Starting phenix.real_space_refine on Wed Feb 4 00:12:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n96_49161/02_2026/9n96_49161.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n96_49161/02_2026/9n96_49161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n96_49161/02_2026/9n96_49161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n96_49161/02_2026/9n96_49161.map" model { file = "/net/cci-nas-00/data/ceres_data/9n96_49161/02_2026/9n96_49161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n96_49161/02_2026/9n96_49161.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 43 5.49 5 S 45 5.16 5 C 4861 2.51 5 N 1393 2.21 5 O 1579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7921 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain breaks: 1 Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "D" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 Chain: "E" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 614 Classifications: {'peptide': 74} Link IDs: {'TRANS': 73} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "G" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2439 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain: "Y" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 343 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain breaks: 1 Chain: "Z" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 564 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 14} Link IDs: {'rna2p': 7, 'rna3p': 19} Time building chain proxies: 1.78, per 1000 atoms: 0.22 Number of scatterers: 7921 At special positions: 0 Unit cell: (81.225, 96.387, 127.794, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 43 15.00 O 1579 8.00 N 1393 7.00 C 4861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 166.7 milliseconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 36.7% alpha, 25.4% beta 13 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 removed outlier: 3.693A pdb=" N LYS A 8 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.620A pdb=" N LEU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 16 removed outlier: 4.159A pdb=" N ILE C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 removed outlier: 4.198A pdb=" N LEU C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 100 Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.640A pdb=" N GLU D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 166 removed outlier: 3.777A pdb=" N ILE D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 28 Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'G' and resid 9 through 13 removed outlier: 3.516A pdb=" N MET G 13 " --> pdb=" O LYS G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'J' and resid 36 through 45 removed outlier: 3.748A pdb=" N LEU J 45 " --> pdb=" O ASN J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 64 removed outlier: 4.127A pdb=" N VAL J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 61 " --> pdb=" O GLN J 57 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE J 62 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 74 removed outlier: 3.570A pdb=" N PHE J 73 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 79 removed outlier: 3.786A pdb=" N ALA J 79 " --> pdb=" O ASP J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 83 Processing helix chain 'J' and resid 85 through 103 removed outlier: 4.300A pdb=" N ARG J 89 " --> pdb=" O SER J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 119 removed outlier: 3.594A pdb=" N ILE J 111 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ALA J 112 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN J 113 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN J 115 " --> pdb=" O ILE J 111 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU J 117 " --> pdb=" O ASN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 147 removed outlier: 4.040A pdb=" N GLN J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS J 138 " --> pdb=" O THR J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 removed outlier: 3.802A pdb=" N MET J 160 " --> pdb=" O ALA J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 176 through 194 Processing helix chain 'J' and resid 224 through 244 removed outlier: 3.647A pdb=" N LEU J 228 " --> pdb=" O GLN J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 267 removed outlier: 3.599A pdb=" N GLY J 258 " --> pdb=" O THR J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 279 removed outlier: 3.834A pdb=" N ILE J 275 " --> pdb=" O MET J 271 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN J 276 " --> pdb=" O SER J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 311 Processing helix