Starting phenix.real_space_refine on Sun Aug 24 06:27:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x32_38026/08_2025/8x32_38026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x32_38026/08_2025/8x32_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_38026/08_2025/8x32_38026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x32_38026/08_2025/8x32_38026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x32_38026/08_2025/8x32_38026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x32_38026/08_2025/8x32_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.88, per 1000 atoms: 0.23 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: 1.37 Conformation dependent library (CDL) restraints added in 514.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.00 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: 3.89 Time building geometry restraints manager: 1.88 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: 1.780 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 19.080 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.980 ------------------------------------------------------------------------------- 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 aren 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 : 0.498 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: 0.7638 (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: 0.4811 (mtmm) REVERT: M 68 ILE cc_start: 0.6356 (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: 0.7326 (m) cc_final: 0.6985 (m) REVERT: B 50 ILE cc_start: 0.8008 (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: 0.7633 (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: 0.8114 (mt) cc_final: 0.7712 (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: 0.6413 (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: 0.1836 time to fit residues: 97.7801 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 : 0.492 ------------------------------------------------------------------------------- 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 aren 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 : 0.553 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: 0.7439 (tp) REVERT: B 68 ASP cc_start: 0.7695 (p0) cc_final: 0.6684 (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: 0.1785 time to fit residues: 80.4495 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 : 0.507 ------------------------------------------------------------------------------- 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 aren 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 : 0.525 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: 0.8022 (tt0) cc_final: 0.7688 (tt0) REVERT: A 104 PHE cc_start: 0.7701 (m-80) cc_final: 0.7363 (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: 0.7643 (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: 0.8640 (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: 0.7451 (t80) REVERT: H 64 ILE cc_start: 0.6910 (mm) cc_final: 0.6621 (mm) REVERT: H 73 PHE cc_start: 0.6990 (m-10) cc_final: 0.6672 (m-10) outliers start: 1 outliers final: 1 residues processed: 314 average time/residue: 0.1831 time to fit residues: 80.1552 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 : 0.533 ------------------------------------------------------------------------------- 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 aren 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 : 0.392 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: 0.6318 (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: 0.8050 (mm) REVERT: K 391 LEU cc_start: 0.8354 (tp) cc_final: 0.8116 (tp) REVERT: K 408 ASP cc_start: 0.6986 (p0) cc_final: 0.6481 (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: 0.3330 (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: 0.8298 (mm) cc_final: 0.8085 (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 64 ILE cc_start: 0.7151 (tt) cc_final: 0.6951 (pt) 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: 0.1813 time to fit residues: 76.0149 Evaluate side-chains 258 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 = 0.4663 r_free = 0.4663 target = 0.175083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.154101 restraints weight = 76525.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.156557 restraints weight = 59566.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.157651 restraints weight = 47686.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.159015 restraints weight = 41012.