Starting phenix.real_space_refine on Thu Feb 5 12:50:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x32_38026/02_2026/8x32_38026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x32_38026/02_2026/8x32_38026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x32_38026/02_2026/8x32_38026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x32_38026/02_2026/8x32_38026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x32_38026/02_2026/8x32_38026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x32_38026/02_2026/8x32_38026.map" } resolution = 4.4 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= 0.022 sd= 0.415 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1064 atoms to isotropic. 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 290 5.49 5 S 23 5.16 5 C 9819 2.51 5 N 3043 2.21 5 O 3769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s 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: 16944 Number of models: 1 Model: "" Number of chains: 14 Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 205 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "N" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Chain: "K" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2309 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 261} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1919 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 750 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Time building chain proxies: 4.02, per 1000 atoms: 0.24 Number of scatterers: 16944 At special positions: 0 Unit cell: (134.16, 136.24, 127.92, 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 23 16.00 P 290 15.00 O 3769 8.00 N 3043 7.00 C 9819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 597.9 milliseconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 5 sheets defined 52.4% alpha, 2.7% beta 143 base pairs and 226 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'N' and resid 3 through 10 removed outlier: 4.260A pdb=" N LEU N 7 " --> pdb=" O PRO N 3 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN N 9 " --> pdb=" O LEU N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 29 removed outlier: 4.259A pdb=" N LEU N 25 " --> pdb=" O PHE N 21 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLU N 27 " --> pdb=" O TYR N 23 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE N 28 " --> pdb=" O LEU N 24 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 39 removed outlier: 3.772A pdb=" N GLU N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 4.072A pdb=" N LYS N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS N 87 " --> pdb=" O GLN N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 82 through 87' Processing helix chain 'N' and resid 87 through 92 Processing helix chain 'N' and resid 94 through 96 No H-bonds generated for 'chain 'N' and resid 94 through 96' Processing helix chain 'N' and resid 97 through 105 removed outlier: 4.077A pdb=" N LEU N 101 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN N 102 " --> pdb=" O ALA N 98 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 111 removed outlier: 4.029A pdb=" N ALA N 109 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 212 through 217 Processing helix chain 'K' and resid 246 through 259 removed outlier: 4.018A pdb=" N ASN K 250 " --> pdb=" O THR K 246 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU K 251 " --> pdb=" O TRP K 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N CYS K 252 " --> pdb=" O CYS K 248 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU K 253 " --> pdb=" O ARG K 249 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER K 255 " --> pdb=" O LEU K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 318 Processing helix chain 'K' and resid 323 through 332 removed outlier: 3.744A pdb=" N LEU K 327 " --> pdb=" O PHE K 323 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS K 329 " --> pdb=" O TYR K 325 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS K 330 " --> pdb=" O GLU K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 363 removed outlier: 4.863A pdb=" N ALA K 351 " --> pdb=" O LEU K 347 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP K 355 " --> pdb=" O ALA K 351 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR K 356 " --> pdb=" O TYR K 352 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU K 357 " --> pdb=" O TRP K 353 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE K 358 " --> pdb=" O SER K 354 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU K 360 " --> pdb=" O THR K 356 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU K 361 " --> pdb=" O LEU K 357 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU K 363 " --> pdb=" O THR K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 385 Processing helix chain 'K' and resid 388 through 392 Processing helix chain 'K' and resid 414 through 419 Processing helix chain 'M' and resid 153 through 159 Processing helix chain 'M' and resid 165 through 170 removed outlier: 4.009A pdb=" N GLU M 169 " --> pdb=" O ASP M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 196 removed outlier: 3.884A pdb=" N LEU M 192 " --> pdb=" O GLU M 188 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER M 194 " --> pdb=" O GLU M 190 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE M 196 " --> pdb=" O LEU M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 214 removed outlier: 3.864A pdb=" N ILE M 214 " --> pdb=" O PRO M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 219 Processing helix chain 'M' and resid 220 through 225 removed outlier: 3.886A pdb=" N ILE M 225 " --> pdb=" O LYS M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 259 removed outlier: 