chain 'J' and resid 312 through 316 removed outlier: 4.283A pdb=" N GLU J 316 " --> pdb=" O ALA J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 326 removed outlier: 4.053A pdb=" N THR J 322 " --> pdb=" O GLN J 318 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR J 323 " --> pdb=" O ALA J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 329 No H-bonds generated for 'chain 'J' and resid 327 through 329' Processing helix chain 'J' and resid 331 through 336 removed outlier: 3.527A pdb=" N ILE J 335 " --> pdb=" O PRO J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 339 No H-bonds generated for 'chain 'J' and resid 337 through 339' Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 removed outlier: 6.675A pdb=" N GLY A 30 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 46 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU A 32 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER A 44 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 43 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU A 59 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 73 removed outlier: 4.219A pdb=" N LEU B 69 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 73 removed outlier: 4.219A pdb=" N LEU B 69 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS B 43 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE B 31 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N CYS B 45 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY B 29 " --> pdb=" O CYS B 45 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU B 47 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE B 27 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG B 16 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 79 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.885A pdb=" N HIS C 40 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR C 30 " --> pdb=" O HIS C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 339 through 343 removed outlier: 6.734A pdb=" N ILE D 173 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL D 182 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL D 171 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 168 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 355 " --> pdb=" O HIS D 172 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG D 174 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL D 353 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU F 61 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER F 56 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYR F 50 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS F 58 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU F 48 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY F 60 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET F 42 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL F 36 " --> pdb=" O MET F 42 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU F 44 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL F 34 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASN F 46 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TYR F 32 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY F 74 " --> pdb=" O PRO F 18 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N MET F 20 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE F 72 " --> pdb=" O MET F 20 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS F 22 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG E 76 " --> pdb=" O GLY F 74 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA E 61 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG E 76 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP E 59 " --> pdb=" O ARG E 76 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET E 78 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL E 57 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU E 58 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE E 48 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASP E 60 " --> pdb=" O CYS E 46 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N CYS E 46 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET E 41 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU E 35 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU E 86 " --> pdb=" O TRP E 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 54 through 62 removed outlier: 7.254A pdb=" N GLN G 54 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET G 48 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN G 56 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL G 46 " --> pdb=" O ASN G 56 