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.159729 restraints weight = 34845.453| |-----------------------------------------------------------------------------| r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5325 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17855 Z= 0.159 Angle : 0.752 11.610 25347 Z= 0.408 Chirality : 0.043 0.282 2859 Planarity : 0.005 0.063 2191 Dihedral : 29.340 101.980 4760 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.17 % Allowed : 5.52 % Favored : 94.31 % 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 aren not related in a simple way. whole: -3.28 (0.21), residues: 1320 helix: -1.83 (0.18), residues: 649 sheet: -1.34 (1.17), residues: 28 loop : -2.58 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 63 TYR 0.034 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 E 113 Details of bonding type rmsd covalent geometry : bond 0.00336 (17855) covalent geometry : angle 0.75197 (25347) hydrogen bonds : bond 0.05633 ( 741) hydrogen bonds : angle 4.61794 ( 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 : 0.440 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: 0.3054 (tm-30) cc_final: 0.2622 (tm-30) REVERT: K 214 TYR cc_start: 0.6392 (t80) cc_final: 0.6136 (t80) REVERT: K 346 LEU cc_start: 0.8179 (mm) cc_final: 0.7578 (mm) REVERT: M 128 MET cc_start: 0.0453 (ptt) cc_final: 0.0120 (ptt) REVERT: M 229 MET cc_start: 0.3216 (mmm) cc_final: 0.2981 (mmm) REVERT: B 50 ILE cc_start: 0.7573 (tp) cc_final: 0.7322 (tp) REVERT: B 68 ASP cc_start: 0.7805 (m-30) cc_final: 0.7064 (m-30) REVERT: B 73 THR cc_start: 0.6817 (t) cc_final: 0.6102 (t) REVERT: B 88 TYR cc_start: 0.5490 (m-10) cc_final: 0.4832 (m-10) REVERT: B 90 LEU cc_start: 0.6420 (pp) cc_final: 0.6133 (pp) REVERT: C 33 ARG cc_start: 0.6986 (tmm160) cc_final: 0.6623 (tmm160) REVERT: D 75 ARG cc_start: 0.6299 (ttt180) cc_final: 0.5883 (ttt180) REVERT: D 87 ASN cc_start: 0.7748 (p0) cc_final: 0.7481 (p0) REVERT: D 119 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7559 (ttp80) REVERT: E 126 LEU cc_start: 0.7436 (mm) cc_final: 0.6584 (mm) REVERT: F 34 ILE cc_start: 0.8245 (tp) cc_final: 0.7964 (tp) REVERT: F 37 LEU cc_start: 0.7902 (mt) cc_final: 0.7635 (mt) REVERT: F 61 PHE cc_start: 0.7605 (t80) cc_final: 0.7331 (t80) outliers start: 2 outliers final: 0 residues processed: 305 average time/residue: 0.1800 time to fit residues: 76.1235 Evaluate side-chains 267 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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: 0.0010 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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** ** F 93 GLN ** 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 = 0.4658 r_free = 0.4658 target = 0.174619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.152373 restraints weight = 72729.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.154653 restraints weight = 57464.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.155601 restraints weight = 47725.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.157126 restraints weight = 42340.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.157928 restraints weight = 35576.418| |-----------------------------------------------------------------------------| r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5444 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17855 Z= 0.165 Angle : 0.764 11.308 25347 Z= 0.417 Chirality : 0.044 0.282 2859 Planarity : 0.005 0.053 2191 Dihedral : 29.157 96.473 4760 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.40 % 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 aren not related in a simple way. whole: -3.24 (0.21), residues: 1320 helix: -1.77 (0.18), residues: 646 sheet: -1.93 (1.07), residues: 28 loop : -2.57 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 30 TYR 0.045 0.002 TYR B 72 PHE 0.032 0.002 PHE A 104 TRP 0.027 0.002 TRP K 353 HIS 0.007 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00350 (17855) covalent geometry : angle 0.76387 (25347) hydrogen bonds : bond 0.05816 ( 741) hydrogen bonds : angle 4.63714 ( 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 299 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.555 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: K 189 LEU cc_start: 0.6530 (pp) cc_final: 0.5920 (pt) REVERT: K 214 TYR cc_start: 0.6475 (t80) cc_final: 0.6232 (t80) REVERT: K 316 TYR cc_start: 0.5591 (p90) cc_final: 0.5358 (p90) REVERT: K 346 LEU cc_start: 0.8186 (mm) cc_final: 0.7608 (mm) REVERT: M 128 MET cc_start: 0.0561 (ptt) cc_final: 0.0076 (ptt) REVERT: A 61 LEU