE 0.038 0.002 PHE I 29 TYR 0.021 0.002 TYR E 52 ARG 0.007 0.001 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 262) hydrogen bonds : angle 5.69536 ( 666) SS BOND : bond 0.00210 ( 4) SS BOND : angle 0.98874 ( 8) covalent geometry : bond 0.00327 ( 8830) covalent geometry : angle 0.61958 (11950) *********************** 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 383 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 336 time to evaluate : 0.902 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: A 269 ASN cc_start: 0.7616 (m-40) cc_final: 0.7294 (m-40) REVERT: A 314 PHE cc_start: 0.8222 (t80) cc_final: 0.7911 (t80) REVERT: A 361 LYS cc_start: 0.9067 (mttt) cc_final: 0.8493 (mttm) REVERT: B 27 PHE cc_start: 0.8658 (p90) cc_final: 0.7860 (p90) REVERT: B 28 THR cc_start: 0.8220 (m) cc_final: 0.7872 (m) REVERT: B 33 TYR cc_start: 0.8062 (m-10) cc_final: 0.7816 (m-10) REVERT: B 54 GLU cc_start: 0.8180 (tt0) cc_final: 0.7595 (tt0) REVERT: B 58 TYR cc_start: 0.8750 (m-10) cc_final: 0.8325 (m-10) REVERT: B 71 THR cc_start: 0.8181 (m) cc_final: 0.7715 (p) REVERT: B 79 SER cc_start: 0.8563 (m) cc_final: 0.7963 (p) REVERT: B 101 ASP cc_start: 0.6773 (OUTLIER) cc_final: 0.6251 (p0) REVERT: B 104 TYR cc_start: 0.7814 (m-10) cc_final: 0.7498 (m-10) REVERT: C 5 THR cc_start: 0.8582 (t) cc_final: 0.8209 (p) REVERT: C 14 SER cc_start: 0.9052 (m) cc_final: 0.8771 (t) REVERT: C 18 LYS cc_start: 0.8721 (tttt) cc_final: 0.8433 (tttt) REVERT: C 32 MET cc_start: 0.6523 (ttm) cc_final: 0.6287 (ttp) REVERT: C 61 PHE cc_start: 0.8737 (m-10) cc_final: 0.8409 (m-80) REVERT: C 74 ILE cc_start: 0.8361 (mt) cc_final: 0.8124 (mt) REVERT: C 101 THR cc_start: 0.7548 (m) cc_final: 0.7089 (p) REVERT: D 343 ASP cc_start: 0.8446 (t70) cc_final: 0.8196 (t70) REVERT: D 361 LYS cc_start: 0.9214 (mttt) cc_final: 0.8806 (mttm) REVERT: D 362 THR cc_start: 0.8561 (p) cc_final: 0.8299 (t) REVERT: E 10 GLU cc_start: 0.7236 (tt0) cc_final: 0.6916 (tt0) REVERT: E 19 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7972 (tmtt) REVERT: E 38 LYS cc_start: 0.8482 (ttpt) cc_final: 0.8115 (tttt) REVERT: E 46 GLU cc_start: 0.7273 (pt0) cc_final: 0.6931 (pt0) REVERT: E 82 GLN cc_start: 0.7867 (mm110) cc_final: 0.7592 (mm110) REVERT: E 106 TYR cc_start: 0.7995 (m-80) cc_final: 0.7772 (m-80) REVERT: E 107 TRP cc_start: 0.8081 (m100) cc_final: 0.7707 (m-10) REVERT: E 112 SER cc_start: 0.8356 (t) cc_final: 0.7857 (p) REVERT: F 20 SER cc_start: 0.8714 (t) cc_final: 0.8166 (p) REVERT: F 32 ASN cc_start: 0.6685 (t0) cc_final: 0.6203 (t0) REVERT: F 50 SER cc_start: 0.7606 (m) cc_final: 0.7196 (t) REVERT: F 87 PHE cc_start: 0.8497 (m-10) cc_final: 0.8205 (m-10) REVERT: F 93 SER cc_start: 0.7812 (t) cc_final: 0.7476 (p) REVERT: G 22 CYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7376 (t) REVERT: G 27 PHE cc_start: 0.8361 (p90) cc_final: 0.7728 (p90) REVERT: G 29 PHE cc_start: 0.8821 (t80) cc_final: 0.8583 (t80) REVERT: G 34 MET cc_start: 0.6993 (mtp) cc_final: 0.6589 (mtp) REVERT: G 46 GLU cc_start: 0.7576 (tt0) cc_final: 0.6954 (tt0) REVERT: G 54 GLU cc_start: 0.8200 (tt0) cc_final: 0.7826 (tt0) REVERT: G 79 SER cc_start: 0.8684 (m) cc_final: 0.7957 (p) REVERT: G 108 MET cc_start: 0.7168 (mpp) cc_final: 0.6442 (mpp) REVERT: H 10 ILE cc_start: 0.8811 (pt) cc_final: 0.8401 (mm) REVERT: H 29 VAL cc_start: 0.8538 (t) cc_final: 0.8195 (m) REVERT: H 34 TRP cc_start: 0.8047 (m100) cc_final: 0.7826 (m100) REVERT: H 37 GLN cc_start: 0.8220 (tt0) cc_final: 0.7821 (tt0) REVERT: H 48 TYR cc_start: 0.7231 (p90) cc_final: 0.6660 (p90) REVERT: H 55 SER cc_start: 0.8346 (t) cc_final: 0.8082 (p) REVERT: H 61 PHE cc_start: 0.8946 (m-10) cc_final: 0.8605 (m-10) REVERT: H 65 ARG cc_start: 0.8192 (ttt180) cc_final: 0.7815 (ptm-80) REVERT: H 82 VAL cc_start: 0.9182 (t) cc_final: 0.8928 (m) REVERT: H 85 TYR cc_start: 0.8164 (m-80) cc_final: 0.7802 (m-10) REVERT: H 89 GLN cc_start: 0.7271 (mt0) cc_final: 0.6869 (mt0) REVERT: H 101 THR cc_start: 0.7828 (m) cc_final: 0.7306 (p) REVERT: I 27 TYR cc_start: 0.5595 (t80) cc_final: 0.4545 (t80) REVERT: I 28 THR cc_start: 0.7948 (m) cc_final: 0.6822 (p) REVERT: I 30 THR cc_start: 0.8741 (p) cc_final: 0.8215 (t) REVERT: I 36 TRP cc_start: 0.8394 (m100) cc_final: 0.7927 (m-10) REVERT: I 38 LYS cc_start: 0.8612 (tttp) cc_final: 0.8301 (tttm) REVERT: I 46 GLU cc_start: 0.7196 (pt0) cc_final: 0.6822 (pt0) REVERT: I 57 SER cc_start: 0.9394 (m) cc_final: 0.8928 (p) REVERT: I 104 MET cc_start: 0.7222 (mtt) cc_final: 0.6937 (mmt) REVERT: I 113 VAL cc_start: 0.8552 (t) cc_final: 0.8097 (m) REVERT: J 44 PRO cc_start: 0.7179 (Cg_endo) cc_final: 0.6895 (Cg_exo) REVERT: J 50 SER cc_start: 0.7492 (m) cc_final: 0.7008 (t) REVERT: J 61 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7960 (ptm160) REVERT: J 92 ASN cc_start: 0.8700 (t0) cc_final: 0.8165 (t0) REVERT: J 103 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7783 (mtpt) outliers start: 47 outliers final: 37 residues processed: 352 average time/residue: 0.2074 time to fit residues: 98.2350 Evaluate side-chains 376 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 335 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 347 LYS 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 34 TRP Chi-restraints excluded: chain C residue 36 GLN 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 18 VAL Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 63 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 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 93 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 82 GLN 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 61 ARG Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 74 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 60 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 C 36 GLN D 349 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN H 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114121 restraints weight = 14451.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118217 restraints weight = 6681.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120879 restraints weight = 3701.739| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4170 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= 0.174 Angle : 0.644 6.663 11958 Z= 0.341 Chirality : 0.044 0.173 1270 Planarity : 0.004 0.035 1528 Dihedral : 4.751 23.355 1206 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 4.69 % Allowed : 23.13 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.26), residues: 1090 helix: -1.34 (0.68), residues: 62 sheet: -0.55 (0.26), residues: 426 loop : -1.36 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP E 36 HIS 0.004 0.001 HIS G 61 PHE 0.039 0.002 PHE I 29 TYR 0.021 0.002 TYR E 52 ARG 0.006 0.001 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 262) hydrogen bonds : angle 5.73128 ( 666) SS BOND : bond 0.00272 ( 4) SS BOND : angle 0.83927 ( 8) covalent geometry : bond 0.00382 ( 8830) covalent geometry : angle 0.64352 (11950) ********************** 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 386 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 342 time to evaluate : 1.051 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: A 261 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8270 (ttmm) REVERT: A 269 ASN cc_start: 0.7651 (m110) cc_final: 0.7439 (m110) REVERT: A 314 PHE cc_start: 0.8251 (t80) cc_final: 0.7928 (t80) REVERT: A 361 LYS cc_start: 0.9072 (mttt) cc_final: 0.8458 (mttm) REVERT: B 27 PHE cc_start: 0.8671 (p90) cc_final: 0.7885 (p90) REVERT: B 28 THR cc_start: 0.8220 (m) cc_final: 0.7914 (m) REVERT: B 33 TYR cc_start: 0.8070 (m-10) cc_final: 0.7816 (m-10) REVERT: B 54 GLU cc_start: 0.8195 (tt0) cc_final: 0.7582 (tt0) REVERT: B 58 TYR cc_start: 0.8754 (m-10) cc_final: 0.8292 (m-10) REVERT: B 71 THR cc_start: 0.8186 (m) cc_final: 0.7707 (p) REVERT: B 79 SER cc_start: 0.8514 (m) cc_final: 0.7887 (p) REVERT: B 101 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.6299 (p0) REVERT: B 104 TYR cc_start: 0.7826 (m-10) cc_final: 0.7506 (m-10) REVERT: C 5 THR cc_start: 0.8618 (t) cc_final: 0.8261 (p) REVERT: C 14 SER cc_start: 0.9049 (m) cc_final: 0.8769 (t) REVERT: C 18 LYS cc_start: 0.8729 (tttt) cc_final: 0.8441 (tttt) REVERT: C 32 MET cc_start: 0.6520 (ttm) cc_final: 0.6309 (ttp) REVERT: C 51 SER cc_start: 0.8433 (p) cc_final: 0.8173 (m) REVERT: C 61 PHE cc_start: 0.8750 (m-10) cc_final: 0.8435 (m-80) REVERT: C 74 ILE cc_start: 0.8456 (mt) cc_final: 0.8244 (mt) REVERT: C 101 THR cc_start: 0.7506 (m) cc_final: 0.7110 (p) REVERT: D 343 ASP cc_start: 0.8486 (t70) cc_final: 0.8231 (t70) REVERT: D 361 LYS cc_start: 0.9213 (mttt) cc_final: 0.8874 (mttm) REVERT: D 362 THR cc_start: 0.8569 (p) cc_final: 0.8330 (t) REVERT: E 10 GLU cc_start: 0.7268 (tt0) cc_final: 0.6936 (tt0) REVERT: E 19 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8022 (tmtt) REVERT: E 38 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8043 (ttpp) REVERT: E 46 GLU cc_start: 0.7282 (pt0) cc_final: 0.6912 (pt0) REVERT: E 81 MET cc_start: 0.6759 (ttp) cc_final: 0.6332 (ttp) REVERT: E 107 TRP cc_start: 0.8084 (m100) cc_final: 0.7665 (m-10) REVERT: E 112 SER cc_start: 0.8384 (t) cc_final: 0.7856 (p) REVERT: F 17 ASP cc_start: 0.7280 (p0) cc_final: 0.6573 (p0) REVERT: F 20 SER cc_start: 0.8705 (t) cc_final: 0.8184 (p) REVERT: F 32 ASN cc_start: 0.6714 (t0) cc_final: 0.6220 (t0) REVERT: F 50 SER cc_start: 0.7648 (m) cc_final: 0.7211 (t) REVERT: F 87 PHE cc_start: 0.8539 (m-10) cc_final: 0.8212 (m-10) REVERT: F 93 SER cc_start: 0.7821 (t) cc_final: 0.7482 (p) REVERT: G 22 CYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7446 (t) REVERT: G 27 PHE cc_start: 0.8343 (p90) cc_final: 0.7710 (p90) REVERT: G 29 PHE cc_start: 0.8814 (t80) cc_final: 0.8579 (t80) REVERT: G 34 MET cc_start: 0.7028 (mtp) cc_final: 0.6620 (mtp) REVERT: G 46 GLU cc_start: 0.7608 (tt0) cc_final: 0.7022 (tt0) REVERT: G 54 GLU cc_start: 0.8195 (tt0) cc_final: 0.7826 (tt0) REVERT: G 79 SER cc_start: 0.8690 (m) cc_final: 0.7964 (p) REVERT: G 108 MET cc_start: 0.7170 (mpp) cc_final: 0.6468 (mpp) REVERT: H 10 ILE cc_start: 0.8806 (pt) cc_final: 0.8393 (mm) REVERT: H 29 VAL cc_start: 0.8543 (t) cc_final: 0.8207 (m) REVERT: H 34 TRP cc_start: 0.8097 (m100) cc_final: 0.7820 (m100) REVERT: H 37 GLN cc_start: 0.8251 (tt0) cc_final: 0.7868 (tt0) REVERT: H 48 TYR cc_start: 0.7224 (p90) cc_final: 0.6671 (p90) REVERT: H 55 SER cc_start: 0.8378 (t) cc_final: 0.8116 (p) REVERT: H 61 PHE cc_start: 0.8936 (m-10) cc_final: 0.8579 (m-10) REVERT: H 65 ARG cc_start: 0.8236 (ttt180) cc_final: 0.7819 (ptm-80) REVERT: H 82 VAL cc_start: 0.9199 (t) cc_final: 0.8943 (m) REVERT: H 85 TYR cc_start: 0.8194 (m-80) cc_final: 0.7835 (m-10) REVERT: H 89 GLN cc_start: 0.7314 (mt0) cc_final: 0.6912 (mt0) REVERT: H 101 THR cc_start: 0.7866 (m) cc_final: 0.7415 (p) REVERT: I 27 TYR cc_start: 0.5654 (t80) cc_final: 0.4562 (t80) REVERT: I 28 THR cc_start: 0.7908 (m) cc_final: 0.6769 (p) REVERT: I 30 THR cc_start: 0.8779 (p) cc_final: 0.8231 (t) REVERT: I 36 TRP cc_start: 0.8339 (m100) cc_final: 0.7940 (m-10) REVERT: I 38 LYS cc_start: 0.8606 (tttp) cc_final: 0.8257 (tttm) REVERT: I 46 GLU cc_start: 0.7428 (pt0) cc_final: 0.7029 (pt0) REVERT: I 57 SER cc_start: 0.9392 (m) cc_final: 0.8931 (p) REVERT: I 104 MET cc_start: 0.7256 (mtt) cc_final: 0.6963 (mmt) REVERT: I 113 VAL cc_start: 0.8559 (t) cc_final: 0.8098 (m) REVERT: J 10 PHE cc_start: 0.7659 (m-10) cc_final: 0.7412 (m-10) REVERT: J 44 PRO cc_start: 0.7343 (Cg_endo) cc_final: 0.7068 (Cg_exo) REVERT: J 50 SER cc_start: 0.7542 (m) cc_final: 0.7051 (t) REVERT: J 61 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7812 (ptm160) REVERT: J 92 ASN cc_start: 0.8724 (t0) cc_final: 0.8202 (t0) REVERT: J 93 SER cc_start: 0.7732 (t) cc_final: 0.7302 (p) REVERT: J 103 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7942 (mtpt) outliers start: 44 outliers final: 38 residues processed: 356 average time/residue: 0.2180 time to fit residues: 103.8803 Evaluate side-chains 384 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 342 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 34 TRP Chi-restraints excluded: chain C residue 36 GLN 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 18 VAL Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 63 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 93 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 82 GLN 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 61 ARG Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 92 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN C 36 GLN D 283 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN H 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.126749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.113794 restraints weight = 14455.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117846 restraints weight = 6715.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120497 restraints weight = 3731.502| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8834 Z= 0.179 Angle : 0.651 6.593 11958 Z= 0.346 Chirality : 0.044 0.176 1270 Planarity : 0.005 0.040 1528 Dihedral : 4.793 24.735 1206 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 5.12 % Allowed : 23.03 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.26), residues: 1090 helix: -1.38 (0.67), residues: 62 sheet: -0.58 (0.26), residues: 426 loop : -1.34 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP E 36 HIS 0.005 0.001 HIS C 33 PHE 0.039 0.002 PHE I 29 TYR 0.021 0.002 TYR E 52 ARG 0.006 0.001 ARG H 60 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 262) hydrogen bonds : angle 5.74770 ( 666) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.89663 ( 8) covalent geometry : bond 0.00393 ( 8830) covalent geometry : angle 0.65126 (11950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3580.65 seconds wall clock time: 63 minutes 0.61 seconds (3780.61 seconds total)