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLY G 58 " --> pdb=" O GLU G 44 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU G 44 " --> pdb=" O GLY G 58 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL G 41 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS G 45 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN G 28 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLU G 47 " --> pdb=" O HIS G 26 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N HIS G 26 " --> pdb=" O GLU G 47 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2156 1.33 - 1.46: 1556 1.46 - 1.58: 4256 1.58 - 1.70: 84 1.70 - 1.82: 78 Bond restraints: 8130 Sorted by residual: bond pdb=" C VAL A 5 " pdb=" N PRO A 6 " ideal model delta sigma weight residual 1.335 1.409 -0.074 1.36e-02 5.41e+03 2.96e+01 bond pdb=" C MET D 148 " pdb=" N PRO D 149 " ideal model delta sigma weight residual 1.335 1.378 -0.043 9.40e-03 1.13e+04 2.11e+01 bond pdb=" CA PHE D 193 " pdb=" C PHE D 193 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.80e-02 3.09e+03 3.12e+00 bond pdb=" CA ARG D 142 " pdb=" CB ARG D 142 " ideal model delta sigma weight residual 1.527 1.556 -0.029 1.75e-02 3.27e+03 2.75e+00 bond pdb=" CB GLN J 332 " pdb=" CG GLN J 332 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.53e+00 ... (remaining 8125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 10797 2.30 - 4.61: 300 4.61 - 6.91: 46 6.91 - 9.21: 20 9.21 - 11.51: 5 Bond angle restraints: 11168 Sorted by residual: angle pdb=" CA LYS C 8 " pdb=" CB LYS C 8 " pdb=" CG LYS C 8 " ideal model delta sigma weight residual 114.10 123.83 -9.73 2.00e+00 2.50e-01 2.37e+01 angle pdb=" N GLU J 230 " pdb=" CA GLU J 230 " pdb=" CB GLU J 230 " ideal model delta sigma weight residual 110.40 117.65 -7.25 1.63e+00 3.76e-01 1.98e+01 angle pdb=" CA GLN J 332 " pdb=" CB GLN J 332 " pdb=" CG GLN J 332 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.75e+01 angle pdb=" CA GLU E 37 " pdb=" CB GLU E 37 " pdb=" CG GLU E 37 " ideal model delta sigma weight residual 114.10 122.32 -8.22 2.00e+00 2.50e-01 1.69e+01 angle pdb=" CB MET B 17 " pdb=" CG MET B 17 " pdb=" SD MET B 17 " ideal model delta sigma weight residual 112.70 124.21 -11.51 3.00e+00 1.11e-01 1.47e+01 ... (remaining 11163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4404 17.87 - 35.74: 449 35.74 - 53.61: 99 53.61 - 71.48: 51 71.48 - 89.35: 15 Dihedral angle restraints: 5018 sinusoidal: 2474 harmonic: 2544 Sorted by residual: dihedral pdb=" CA GLN A 42 " pdb=" C GLN A 42 " pdb=" N MET A 43 " pdb=" CA MET A 43 " ideal model delta harmonic sigma weight residual -180.00 -158.16 -21.84 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA MET F 40 " pdb=" C MET F 40 " pdb=" N ASN F 41 " pdb=" CA ASN F 41 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TRP F 25 " pdb=" C TRP F 25 " pdb=" N GLY F 26 " pdb=" CA GLY F 26 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 901 0.044 - 0.088: 304 0.088 - 0.131: 106 0.131 - 0.175: 21 0.175 - 0.219: 5 Chirality restraints: 1337 Sorted by residual: chirality pdb=" CB VAL A 5 " pdb=" CA VAL A 5 " pdb=" CG1 VAL A 5 " pdb=" CG2 VAL A 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL C 88 " pdb=" CA VAL C 88 " pdb=" CG1 VAL C 88 " pdb=" CG2 VAL C 88 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA GLU E 37 " pdb=" N GLU E 37 " pdb=" C GLU E 37 " pdb=" CB GLU E 37 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 1334 not shown) Planarity restraints: 1266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS J 245 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO J 246 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO J 246 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO J 246 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 84 " 0.053 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO C 85 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 80 " -0.050 5.00e-02 4.00e+02 7.69e-02 9.45e+00 pdb=" N PRO A 81 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.042 5.00e-02 4.00e+02 ... (remaining 1263 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 3864 3.01 - 3.49: 7694 3.49 - 3.96: 12599 3.96 - 4.43: 14590 4.43 - 4.90: 23140 Nonbonded interactions: 61887 Sorted by model distance: nonbonded pdb=" O5' U Z 29 " pdb=" O4' U Z 29 " model vdw 2.543 2.432 nonbonded pdb=" O4' C Z 14 " pdb=" C6 C Z 14 " model vdw 2.547 2.672 nonbonded pdb=" O ASP G 14 " pdb=" OD1 ASP G 14 " model vdw 2.556 3.040 nonbonded pdb=" O4' U Z 13 " pdb=" C6 U Z 13 " model vdw 2.562 2.672 nonbonded pdb=" O5' A Z 8 " pdb=" O4' A Z 8 " model vdw 2.567 2.432 ... (remaining 61882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 