cc_start: 0.6322 (mp) cc_final: 0.6023 (mp) REVERT: B 88 TYR cc_start: 0.5078 (m-10) cc_final: 0.4867 (m-10) REVERT: B 90 LEU cc_start: 0.6510 (pp) cc_final: 0.6216 (pp) REVERT: C 63 GLU cc_start: 0.3814 (pm20) cc_final: 0.3613 (pm20) REVERT: D 119 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7608 (ttp80) REVERT: E 84 PHE cc_start: 0.6962 (m-10) cc_final: 0.6461 (m-10) REVERT: F 34 ILE cc_start: 0.8519 (tp) cc_final: 0.7964 (tp) REVERT: F 61 PHE cc_start: 0.7722 (t80) cc_final: 0.7322 (t80) REVERT: H 70 ASN cc_start: 0.7499 (m110) cc_final: 0.7231 (m110) REVERT: H 108 GLU cc_start: 0.7051 (pp20) cc_final: 0.6767 (pm20) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.1818 time to fit residues: 75.2752 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 : 0.481 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 0.0040 chunk 124 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.175980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.153881 restraints weight = 72766.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.155868 restraints weight = 59164.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.156925 restraints weight = 49766.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.158318 restraints weight = 43700.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.158891 restraints weight = 37610.756| |-----------------------------------------------------------------------------| r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 moved from start: 0.6777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17855 Z= 0.159 Angle : 0.765 12.735 25347 Z= 0.413 Chirality : 0.043 0.203 2859 Planarity : 0.005 0.060 2191 Dihedral : 29.071 91.892 4760 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.08 % Allowed : 2.51 % Favored : 97.41 % 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 aren not related in a simple way. whole: -3.23 (0.21), residues: 1320 helix: -1.71 (0.18), residues: 650 sheet: -2.26 (1.00), residues: 29 loop : -2.59 (0.22), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 72 TYR 0.037 0.002 TYR B 72 PHE 0.032 0.002 PHE E 104 TRP 0.036 0.003 TRP K 247 HIS 0.007 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00334 (17855) covalent geometry : angle 0.76522 (25347) hydrogen bonds : bond 0.05615 ( 741) hydrogen bonds : angle 4.45302 ( 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 303 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 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: L 35 GLU cc_start: 0.2992 (tm-30) cc_final: 0.2541 (tm-30) REVERT: K 189 LEU cc_start: 0.6236 (pp) cc_final: 0.5830 (pt) REVERT: K 333 LYS cc_start: 0.6498 (mmmt) cc_final: 0.5981 (mmmt) REVERT: K 346 LEU cc_start: 0.8208 (mm) cc_final: 0.8002 (mm) REVERT: B 87 VAL cc_start: 0.6763 (p) cc_final: 0.6469 (p) REVERT: B 88 TYR cc_start: 0.5512 (m-10) cc_final: 0.5053 (m-10) REVERT: C 97 SER cc_start: 0.6295 (p) cc_final: 0.6046 (m) REVERT: C 102 THR cc_start: 0.6019 (p) cc_final: 0.5438 (p) REVERT: D 72 ILE cc_start: 0.7977 (pt) cc_final: 0.7594 (pt) REVERT: E 104 PHE cc_start: 0.7166 (m-10) cc_final: 0.6353 (t80) REVERT: F 61 PHE cc_start: 0.7721 (t80) cc_final: 0.7376 (t80) REVERT: G 97 SER cc_start: 0.6342 (t) cc_final: 0.6119 (m) REVERT: H 70 ASN cc_start: 0.7460 (m110) cc_final: 0.7222 (m110) REVERT: H 108 GLU cc_start: 0.7018 (pp20) cc_final: 0.6629 (pm20) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.1856 time to fit residues: 77.3155 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 : 0.506 ------------------------------------------------------------------------------- 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: 8.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ** 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 = 0.4649 r_free = 0.4649 target = 0.173917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.151347 restraints weight = 72928.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.153495 restraints weight = 58445.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.154402 restraints weight = 48574.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.155899 restraints weight = 43275.