3.873A pdb=" N GLN M 258 " --> pdb=" O PRO M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 272 removed outlier: 3.775A pdb=" N ILE M 268 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS M 270 " --> pdb=" O GLN M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 275 No H-bonds generated for 'chain 'M' and resid 273 through 275' Processing helix chain 'M' and resid 276 through 281 removed outlier: 4.090A pdb=" N GLU M 281 " --> pdb=" O ASP M 277 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 287 Processing helix chain 'M' and resid 328 through 332 removed outlier: 3.659A pdb=" N SER M 331 " --> pdb=" O ILE M 328 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN M 332 " --> pdb=" O LEU M 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 328 through 332' Processing helix chain 'M' and resid 333 through 339 removed outlier: 3.740A pdb=" N ALA M 336 " --> pdb=" O ARG M 333 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS M 338 " --> pdb=" O ARG M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 349 Processing helix chain 'M' and resid 352 through 357 Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.129A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 4.236A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.781A pdb=" N ILE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.975A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 48 through 61 removed outlier: 3.751A pdb=" N ALA C 55 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL C 56 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.668A pdb=" N ALA C 72 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 73 " --> pdb=" O ASN C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 73' Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.937A pdb=" N GLU C 94 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 58 through 87 Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 107 through 127 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.501A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.513A pdb=" N ILE E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.795A pdb=" N ASP F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 19 through 23 Processing helix chain 'G' and resid 28 through 39 Processing helix chain 'G' and resid 47 through 50 Processing helix chain 'G' and resid 51 through 57 removed outlier: 3.596A pdb=" N LEU G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 67 removed outlier: 3.844A pdb=" N LEU G 65 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 74 removed outlier: 4.340A pdb=" N ALA G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 91 removed outlier: 4.003A pdb=" N LEU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 97 removed outlier: 4.413A pdb=" N ASP G 96 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 52 removed outlier: 4.405A pdb=" N ILE H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 84 Processing helix chain 'H' and resid 93 through 104 removed outlier: 4.064A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 123 Processing sheet with id=AA1, first strand: chain 'K' and resid 170 through 172 removed outlier: 6.759A pdb=" N ILE K 171 " --> pdb=" O ILE K 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 226 through 230 removed outlier: 5.433A pdb=" N GLU K 227 " --> pdb=" O GLU K 238 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU K 238 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR K 229 " --> pdb=" O PHE K 236 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR K 274 " --> pdb=" O TYR K 289 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYR K 289 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET K 276 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR K 289 " --> pdb=" O LEU K 306 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU K 306 " --> pdb=" O TYR K 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.420A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 397 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 226 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2362 1.32 - 1.44: 6210 1.44 - 1.57: 8667 1.57 - 1.69: 580 1.69 - 1.82: 36 Bond restraints: 17855 Sorted by residual: bond pdb=" C LEU E 61 " pdb=" N ILE E 62 " ideal model delta sigma weight residual 1.327 1.261 0.066 9.50e-03 1.11e+04 4.77e+01 bond pdb=" C GLN C 25 " pdb=" N PHE C 26 " ideal model delta sigma weight residual 1.333 1.493 -0.160 2.74e-02 1.33e+03 3.43e+01 bond pdb=" C1' DT I 112 " pdb=" N1 DT I 112 " ideal model delta sigma weight residual 1.490 1.352 0.138 3.00e-02 1.11e+03 2.12e+01 bond pdb=" C1' DC J 195 " pdb=" N1 DC J 195 " ideal model delta sigma weight residual 1.490 1.365 0.125 3.00e-02 1.11e+03 1.74e+01 bond pdb=" C1' DC I 60 " pdb=" N1 DC I 60 " ideal model delta sigma weight residual 1.490 1.366 0.124 3.00e-02 1.11e+03 1.70e+01 ... (remaining 17850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 24531 3.58 - 7.16: 708 7.16 - 10.74: 89 10.74 - 14.31: 12 14.31 - 17.89: 7 Bond angle restraints: 25347 Sorted by residual: angle pdb=" CA LEU D 105 " pdb=" C LEU D 105 " pdb=" N PRO D 106 " ideal model delta sigma weight residual 117.59 124.12 -6.53 9.90e-01 1.02e+00 4.35e+01 angle pdb=" CA ALA G 20 " pdb=" C ALA G 20 " pdb=" N ARG G 21 " ideal model delta sigma weight residual 118.14 110.19 7.95 1.31e+00 5.83e-01 3.68e+01 angle pdb=" C GLU E 105 " pdb=" N ASP E 106 " pdb=" CA ASP E 106 " ideal model delta sigma weight residual 122.06 111.45 10.61 1.86e+00 2.89e-01 3.25e+01 angle pdb=" C GLY F 48 " pdb=" N LEU F 49 " pdb=" CA LEU F 49 " ideal model delta sigma weight residual 121.54 132.26 -10.72 1.91e+00 2.74e-01 3.15e+01 angle pdb=" O LEU D 105 " pdb=" C LEU D 105 " pdb=" N