8130 Z= 0.225 Angle : 0.974 11.514 11168 Z= 0.504 Chirality : 0.051 0.219 1337 Planarity : 0.008 0.095 1266 Dihedral : 16.342 89.349 3362 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.27), residues: 859 helix: -1.31 (0.27), residues: 281 sheet: -1.52 (0.39), residues: 177 loop : -1.19 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 161 TYR 0.021 0.002 TYR F 71 PHE 0.018 0.002 PHE A 70 TRP 0.024 0.003 TRP F 25 HIS 0.005 0.001 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 8130) covalent geometry : angle 0.97401 (11168) hydrogen bonds : bond 0.16176 ( 317) hydrogen bonds : angle 7.51625 ( 893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: C 44 ASP cc_start: 0.7725 (m-30) cc_final: 0.7462 (m-30) REVERT: D 196 MET cc_start: 0.8102 (mpp) cc_final: 0.7466 (mtm) REVERT: E 71 ARG cc_start: 0.7979 (mmp-170) cc_final: 0.7741 (mmt180) REVERT: G 13 MET cc_start: 0.7989 (mmt) cc_final: 0.7777 (mmm) REVERT: G 48 MET cc_start: 0.7564 (mmm) cc_final: 0.7288 (mmm) REVERT: J 73 PHE cc_start: 0.9056 (m-80) cc_final: 0.8817 (m-80) REVERT: J 84 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7798 (pttp) REVERT: J 142 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7859 (tm-30) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0864 time to fit residues: 17.6611 Evaluate side-chains 134 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN D 344 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.187276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.142346 restraints weight = 9350.230| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.25 r_work: 0.3643 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8130 Z= 0.163 Angle : 0.632 7.734 11168 Z= 0.325 Chirality : 0.042 0.163 1337 Planarity : 0.005 0.067 1266 Dihedral : 14.812 77.147 1585 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.66 % Allowed : 7.77 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.29), residues: 859 helix: -0.40 (0.30), residues: 297 sheet: -1.69 (0.38), residues: 176 loop : -0.85 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 29 TYR 0.017 0.001 TYR F 71 PHE 0.020 0.002 PHE A 70 TRP 0.009 0.001 TRP J 229 HIS 0.007 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8130) covalent geometry : angle 0.63167 (11168) hydrogen bonds : bond 0.04606 ( 317) hydrogen bonds : angle 5.38261 ( 893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8052 (mmm) cc_final: 0.7717 (mmm) REVERT: D 196 MET cc_start: 0.8121 (mpp) cc_final: 0.7368 (mpp) REVERT: G 13 MET cc_start: 0.7719 (mmt) cc_final: 0.7492 (mmm) REVERT: G 48 MET cc_start: 0.7208 (mmm) cc_final: 0.6928 (mmm) REVERT: J 73 PHE cc_start: 0.8680 (m-80) cc_final: 0.8478 (m-80) REVERT: J 84 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7741 (pttp) REVERT: J 142 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7644 (tm-30) REVERT: J 231 GLU cc_start: 0.8251 (tp30) cc_final: 0.7964 (tp30) outliers start: 13 outliers final: 8 residues processed: 150 average time/residue: 0.0898 time to fit residues: 17.6581 Evaluate side-chains 141 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 335 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 39 optimal weight: 0.0570 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 GLN D 143 ASN ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.188328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.146978 restraints weight = 9450.709| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.16 r_work: 0.3726 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8130 Z= 0.102 Angle : 0.542 8.253 11168 Z= 0.279 Chirality : 0.040 0.164 1337 Planarity : 0.004 0.053 1266 Dihedral : 14.553 78.039 1585 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.02 % Allowed : 9.68 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.30), residues: 859 helix: 0.26 (0.31), residues: 290 sheet: -1.54 (0.37), residues: 196 loop : -0.67 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 161 TYR 0.009 0.001 TYR F 71 PHE 0.010 0.001 PHE D 190 TRP 0.010 0.001 TRP J 229 HIS 0.003 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8130) covalent geometry : angle 0.54189 (11168) hydrogen bonds : bond 0.03701 ( 317) hydrogen bonds : angle 4.94109 ( 893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: B 46 ASP cc_start: 0.7915 (m-30) cc_final: 0.7704 (m-30) REVERT: D 161 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7435 (ttp-110) REVERT: D 196 MET cc_start: 0.7982 (mpp) cc_final: 0.7618 (mpp) REVERT: G 13 MET cc_start: 0.7723 (mmt) cc_final: 0.7494 (mmm) REVERT: G 48 MET cc_start: 0.7500 (mmm) cc_final: 0.7211 (mmm) REVERT: J 73 PHE cc_start: 0.8702 (m-80) cc_final: 