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.156433 restraints weight = 36880.496| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17855 Z= 0.187 Angle : 0.799 11.345 25347 Z= 0.434 Chirality : 0.045 0.444 2859 Planarity : 0.006 0.066 2191 Dihedral : 28.985 89.813 4760 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.08 % Allowed : 1.76 % Favored : 98.16 % 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 aren not related in a simple way. whole: -3.20 (0.21), residues: 1320 helix: -1.76 (0.18), residues: 654 sheet: -4.00 (1.17), residues: 12 loop : -2.47 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 72 TYR 0.035 0.002 TYR B 72 PHE 0.044 0.002 PHE K 205 TRP 0.052 0.004 TRP K 247 HIS 0.005 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00402 (17855) covalent geometry : angle 0.79946 (25347) hydrogen bonds : bond 0.06207 ( 741) hydrogen bonds : angle 4.51380 ( 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 285 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.452 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: K 189 LEU cc_start: 0.6452 (pp) cc_final: 0.5871 (pt) REVERT: K 333 LYS cc_start: 0.6723 (mmmt) cc_final: 0.6180 (mmmt) REVERT: K 346 LEU cc_start: 0.8087 (mm) cc_final: 0.7702 (mm) REVERT: M 128 MET cc_start: 0.0210 (ptm) cc_final: -0.0203 (ptm) REVERT: B 87 VAL cc_start: 0.6762 (p) cc_final: 0.6396 (p) REVERT: B 88 TYR cc_start: 0.6225 (m-10) cc_final: 0.5393 (m-10) REVERT: E 84 PHE cc_start: 0.7407 (m-10) cc_final: 0.7141 (m-10) REVERT: E 104 PHE cc_start: 0.7171 (m-10) cc_final: 0.6912 (m-10) REVERT: F 34 ILE cc_start: 0.8162 (tp) cc_final: 0.7706 (tp) REVERT: F 61 PHE cc_start: 0.7685 (t80) cc_final: 0.7325 (t80) REVERT: G 97 SER cc_start: 0.6482 (t) cc_final: 0.6198 (m) REVERT: H 70 ASN cc_start: 0.7607 (m110) cc_final: 0.7299 (m110) REVERT: H 108 GLU cc_start: 0.7022 (pp20) cc_final: 0.6504 (pm20) outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.1801 time to fit residues: 71.1605 Evaluate side-chains 255 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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: 1.9990 chunk 122 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 140 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** B 93 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.174426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.152975 restraints weight = 73502.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.155176 restraints weight = 58590.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.156127 restraints weight = 47587.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.157406 restraints weight = 40861.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.157671 restraints weight = 36360.015| |-----------------------------------------------------------------------------| r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5486 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17855 Z= 0.173 Angle : 0.792 11.161 25347 Z= 0.430 Chirality : 0.045 0.224 2859 Planarity : 0.006 0.059 2191 Dihedral : 28.975 88.803 4760 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.17 % Allowed : 0.50 % Favored : 99.33 % 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 aren not related in a simple way. whole: -3.25 (0.21), residues: 1320 helix: -1.77 (0.18), residues: 666 sheet: -1.97 (1.29), residues: 18 loop : -2.59 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 72 TYR 0.036 0.002 TYR B 72 PHE 0.028 0.002 PHE K 404 TRP 0.041 0.004 TRP K 247 HIS 0.006 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00369 (17855) covalent geometry : angle 0.79155 (25347) hydrogen bonds : bond 0.05967 ( 741) hydrogen bonds : angle 4.55555 ( 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 287 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 285 time to evaluate : 0.552 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: K 189 LEU cc_start: 0.6548 (pp) cc_final: 0.6012 (pt) REVERT: K 214 TYR cc_start: 0.6475 (t80) cc_final: 0.6248 (t80) REVERT: K 333 LYS cc_start: 0.6752 (mmmt) cc_final: 0.6276 (mmmt) REVERT: M 128 MET cc_start: 0.0264 (ptm) cc_final: -0.0199 (ptm) REVERT: M 144 THR cc_start: 0.6539 (p) cc_final: 0.6333 (p) REVERT: M 164 MET cc_start: 0.3710 (ttp) cc_final: 0.3011 (ttp) REVERT: B 61 PHE cc_start: 0.7626 (t80) cc_final: 0.7185 (t80) REVERT: B 87 VAL cc_start: 0.6914 (p) cc_final: 0.6342 (p) REVERT: C 35 LEU cc_start: 0.7654 (pp) cc_final: 0.7454 (pp) REVERT: C 97 SER cc_start: 0.6640 (p) cc_final: 0.6030 (p) REVERT: C 102 THR cc_start: 0.6080 (p) cc_final: 0.5756 (t) REVERT: D 72 ILE cc_start: 0.7871 (pt) cc_final: 0.7472 (pt) REVERT: D 116 GLU cc_start: 0.7224 (pp20) cc_final: 0.6804 (pp20) REVERT: E 84 PHE cc_start: 0.7336 (m-10) cc_final: 0.7063 (m-10) REVERT: E 100 LEU cc_start: 0.7647 (pp) cc_final: 0.7371 (pp) REVERT: F 34 ILE cc_start: 0.8153 (tp) cc_final: 0.7654 (tp) REVERT: F 61 PHE cc_start: 0.7644 (t80) cc_final: 0.7329 (t80) REVERT: G 97 SER cc_start: 0.6005 (t) cc_final: 0.5575 (m) outliers start: 2 outliers final: 1 residues processed: 287 average time/residue: 0.1746 time to fit residues: 70.0240 Evaluate side-chains 256 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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: 0.9990 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 A 93 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.174018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.152266 restraints weight = 72225.