PRO D 106 " ideal model delta sigma weight residual 121.32 116.57 4.75 8.50e-01 1.38e+00 3.12e+01 ... (remaining 25342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.82: 7792 25.82 - 51.63: 1829 51.63 - 77.45: 468 77.45 - 103.26: 18 103.26 - 129.08: 2 Dihedral angle restraints: 10109 sinusoidal: 6135 harmonic: 3974 Sorted by residual: dihedral pdb=" CA LEU G 57 " pdb=" C LEU G 57 " pdb=" N GLU G 58 " pdb=" CA GLU G 58 " ideal model delta harmonic sigma weight residual -180.00 -128.26 -51.74 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA GLN D 59 " pdb=" C GLN D 59 " pdb=" N LYS D 60 " pdb=" CA LYS D 60 " ideal model delta harmonic sigma weight residual 180.00 136.70 43.30 0 5.00e+00 4.00e-02 7.50e+01 dihedral pdb=" CA THR E 80 " pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta harmonic sigma weight residual 180.00 -136.81 -43.19 0 5.00e+00 4.00e-02 7.46e+01 ... (remaining 10106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2505 0.117 - 0.234: 319 0.234 - 0.350: 32 0.350 - 0.467: 1 0.467 - 0.584: 2 Chirality restraints: 2859 Sorted by residual: chirality pdb=" CG LEU E 70 " pdb=" CB LEU E 70 " pdb=" CD1 LEU E 70 " pdb=" CD2 LEU E 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" CG LEU B 97 " pdb=" CB LEU B 97 " pdb=" CD1 LEU B 97 " pdb=" CD2 LEU B 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE C 51 " pdb=" CA ILE C 51 " pdb=" CG1 ILE C 51 " pdb=" CG2 ILE C 51 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 2856 not shown) Planarity restraints: 2191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 404 " -0.034 2.00e-02 2.50e+03 2.86e-02 1.43e+01 pdb=" CG PHE K 404 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE K 404 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE K 404 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE K 404 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE K 404 " -0.025 2.00e-02 2.50e+03 pdb=" CZ PHE K 404 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 122 " -0.046 2.00e-02 2.50e+03 2.13e-02 1.36e+01 pdb=" N9 DG I 122 " 0.049 2.00e-02 2.50e+03 pdb=" C8 DG I 122 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 122 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DG I 122 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DG I 122 " 0.010 2.00e-02 2.50e+03 pdb=" O6 DG I 122 " -0.024 2.00e-02 2.50e+03 pdb=" N1 DG I 122 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG I 122 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 122 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG I 122 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DG I 122 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 105 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO H 106 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO H 106 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 106 " -0.049 5.00e-02 4.00e+02 ... (remaining 2188 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2401 2.74 - 3.28: 16737 3.28 - 3.82: 34391 3.82 - 4.36: 38727 4.36 - 4.90: 53808 Nonbonded interactions: 146064 Sorted by model distance: nonbonded pdb=" OG1 THR M 153 " pdb=" OE1 GLU M 155 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR E 118 " pdb=" O ILE F 46 " model vdw 2.197 3.040 nonbonded pdb=" O ASN N 16 " pdb=" OG SER N 19 " model vdw 2.218 3.040 nonbonded pdb=" O ALA F 33 " pdb=" NH1 ARG F 36 " model vdw 2.224 3.120 nonbonded pdb=" O THR K 356 " pdb=" OG1 THR K 359 " model vdw 2.227 3.040 ... (remaining 146059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 113) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 128) } ncs_group { reference = chain 'I' 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.540 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.160 17855 Z= 0.600 Angle : 1.471 17.892 25347 Z= 0.820 Chirality : 0.079 0.584 2859 Planarity : 0.009 0.091 2191 Dihedral : 26.157 129.078 7531 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 2.09 % Allowed : 9.11 % Favored : 88.80 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.89 % Twisted General : 1.93 % 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: -4.82 (0.18), residues: 1320 helix: -3.66 (0.14), residues: 563 sheet: -1.26 (1.49), residues: 14 loop : -2.92 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.002 ARG G 21 TYR 0.057 0.005 TYR H 124 PHE 0.060 0.005 PHE K 404 TRP 0.037 0.006 TRP K 353 HIS 0.025 0.004 HIS G 84 Details of bonding type rmsd covalent geometry : bond 0.01250 (17855) covalent geometry : angle 1.47132 (25347) hydrogen bonds : bond 0.22712 ( 741) hydrogen bonds : angle 7.83661 ( 1799) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 373 time to evaluate : 0.512 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: 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: K 214 TYR cc_start: 0.7639 (t80) cc_final: 0.6991 (t80) REVERT: K 379 MET cc_start: 0.4185 (tpt) cc_final: 0.3294 (tpp) REVERT: K 391 LEU cc_start: 0.9087 (tp) cc_final: 0.8826 (tp) REVERT: M 67 LYS cc_start: 0.6024 (tmmt) cc_final: 0.4810 (mtmm) REVERT: M 68 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.5723 (tp) REVERT: M 128 MET cc_start: 0.1349 (ptm) cc_final: 0.0966 (ptm) REVERT: M 264 LEU cc_start: 0.2585 (OUTLIER) cc_final: 0.2289 (pp) REVERT: A 85 GLN cc_start: 0.6107 (tm-30) cc_final: 0.5446 (tp40) REVERT: A 118 THR cc_start: 0.7325 (m) cc_final: 0.6985 (m) REVERT: B 50 ILE cc_start: 0.8007 (tp) cc_final: 0.7499 (tp) REVERT: B 55 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7048 (ptp-170) REVERT: B 68 ASP cc_start: 0.7632 (p0) cc_final: 0.7333 (m-30) REVERT: C 52 TYR cc_start: 0.8085 (t80) cc_final: 0.7757 (t80) REVERT: C 102 THR cc_start: 0.7453 (p) cc_final: 0.7192 (t) REVERT: D 39 THR cc_start: 0.6777 (t) cc_final: 0.6145 (t) REVERT: D 64 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6641 (mt) REVERT: D 68 PHE cc_start: 0.6132 (t80) cc_final: 0.5689 (t80) REVERT: D 123 LYS cc_start: 0.7547 (pttp) cc_final: 0.7188 (pttp) REVERT: F 34 ILE cc_start: 0.8731 (tp) cc_final: 0.8525 (tp) REVERT: F 37 LEU cc_start: 0.8113 (mt) cc_final: 0.7711 (mt) REVERT: F 53 GLU cc_start: 0.7978 (pm20) cc_final: 0.7665 (pm20) REVERT: F 58 LEU cc_start: 0.8634 (tt) cc_final: 0.7979 (tp) REVERT: F 61 PHE cc_start: 0.7992 (t80) cc_final: 0.7764 (t80) REVERT: G 35 LEU cc_start: 0.5049 (mp) cc_final: 0.4707 (tp) REVERT: G 87 LEU cc_start: 0.8127 (pp) cc_final: 0.7801 (pp) REVERT: G 110 PRO cc_start: 0.5284 (Cg_endo) cc_final: 0.3737 (Cg_exo) REVERT: H 40 TYR cc_start: 0.6414 (m-10) cc_final: 0.5226 (m-10) REVERT: H 52 HIS cc_start: 0.5764 (m-70) cc_final: 0.5556 (m-70) outliers start: 25 outliers final: 5 residues processed: 386 average time/residue: 0.1693 time to fit residues: 90.1875 Evaluate side-chains 306 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 297 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 9 GLN N 16 ASN K 222 HIS K 250 ASN M 332 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.172004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.150596 restraints weight = 72353.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.152735 restraints weight = 55183.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.154440 restraints weight = 44832.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.155781 restraints weight = 37507.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.156676 restraints weight = 32384.832| |-----------------------------------------------------------------------------| r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5335 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17855 Z= 0.196 Angle : 0.854 12.538 25347 Z= 0.471 Chirality : 0.047 0.254 2859 Planarity : 0.007 0.083 2191 Dihedral : 30.121 117.619 4760 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.42 % Allowed : 8.11 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.01 (0.20), residues: 1320 helix: -2.67 (0.17), residues: 599 sheet: -0.94 (1.41), residues: 19 loop : -2.73 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 119 TYR 0.036 0.003 TYR D 45 PHE 0.043 0.002 PHE E 104 TRP 0.032 0.003 TRP K 353 HIS 0.016 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00414 (17855) covalent geometry : angle 0.85397 (25347) hydrogen bonds : bond 0.06955 ( 741) hydrogen bonds : angle 5.67591 ( 1799) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 320 time to evaluate : 0.630 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: 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: K 316 TYR cc_start: 0.4975 (p90) cc_final: 0.4588 (p90) REVERT: K 328 SER cc_start: 0.7740 (m) cc_final: 0.7339 (p) REVERT: K 329 LYS cc_start: 0.7284 (mtmm) cc_final: 0.7029 (mtmm) REVERT: K 358 ILE cc_start: 0.5445 (pt) cc_final: 0.4643 (pt) REVERT: K 391 LEU cc_start: 0.8324 (tp) cc_final: 0.8064 (tp) REVERT: A 62 ILE cc_start: 0.7312 (mm) cc_final: 0.6987 (mm) REVERT: A 118 THR cc_start: 0.6528 (m) cc_final: 0.6147 (m) REVERT: A 123 ASP cc_start: 0.5892 (m-30) cc_final: 0.3681 (m-30) REVERT: B 50 ILE cc_start: 0.7703 (tp) cc_final: 0.7438 (tp) REVERT: B 68 ASP cc_start: 0.7695 (p0) cc_final: 0.6683 (m-30) REVERT: C 102 THR cc_start: 0.7477 (p) cc_final: 0.7180 (t) REVERT: D 72 ILE cc_start: 0.8112 (pt) cc_final: 0.7832 (pt) REVERT: E 100 LEU cc_start: 0.7520 (pp) cc_final: 0.7307 (pp) REVERT: E 104 PHE cc_start: 0.7767 (m-80) cc_final: 0.7441 (m-10) REVERT: F 34 ILE cc_start: 0.8891 (tp) cc_final: 0.8484 (tp) REVERT: F 37 LEU cc_start: 0.7983 (mt) cc_final: 0.7753 (mt) REVERT: H 70 ASN cc_start: 0.7693 (m-40) cc_final: 0.7485 (m-40) REVERT: H 112 HIS cc_start: 0.6289 (t70) cc_final: 0.5755 (t70) outliers start: 5 outliers final: 2 residues processed: 324 average time/residue: 0.1654 time to fit residues: 74.5107 Evaluate side-chains 270 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 268 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 143 optimal weight: 0.0770 chunk 49 optimal weight: 0.0980 chunk 114 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN K 166 ASN K 285 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.172601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.151570 restraints weight = 75060.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.153781 restraints weight = 58781.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.154851 restraints weight = 48658.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.156276 restraints weight = 41990.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.157188 restraints weight = 35237.573| |-----------------------------------------------------------------------------| r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17855 Z= 0.179 Angle : 0.791 11.327 25347 Z= 0.437 Chirality : 0.045 0.278 2859 Planarity : 0.006 0.074 2191 Dihedral : 29.805 108.534 4760 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.08 % Allowed : 7.19 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.20), residues: 1320 helix: -2.32 (0.18), residues: 642 sheet: -2.11 (1.02), residues: 30 loop : -2.64 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 83 TYR 0.034 0.002 TYR B 72 PHE 0.034 0.002 PHE K 404 TRP 0.041 0.003 TRP K 247 HIS 0.008 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00381 (17855) covalent geometry : angle 0.79123 (25347) hydrogen bonds : bond 0.06390 ( 741) hydrogen bonds : angle 5.12375 ( 1799) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash REVERT: K 167 LEU cc_start: 0.5778 (tp) cc_final: 0.5572 (tp) REVERT: K 214 TYR cc_start: 0.6397 (t80) cc_final: 0.6156 (t80) REVERT: K 328 SER cc_start: 0.7957 (m) cc_final: 0.7402 (p) REVERT: K 329 LYS cc_start: 0.7370 (mtmm) cc_final: 0.7160 (mtmm) REVERT: K 346 LEU cc_start: 0.7961 (mm) cc_final: 0.7653 (mm) REVERT: K 391 LEU cc_start: 0.8290 (tp) cc_final: 0.8008 (tp) REVERT: K 403 ILE cc_start: 0.7547 (mm) cc_final: 0.7337 (mm) REVERT: K 408 ASP cc_start: 0.6873 (p0) cc_final: 0.6247 (p0) REVERT: M 128 MET cc_start: 0.0546 (ptt) cc_final: 0.0192 (ptt) REVERT: A 62 ILE cc_start: 0.7071 (mm) cc_final: 0.6717 (mm) REVERT: A 73 GLU cc_start: 0.8021 (tt0) cc_final: 0.7688 (tt0) REVERT: A 104 PHE cc_start: 0.7701 (m-80) cc_final: 0.7362 (m-80) REVERT: A 123 ASP cc_start: 0.6048 (m-30) cc_final: 0.4892 (m-30) REVERT: B 50 ILE cc_start: 0.7600 (tp) cc_final: 0.7269 (tp) REVERT: D 72 ILE cc_start: 0.7951 (pt) cc_final: 0.7644 (pt) REVERT: D 76 ILE cc_start: 0.8401 (pt) cc_final: 0.8179 (pt) REVERT: D 116 GLU cc_start: 0.7642 (pp20) cc_final: 0.7050 (pp20) REVERT: E 104 PHE cc_start: 0.7611 (m-80) cc_final: 0.7248 (m-10) REVERT: F 34 ILE cc_start: 0.8641 (tp) cc_final: 0.8164 (tp) REVERT: F 37 LEU cc_start: 0.7947 (mt) cc_final: 0.7587 (mt) REVERT: F 61 PHE cc_start: 0.7728 (t80) cc_final: 0.7452 (t80) REVERT: H 64 ILE cc_start: 0.6910 (mm) cc_final: 0.6621 (mm) REVERT: H 73 PHE cc_start: 0.6991 (m-10) cc_final: 0.6672 (m-10) outliers start: 1 outliers final: 1 residues processed: 314 average time/residue: 0.1617 time to fit residues: 70.5266 Evaluate side-chains 267 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 120 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 148 optimal weight: 0.3980 chunk 86 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN K 166 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.172630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.150854 restraints weight = 73471.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.153129 restraints weight = 58499.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.154091 restraints weight = 48349.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.155256 restraints weight = 41801.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.155957 restraints weight = 36434.720| |-----------------------------------------------------------------------------| r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5443 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 17855 Z= 0.178 Angle : 0.778 14.051 25347 Z= 0.427 Chirality : 0.044 0.213 2859 Planarity : 0.006 0.101 2191 Dihedral : 29.561 105.399 4760 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.17 % Allowed : 5.94 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.21), residues: 1320 helix: -1.96 (0.18), residues: 639 sheet: -1.72 (1.09), residues: 28 loop : -2.69 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 119 TYR 0.036 0.002 TYR B 72 PHE 0.031 0.002 PHE K 404 TRP 0.023 0.003 TRP K 353 HIS 0.011 0.001 HIS G 84 Details of bonding type rmsd covalent geometry : bond 0.00386 (17855) covalent geometry : angle 0.77765 (25347) hydrogen bonds : bond 0.06089 ( 741) hydrogen bonds : angle 4.85552 ( 1799) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 302 time to evaluate : 0.495 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 214 TYR cc_start: 0.6317 (t80) cc_final: 0.6107 (t80) REVERT: K 268 VAL cc_start: 0.7185 (m) cc_final: 0.6454 (t) REVERT: K 328 SER cc_start: 0.7838 (m) cc_final: 0.7404 (p) REVERT: K 346 LEU cc_start: 0.8294 (mm) cc_final: 0.8051 (mm) REVERT: K 391 LEU cc_start: 0.8354 (tp) cc_final: 0.8116 (tp) REVERT: K 408 ASP cc_start: 0.6987 (p0) cc_final: 0.6482 (p0) REVERT: M 128 MET cc_start: 0.0837 (ptt) cc_final: 0.0445 (ptt) REVERT: M 229 MET cc_start: 0.3541 (mmm) cc_final: 0.3331 (mmm) REVERT: A 73 GLU cc_start: 0.7894 (tt0) cc_final: 0.7570 (tt0) REVERT: A 104 PHE cc_start: 0.7566 (m-80) cc_final: 0.7276 (m-80) REVERT: A 109 LEU cc_start: 0.8299 (mm) cc_final: 0.8086 (tp) REVERT: B 50 ILE cc_start: 0.7766 (tp) cc_final: 0.7431 (tp) REVERT: C 32 LYS cc_start: 0.6440 (tptt) cc_final: 0.6195 (tptt) REVERT: D 116 GLU cc_start: 0.7569 (pp20) cc_final: 0.7175 (pp20) REVERT: E 104 PHE cc_start: 0.7416 (m-80) cc_final: 0.7165 (m-10) REVERT: F 34 ILE cc_start: 0.8267 (tp) cc_final: 0.8059 (tp) REVERT: F 61 PHE cc_start: 0.7705 (t80) cc_final: 0.7374 (t80) outliers start: 2 outliers final: 0 residues processed: 304 average time/residue: 0.1558 time to fit residues: 65.4188 Evaluate side-chains 259 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 96 optimal weight: 0.0170 chunk 134 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 0.0870 chunk 83 optimal weight: 4.9990 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN K 166 ASN M 252 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.175338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.154100 restraints weight = 75305.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.156073 restraints weight = 60637.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.157076 restraints weight = 51620.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.158587 restraints weight = 44593.