0.8456 (m-80) REVERT: J 84 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7910 (pttp) outliers start: 8 outliers final: 7 residues processed: 151 average time/residue: 0.0835 time to fit residues: 16.5947 Evaluate side-chains 141 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain G residue 37 PHE Chi-restraints excluded: chain J residue 203 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.186811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.141583 restraints weight = 9416.927| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.27 r_work: 0.3644 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8130 Z= 0.137 Angle : 0.574 7.070 11168 Z= 0.297 Chirality : 0.041 0.169 1337 Planarity : 0.004 0.048 1266 Dihedral : 14.406 74.911 1585 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.91 % Allowed : 10.83 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.30), residues: 859 helix: 0.55 (0.31), residues: 290 sheet: -1.52 (0.38), residues: 193 loop : -0.53 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 298 TYR 0.015 0.001 TYR F 71 PHE 0.017 0.001 PHE B 31 TRP 0.007 0.001 TRP J 229 HIS 0.006 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8130) covalent geometry : angle 0.57365 (11168) hydrogen bonds : bond 0.03921 ( 317) hydrogen bonds : angle 4.81775 ( 893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.315 Fit side-chains REVERT: B 46 ASP cc_start: 0.7745 (m-30) cc_final: 0.7532 (m-30) REVERT: D 196 MET cc_start: 0.8010 (mpp) cc_final: 0.7560 (mpp) REVERT: G 13 MET cc_start: 0.7642 (mmt) cc_final: 0.7403 (mmm) REVERT: G 48 MET cc_start: 0.7242 (mmm) cc_final: 0.6956 (mmm) REVERT: J 73 PHE cc_start: 0.8689 (m-80) cc_final: 0.8468 (m-80) REVERT: J 84 LYS cc_start: 0.8399 (ttpt) cc_final: 0.7857 (pttp) REVERT: J 231 GLU cc_start: 0.8158 (tp30) cc_final: 0.7935 (tp30) outliers start: 15 outliers final: 10 residues processed: 144 average time/residue: 0.1061 time to fit residues: 19.9951 Evaluate side-chains 136 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 60 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 0.0370 chunk 7 optimal weight: 0.0030 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.0570 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 overall best weight: 0.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 GLN E 26 GLN ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.190298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.148074 restraints weight = 9655.029| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.28 r_work: 0.3727 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8130 Z= 0.097 Angle : 0.521 7.453 11168 Z= 0.270 Chirality : 0.040 0.156 1337 Planarity : 0.004 0.047 1266 Dihedral : 14.267 77.597 1585 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.04 % Allowed : 12.10 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.30), residues: 859 helix: 0.75 (0.31), residues: 291 sheet: -1.41 (0.38), residues: 198 loop : -0.48 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 298 TYR 0.008 0.001 TYR C 81 PHE 0.009 0.001 PHE D 190 TRP 0.009 0.001 TRP J 229 HIS 0.003 0.001 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8130) covalent geometry : angle 0.52101 (11168) hydrogen bonds : bond 0.03305 ( 317) hydrogen bonds : angle 4.63186 ( 893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.301 Fit side-chains REVERT: D 148 MET cc_start: 0.7786 (mtp) cc_final: 0.7561 (mtp) REVERT: F 28 GLU cc_start: 0.8127 (tt0) cc_final: 0.7802 (tt0) REVERT: F 30 LYS cc_start: 0.8625 (tttp) cc_final: 0.8395 (ttmm) REVERT: G 13 MET cc_start: 0.7642 (mmt) cc_final: 0.7384 (mmm) REVERT: G 48 MET cc_start: 0.7532 (mmm) cc_final: 0.7215 (mmm) REVERT: J 73 PHE cc_start: 0.8699 (m-80) cc_final: 0.8483 (m-80) REVERT: J 84 LYS cc_start: 0.8516 (ttpt) cc_final: 0.7953 (pttp) REVERT: J 298 ARG cc_start: 0.8005 (mmp80) cc_final: 0.7783 (mmp80) outliers start: 16 outliers final: 13 residues processed: 160 average time/residue: 0.1004 time to fit residues: 21.2267 Evaluate side-chains 153 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain G residue 37 PHE Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 254 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.181886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136009 restraints weight = 9416.254| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.25 r_work: 0.3577 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 8130 Z= 0.253 Angle : 0.707 8.394 11168 Z= 0.366 Chirality : 0.045 0.181 1337 Planarity : 0.005 0.058 1266 Dihedral : 14.360 73.305 1585 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.17 % Allowed : 14.27 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.29), residues: 859 helix: 0.51 (0.31), residues: 289 sheet: -0.65 (0.46), residues: 127 loop : -1.01 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 64 TYR 0.021 0.002 TYR F 71 PHE 0.033 0.003 PHE A 70 TRP 0.011 0.002 TRP D 194 HIS 0.007 0.002 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 8130) covalent geometry : angle 0.70670 (11168) hydrogen bonds : bond 0.04893 ( 317) hydrogen bonds : angle 5.07710 ( 893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.178 Fit side-chains REVERT: D 196 MET cc_start: 0.8372 (mpp) cc_final: 0.7829 (mpp) REVERT: G 48 MET cc_start: 0.7533 (mmm) cc_final: 0.7295 (mmm) REVERT: J 73 PHE cc_start: 0.8797 (m-80) cc_final: 0.8576 (m-80) REVERT: J 230 GLU cc_start: 0.7507 (pp20) cc_final: 0.7238 (tp30) outliers start: 17 outliers final: 13 residues processed: 153 average time/residue: 0.1017 time to fit residues: 20.3220 Evaluate side-chains 146 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 55 optimal weight: 0.0040 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.0670 chunk 53 optimal weight: 0.7980 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.184953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141665 restraints weight = 9583.292| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.12 r_work: 0.3662 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8130 Z= 0.121 Angle : 0.576 7.973 11168 Z= 0.300 Chirality : 0.041 0.159 1337 Planarity : 0.004 0.045 1266 Dihedral : 14.204 77.450 1585 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.78 % Allowed : 15.80 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.30), residues: 859 helix: 0.69 (0.32), residues: 289 sheet: -0.82 (0.45), residues: 138 loop : -0.77 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 298 TYR 0.010 0.001 TYR F 71 PHE 0.013 0.001 PHE A 70 TRP 0.011 0.001 TRP J 229 HIS 0.004 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8130) covalent geometry : angle 0.57561 (11168) hydrogen bonds : bond 0.03783 ( 317) hydrogen bonds : angle 4.76827 ( 893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.235 Fit side-chains REVERT: D 196 MET cc_start: 0.8156 (mpp) cc_final: 0.7657 (mpp) REVERT: E 41 MET cc_start: 0.7713 (tmm) cc_final: 0.7446 (tmm) REVERT: F 29 TYR cc_start: 0.7988 (m-80) cc_final: 0.7672 (m-80) REVERT: G 13 MET cc_start: 0.7705 (mmt) cc_final: 0.7477 (mmm) REVERT: G 48 MET cc_start: 0.7581 (mmm) cc_final: 0.7304 (mmm) REVERT: J 73 PHE cc_start: 0.8771 (m-80) cc_final: 0.8528 (m-80) REVERT: J 230 GLU cc_start: 0.7381 (pp20) cc_final: 0.7119 (tp30) REVERT: J 298 ARG cc_start: 0.8325 (mmp80) cc_final: 0.8089 (mmp80) outliers start: 14 outliers final: 12 residues processed: 153 average time/residue: 0.0965 time to fit residues: 19.6761 Evaluate side-chains 149 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 203 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 52 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.179928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.136369 restraints weight = 9877.796| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.12 r_work: 0.3609 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 8130 Z= 0.234 Angle : 0.689 8.068 11168 Z= 0.358 Chirality : 0.045 0.172 1337 Planarity : 0.005 0.053 1266 Dihedral : 14.251 73.480 1585 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.68 % Allowed : 15.67 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.30), residues: 859 helix: 0.50 (0.31), residues: 288 sheet: -1.17 (0.43), residues: 143 loop : -0.88 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 298 TYR 0.017 0.002 TYR F 71 PHE 0.029 0.002 PHE A 70 TRP 0.008 0.002 TRP D 194 HIS 0.008 0.002 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 8130) covalent geometry : angle 0.68913 (11168) hydrogen bonds : bond 0.04754 ( 317) hydrogen bonds : angle 5.06301 ( 893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.203 Fit side-chains REVERT: D 196 MET cc_start: 0.8288 (mpp) cc_final: 0.7831 (mpp) REVERT: F 25 TRP cc_start: 0.8020 (OUTLIER) cc_final: 0.5915 (p90) REVERT: G 48 MET cc_start: 0.7539 (mmm) cc_final: 0.7332 (mmm) REVERT: J 73 PHE cc_start: 0.8827 (m-80) cc_final: 0.8587 (m-80) REVERT: J 298 ARG cc_start: 0.8399 (mmp80) cc_final: 0.8146 (mmp80) REVERT: J 332 GLN cc_start: 0.7812 (mm110) cc_final: 0.7595 (tm-30) outliers start: 21 outliers final: 20 residues processed: 153 average time/residue: 0.0932 time to fit residues: 18.6168 Evaluate side-chains 153 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 335 