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.159060 restraints weight = 37855.832| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17855 Z= 0.160 Angle : 0.753 11.781 25347 Z= 0.408 Chirality : 0.043 0.292 2859 Planarity : 0.005 0.063 2191 Dihedral : 29.331 101.798 4760 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.17 % Allowed : 5.60 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.21), residues: 1320 helix: -1.83 (0.18), residues: 649 sheet: -1.32 (1.18), residues: 28 loop : -2.58 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 63 TYR 0.036 0.002 TYR D 45 PHE 0.033 0.002 PHE K 404 TRP 0.018 0.002 TRP K 247 HIS 0.012 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00335 (17855) covalent geometry : angle 0.75285 (25347) hydrogen bonds : bond 0.05646 ( 741) hydrogen bonds : angle 4.60446 ( 1799) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 0.384 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 GLU cc_start: 0.3089 (tm-30) cc_final: 0.2662 (tm-30) REVERT: K 214 TYR cc_start: 0.6371 (t80) cc_final: 0.6122 (t80) REVERT: K 346 LEU cc_start: 0.8141 (mm) cc_final: 0.7665 (mm) REVERT: M 128 MET cc_start: 0.0551 (ptt) cc_final: 0.0210 (ptt) REVERT: M 229 MET cc_start: 0.3216 (mmm) cc_final: 0.2983 (mmm) REVERT: B 50 ILE cc_start: 0.7525 (tp) cc_final: 0.7275 (tp) REVERT: B 68 ASP cc_start: 0.7805 (m-30) cc_final: 0.7054 (m-30) REVERT: B 73 THR cc_start: 0.6784 (t) cc_final: 0.6045 (t) REVERT: B 88 TYR cc_start: 0.5399 (m-10) cc_final: 0.4715 (m-10) REVERT: B 90 LEU cc_start: 0.6380 (pp) cc_final: 0.6105 (pp) REVERT: C 33 ARG cc_start: 0.6959 (tmm160) cc_final: 0.6610 (tmm160) REVERT: D 87 ASN cc_start: 0.7755 (p0) cc_final: 0.7493 (p0) REVERT: D 119 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7570 (ttp80) REVERT: E 126 LEU cc_start: 0.7447 (mm) cc_final: 0.6583 (mm) REVERT: F 34 ILE cc_start: 0.8243 (tp) cc_final: 0.7970 (tp) REVERT: F 37 LEU cc_start: 0.7928 (mt) cc_final: 0.7673 (mt) REVERT: F 61 PHE cc_start: 0.7626 (t80) cc_final: 0.7346 (t80) outliers start: 2 outliers final: 0 residues processed: 305 average time/residue: 0.1643 time to fit residues: 69.4418 Evaluate side-chains 264 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 46 optimal weight: 0.0020 chunk 87 optimal weight: 0.0980 chunk 92 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 2 optimal weight: 0.0030 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN K 166 ASN ** M 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.175705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.154112 restraints weight = 74846.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.156188 restraints weight = 60715.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.157531 restraints weight = 49944.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.158875 restraints weight = 41012.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.159111 restraints weight = 37427.061| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5371 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17855 Z= 0.159 Angle : 0.753 11.272 25347 Z= 0.410 Chirality : 0.043 0.222 2859 Planarity : 0.005 0.054 2191 Dihedral : 29.155 95.417 4760 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.21), residues: 1320 helix: -1.82 (0.18), residues: 656 sheet: -1.83 (1.09), residues: 28 loop : -2.54 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 72 TYR 0.045 0.002 TYR B 72 PHE 0.030 0.002 PHE A 104 TRP 0.020 0.002 TRP K 353 HIS 0.006 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00333 (17855) covalent geometry : angle 0.75266 (25347) hydrogen bonds : bond 0.05645 ( 741) hydrogen bonds : angle 4.58475 ( 1799) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 0.321 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: K 172 MET cc_start: 0.5026 (ppp) cc_final: 0.4494 (pmm) REVERT: K 189 LEU cc_start: 0.6273 (pp) cc_final: 0.5674 (pt) REVERT: K 346 LEU cc_start: 0.8246 (mm) cc_final: 0.8033 (mm) REVERT: K 408 ASP cc_start: 0.7887 (p0) cc_final: 0.7660 (p0) REVERT: M 128 MET cc_start: 0.0392 (ptt) cc_final: -0.0049 (ptt) REVERT: A 61 LEU cc_start: 0.6215 (mp) cc_final: 0.5975 (mp) REVERT: B 72 TYR cc_start: 0.6920 (m-80) cc_final: 0.6587 (m-80) REVERT: B 88 TYR cc_start: 0.4890 (m-10) cc_final: 0.4629 (m-10) REVERT: B 90 LEU cc_start: 0.6449 (pp) cc_final: 0.6098 (pp) REVERT: D 68 PHE cc_start: 0.4961 (t80) cc_final: 0.4428 (t80) REVERT: D 76 ILE cc_start: 0.8573 (pt) cc_final: 0.8373 (pt) REVERT: D 119 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7226 (ttp80) REVERT: D 123 LYS cc_start: 0.7239 (pptt) cc_final: 0.6550 (pptt) REVERT: E 84 PHE cc_start: 0.6860 (m-10) cc_final: 0.6382 (m-10) REVERT: F 34 ILE cc_start: 0.8408 (tp) cc_final: 0.7856 (tp) REVERT: F 58 LEU cc_start: 0.7872 (tp) cc_final: 0.7561 (mt) REVERT: F 61 PHE cc_start: 0.7685 (t80) cc_final: 0.7282 (t80) REVERT: F 64 SER cc_start: 0.8285 (p) cc_final: 0.8080 (p) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.1442 time to fit residues: 58.9120 Evaluate side-chains 261 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 125 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 136 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN K 166 ASN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.177257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.154619 restraints weight = 89876.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.155793 restraints weight = 75750.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.156606 restraints weight = 68877.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.157470 restraints weight = 59513.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.158865 restraints weight = 52651.854| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5514 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17855 Z= 0.167 Angle : 0.762 11.781 25347 Z= 0.413 Chirality : 0.043 0.207 2859 Planarity : 0.005 0.090 2191 Dihedral : 29.049 90.902 4760 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.08 % Allowed : 2.26 % Favored : 97.66 % 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: -3.22 (0.21), residues: 1320 helix: -1.76 (0.18), residues: 653 sheet: -2.27 (1.03), residues: 28 loop : -2.52 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 36 TYR 0.038 0.002 TYR B 72 PHE 0.033 0.002 PHE E 104 TRP 0.044 0.004 TRP K 247 HIS 0.006 0.001 HIS D 112 Details of bonding type rmsd covalent geometry : bond 0.00356 (17855) covalent geometry : angle 0.76207 (25347) hydrogen bonds : bond 0.05711 ( 741) hydrogen bonds : angle 4.47826 ( 1799) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.347 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: symmetry clash revert: symmetry clash REVERT: N 87 CYS cc_start: 0.8635 (p) cc_final: 0.8416 (p) REVERT: K 189 LEU cc_start: 0.6294 (pp) cc_final: 0.5837 (pt) REVERT: K 200 PHE cc_start: 0.4088 (m-80) cc_final: 0.3882 (m-80) REVERT: K 333 LYS cc_start: 0.6504 (mmmt) cc_final: 0.5962 (mmmt) REVERT: K 346 LEU cc_start: 0.7828 (mm) cc_final: 0.7335 (mm) REVERT: K 358 ILE cc_start: 0.5385 (pt) cc_final: 0.4863 (pt) REVERT: M 289 TYR cc_start: 0.5866 (m-80) cc_final: 0.5643 (m-80) REVERT: A 62 ILE cc_start: 0.5708 (tt) cc_final: 0.5298 (tp) REVERT: B 68 ASP cc_start: 0.7603 (m-30) cc_final: 0.7132 (m-30) REVERT: B 88 TYR cc_start: 0.5566 (m-10) cc_final: 0.4664 (m-10) REVERT: D 72 ILE cc_start: 0.7941 (pt) cc_final: 0.7610 (pt) REVERT: D 119 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7115 (ttp80) REVERT: D 123 LYS cc_start: 0.6988 (pptt) cc_final: 0.6222 (pptt) REVERT: E 72 ARG cc_start: 0.5869 (mmm160) cc_final: 0.4845 (mmm160) REVERT: E 83 ARG cc_start: 0.7748 (mmp-170) cc_final: 0.7255 (mmm160) REVERT: E 104 PHE cc_start: 0.7140 (m-10) cc_final: 0.6364 (t80) REVERT: F 36 ARG cc_start: 0.7261 (pmt-80) cc_final: 0.7059 (pmt-80) REVERT: F 61 PHE cc_start: 0.7639 (t80) cc_final: 0.7290 (t80) REVERT: H 70 ASN cc_start: 0.7332 (m110) cc_final: 0.7092 (m110) REVERT: H 108 GLU cc_start: 0.6876 (pp20) cc_final: 0.6545 (pm20) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.1433 time to fit residues: 59.4900 Evaluate side-chains 257 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 121 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 49 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN K 166 ASN A 93 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.173956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.151264 restraints weight = 73896.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.153238 restraints weight = 58751.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.154751 restraints weight = 49282.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.155832 restraints weight = 42592.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.156680 restraints weight = 38171.186| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.7038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17855 Z= 0.182 Angle : 0.793 11.439 25347 Z= 0.430 Chirality : 0.045 0.261 2859 Planarity : 0.005 0.067 2191 Dihedral : 29.013 89.408 4760 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 0.17 % Allowed : 1.42 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.21), residues: 1320 helix: -1.80 (0.18), residues: 665 sheet: -4.15 (1.14), residues: 12 loop : -2.54 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 83 TYR 0.034 0.002 TYR K 233 PHE 0.029 0.002 PHE K 404 TRP 0.046 0.004 TRP K 247 HIS 0.006 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00389 (17855) covalent geometry : angle 0.79259 (25347) hydrogen bonds : bond 0.06092 ( 741) hydrogen bonds : angle 4.62750 ( 1799) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 289 time to evaluate : 0.397 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 189 LEU cc_start: 0.6482 (pp) cc_final: 0.5881 (pt) REVERT: K 316 TYR cc_start: 0.5903 (p90) cc_final: 0.5071 (p90) REVERT: K 333 LYS cc_start: 0.6726 (mmmt) cc_final: 0.6163 (mmmt) REVERT: K 346 LEU cc_start: 0.8170 (mm) cc_final: 0.7952 (mm) REVERT: M 128 MET cc_start: 0.0064 (ptm) cc_final: -0.0314 (ptm) REVERT: B 87 VAL cc_start: 0.6745 (p) cc_final: 0.6502 (p) REVERT: B 88 TYR cc_start: 0.5675 (m-10) cc_final: 0.5137 (m-10) REVERT: E 84 PHE cc_start: 0.7454 (m-10) cc_final: 0.6744 (m-10) REVERT: E 104 PHE cc_start: 0.7197 (m-10) cc_final: 0.6990 (m-10) REVERT: F 34 ILE cc_start: 0.8128 (tp) cc_final: 0.7633 (tp) REVERT: F 58 LEU cc_start: 0.7044 (mt) cc_final: 0.6558 (mt) REVERT: F 61 PHE cc_start: 0.7675 (t80) cc_final: 0.7307 (t80) REVERT: H 70 ASN cc_start: 0.7602 (m110) cc_final: 0.7316 (m110) REVERT: H 109 LEU cc_start: 0.7551 (tp) cc_final: 0.7348 (tp) outliers start: 2 outliers final: 1 residues processed: 291 average time/residue: 0.1468 time to fit residues: 59.5948 Evaluate side-chains 261 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 154 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN K 166 ASN A 93 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.174657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.152985 restraints weight = 72741.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.155185 restraints weight = 58508.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.156762 restraints weight = 46650.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.157375 restraints weight = 38970.