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.182665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139358 restraints weight = 9820.612| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.13 r_work: 0.3643 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8130 Z= 0.155 Angle : 0.629 8.629 11168 Z= 0.326 Chirality : 0.042 0.166 1337 Planarity : 0.004 0.046 1266 Dihedral : 14.185 77.036 1585 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.55 % Allowed : 16.18 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.30), residues: 859 helix: 0.60 (0.31), residues: 289 sheet: -1.26 (0.42), residues: 154 loop : -0.79 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 298 TYR 0.012 0.002 TYR F 71 PHE 0.019 0.002 PHE A 70 TRP 0.010 0.001 TRP J 229 HIS 0.006 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8130) covalent geometry : angle 0.62877 (11168) hydrogen bonds : bond 0.04125 ( 317) hydrogen bonds : angle 4.90271 ( 893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: D 196 MET cc_start: 0.8189 (mpp) cc_final: 0.7645 (mpp) REVERT: F 25 TRP cc_start: 0.7989 (OUTLIER) cc_final: 0.5895 (p90) REVERT: F 29 TYR cc_start: 0.7975 (m-80) cc_final: 0.7624 (m-80) REVERT: G 13 MET cc_start: 0.7763 (mmt) cc_final: 0.7546 (mmm) REVERT: G 48 MET cc_start: 0.7504 (mmm) cc_final: 0.7297 (mmm) REVERT: J 73 PHE cc_start: 0.8781 (m-80) cc_final: 0.8553 (m-80) REVERT: J 84 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8109 (pttp) REVERT: J 298 ARG cc_start: 0.8289 (mmp80) cc_final: 0.8044 (mmp80) outliers start: 20 outliers final: 17 residues processed: 154 average time/residue: 0.1035 time to fit residues: 20.9066 Evaluate side-chains 154 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 85 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 HIS ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.185161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.144858 restraints weight = 9704.631| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.88 r_work: 0.3709 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8130 Z= 0.132 Angle : 0.612 8.980 11168 Z= 0.317 Chirality : 0.041 0.166 1337 Planarity : 0.004 0.045 1266 Dihedral : 14.132 78.006 1585 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.29 % Allowed : 16.56 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.30), residues: 859 helix: 0.73 (0.31), residues: 284 sheet: -1.64 (0.40), residues: 175 loop : -0.53 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 298 TYR 0.010 0.001 TYR F 71 PHE 0.015 0.001 PHE A 70 TRP 0.011 0.001 TRP J 229 HIS 0.004 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8130) covalent geometry : angle 0.61223 (11168) hydrogen bonds : bond 0.03809 ( 317) hydrogen bonds : angle 4.79694 ( 893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: D 196 MET cc_start: 0.8008 (mpp) cc_final: 0.7513 (mpp) REVERT: F 25 TRP cc_start: 0.7980 (OUTLIER) cc_final: 0.5893 (p90) REVERT: F 29 TYR cc_start: 0.7858 (m-80) cc_final: 0.7504 (m-80) REVERT: G 13 MET cc_start: 0.7787 (mmt) cc_final: 0.7554 (mmm) REVERT: G 48 MET cc_start: 0.7492 (mmm) cc_final: 0.7264 (mmm) REVERT: J 73 PHE cc_start: 0.8753 (m-80) cc_final: 0.8520 (m-80) REVERT: J 84 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8089 (pttp) REVERT: J 231 GLU cc_start: 0.8265 (tp30) cc_final: 0.7992 (tp30) REVERT: J 298 ARG cc_start: 0.8342 (mmp80) cc_final: 0.8120 (mmp80) outliers start: 18 outliers final: 16 residues processed: 157 average time/residue: 0.0916 time to fit residues: 18.9225 Evaluate side-chains 161 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 170 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.180853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137158 restraints weight = 9794.913| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.11 r_work: 0.3616 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8130 Z= 0.209 Angle : 0.675 8.845 11168 Z= 0.350 Chirality : 0.044 0.181 1337 Planarity : 0.005 0.048 1266 Dihedral : 14.190 74.939 1585 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.68 % Allowed : 15.92 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.30), residues: 859 helix: 0.60 (0.31), residues: 285 sheet: -1.51 (0.42), residues: 157 loop : -0.77 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 298 TYR 0.016 0.002 TYR F 71 PHE 0.026 0.002 PHE A 70 TRP 0.009 0.001 TRP J 229 HIS 0.009 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 8130) covalent geometry : angle 0.67546 (11168) hydrogen bonds : bond 0.04480 ( 317) hydrogen bonds : angle 4.99084 ( 893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2012.07 seconds wall clock time: 35 minutes 0.85 seconds (2100.85 seconds total)