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.157757 restraints weight = 36325.323| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 moved from start: 0.7444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17855 Z= 0.169 Angle : 0.781 11.366 25347 Z= 0.422 Chirality : 0.044 0.223 2859 Planarity : 0.005 0.068 2191 Dihedral : 28.976 89.538 4760 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.08 % Allowed : 0.92 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.21), residues: 1320 helix: -1.71 (0.19), residues: 652 sheet: -2.21 (1.25), residues: 18 loop : -2.59 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 242 TYR 0.035 0.002 TYR D 45 PHE 0.028 0.002 PHE K 404 TRP 0.044 0.003 TRP K 247 HIS 0.006 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00360 (17855) covalent geometry : angle 0.78080 (25347) hydrogen bonds : bond 0.05808 ( 741) hydrogen bonds : angle 4.49903 ( 1799) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.398 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 87 CYS cc_start: 0.8592 (p) cc_final: 0.8382 (p) REVERT: K 189 LEU cc_start: 0.6520 (pp) cc_final: 0.5963 (pt) REVERT: K 333 LYS cc_start: 0.6743 (mmmt) cc_final: 0.6230 (mmmt) REVERT: M 128 MET cc_start: 0.0454 (ptm) cc_final: -0.0004 (ptm) REVERT: B 88 TYR cc_start: 0.5877 (m-10) cc_final: 0.4752 (m-80) REVERT: B 90 LEU cc_start: 0.6674 (pp) cc_final: 0.6337 (pp) REVERT: D 72 ILE cc_start: 0.7910 (pt) cc_final: 0.7493 (pt) REVERT: D 86 TYR cc_start: 0.5960 (m-10) cc_final: 0.5749 (m-80) REVERT: D 123 LYS cc_start: 0.7161 (pptt) cc_final: 0.6389 (pptt) REVERT: E 45 THR cc_start: 0.4996 (p) cc_final: 0.4769 (p) REVERT: E 84 PHE cc_start: 0.7073 (m-10) cc_final: 0.6681 (m-10) REVERT: F 49 LEU cc_start: 0.6378 (mm) cc_final: 0.6066 (mm) REVERT: F 51 TYR cc_start: 0.6017 (m-80) cc_final: 0.5544 (m-10) REVERT: F 61 PHE cc_start: 0.7659 (t80) cc_final: 0.7383 (t80) REVERT: H 70 ASN cc_start: 0.7622 (m110) cc_final: 0.7416 (m110) outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.1524 time to fit residues: 60.5711 Evaluate side-chains 259 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 114 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 124 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 136 optimal weight: 0.1980 chunk 112 optimal weight: 0.9980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN K 166 ASN M 356 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.174918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.153504 restraints weight = 72745.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.155510 restraints weight = 59017.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.156988 restraints weight = 48212.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.158023 restraints weight = 39439.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.158260 restraints weight = 36329.020| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 moved from start: 0.7758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17855 Z= 0.169 Angle : 0.784 11.626 25347 Z= 0.425 Chirality : 0.044 0.224 2859 Planarity : 0.005 0.049 2191 Dihedral : 28.923 87.929 4760 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.08 % Allowed : 0.67 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.21), residues: 1320 helix: -1.58 (0.19), residues: 639 sheet: -4.24 (1.34), residues: 12 loop : -2.46 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 39 TYR 0.035 0.002 TYR K 233 PHE 0.028 0.002 PHE K 404 TRP 0.056 0.004 TRP K 247 HIS 0.007 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00363 (17855) covalent geometry : angle 0.78411 (25347) hydrogen bonds : bond 0.05818 ( 741) hydrogen bonds : angle 4.54227 ( 1799) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.481 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 87 CYS cc_start: 0.8505 (p) cc_final: 0.8262 (p) REVERT: K 189 LEU cc_start: 0.6418 (pp) cc_final: 0.5946 (pt) REVERT: K 314 MET cc_start: 0.7167 (ptt) cc_final: 0.6583 (ptt) REVERT: K 316 TYR cc_start: 0.6374 (p90) cc_final: 0.5885 (p90) REVERT: K 346 LEU cc_start: 0.8203 (mm) cc_final: 0.7972 (mm) REVERT: M 128 MET cc_start: 0.0407 (ptm) cc_final: -0.0032 (ptm) REVERT: B 61 PHE cc_start: 0.7635 (t80) cc_final: 0.7028 (t80) REVERT: B 88 TYR cc_start: 0.5929 (m-10) cc_final: 0.4805 (m-10) REVERT: C 33 ARG cc_start: 0.7768 (mmp80) cc_final: 0.7439 (mmp80) REVERT: D 72 ILE cc_start: 0.7956 (pt) cc_final: 0.7664 (pt) REVERT: D 123 LYS cc_start: 0.7126 (pptt) cc_final: 0.6576 (pptt) REVERT: E 45 THR cc_start: 0.4722 (p) cc_final: 0.4480 (p) REVERT: F 49 LEU cc_start: 0.6282 (mm) cc_final: 0.5978 (mm) REVERT: H 70 ASN cc_start: 0.7595 (m110) cc_final: 0.7382 (m110) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.1572 time to fit residues: 61.0164 Evaluate side-chains 254 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 128 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN K 166 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.175888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.154395 restraints weight = 73424.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.156434 restraints weight = 59644.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.157054 restraints weight = 49677.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.158031 restraints weight = 44254.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.159501 restraints weight = 39354.246| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5437 moved from start: 0.8023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17855 Z= 0.163 Angle : 0.786 11.587 25347 Z= 0.426 Chirality : 0.044 0.235 2859 Planarity : 0.005 0.051 2191 Dihedral : 28.873 86.494 4760 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.08 % Allowed : 0.75 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.21), residues: 1320 helix: -1.65 (0.19), residues: 652 sheet: -2.15 (1.31), residues: 18 loop : -2.46 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 72 TYR 0.043 0.002 TYR B 72 PHE 0.028 0.002 PHE K 404 TRP 0.038 0.003 TRP K 247 HIS 0.016 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00348 (17855) covalent geometry : angle 0.78639 (25347) hydrogen bonds : bond 0.05651 ( 741) hydrogen bonds : angle 4.48838 ( 1799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2623.62 seconds wall clock time: 46 minutes 15.92 seconds (2775.92 seconds total)