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.154587 restraints weight = 58130.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.155759 restraints weight = 46886.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.156661 restraints weight = 39921.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.156986 restraints weight = 36330.820| |-----------------------------------------------------------------------------| r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.7814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17855 Z= 0.177 Angle : 0.795 11.642 25347 Z= 0.430 Chirality : 0.044 0.229 2859 Planarity : 0.006 0.070 2191 Dihedral : 28.919 89.708 4760 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.08 % Allowed : 1.09 % Favored : 98.83 % 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 aren not related in a simple way. whole: -2.97 (0.21), residues: 1320 helix: -1.51 (0.19), residues: 632 sheet: -2.26 (1.35), residues: 18 loop : -2.45 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 72 TYR 0.035 0.002 TYR D 45 PHE 0.035 0.002 PHE K 205 TRP 0.072 0.004 TRP K 247 HIS 0.007 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00381 (17855) covalent geometry : angle 0.79532 (25347) hydrogen bonds : bond 0.06107 ( 741) hydrogen bonds : angle 4.53868 ( 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 288 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 0.516 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: K 189 LEU cc_start: 0.6458 (pp) cc_final: 0.5947 (pt) REVERT: K 257 LEU cc_start: 0.3818 (tp) cc_final: 0.3609 (tp) REVERT: K 358 ILE cc_start: 0.5908 (pt) cc_final: 0.5565 (pt) REVERT: K 403 ILE cc_start: 0.7560 (mp) cc_final: 0.7349 (mm) REVERT: K 408 ASP cc_start: 0.8089 (p0) cc_final: 0.7678 (p0) REVERT: M 128 MET cc_start: 0.0551 (ptm) cc_final: 0.0006 (ptm) REVERT: B 50 ILE cc_start: 0.8077 (tp) cc_final: 0.7642 (mm) REVERT: C 35 LEU cc_start: 0.7536 (pp) cc_final: 0.7310 (pp) REVERT: C 97 SER cc_start: 0.6942 (p) cc_final: 0.6682 (m) REVERT: C 102 THR cc_start: 0.6722 (p) cc_final: 0.6356 (t) REVERT: D 72 ILE cc_start: 0.7902 (pt) cc_final: 0.7429 (pt) REVERT: E 50 GLU cc_start: 0.4913 (tp30) cc_final: 0.4005 (tp30) REVERT: E 100 LEU cc_start: 0.7794 (pp) cc_final: 0.7388 (pp) REVERT: F 34 ILE cc_start: 0.8298 (tp) cc_final: 0.7899 (tp) REVERT: F 49 LEU cc_start: 0.6570 (mm) cc_final: 0.6307 (mm) REVERT: F 51 TYR cc_start: 0.6133 (m-80) cc_final: 0.5601 (m-10) REVERT: F 61 PHE cc_start: 0.7697 (t80) cc_final: 0.7350 (t80) REVERT: F 67 ARG cc_start: 0.6677 (mmt-90) cc_final: 0.5711 (mmt-90) REVERT: G 97 SER cc_start: 0.5626 (t) cc_final: 0.5310 (m) REVERT: H 70 ASN cc_start: 0.7693 (m110) cc_final: 0.7337 (m110) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.1783 time to fit residues: 71.2256 Evaluate side-chains 256 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 0.2980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 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** A 93 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 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 = 0.4656 r_free = 0.4656 target = 0.175060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.153309 restraints weight = 73433.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.155468 restraints weight = 59343.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.156760 restraints weight = 48379.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.157661 restraints weight = 42847.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.158282 restraints weight = 37713.156| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.8128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17855 Z= 0.170 Angle : 0.797 12.647 25347 Z= 0.431 Chirality : 0.044 0.328 2859 Planarity : 0.006 0.089 2191 Dihedral : 28.896 86.791 4760 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % 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 aren not related in a simple way. whole: -2.89 (0.21), residues: 1320 helix: -1.42 (0.19), residues: 631 sheet: -2.09 (1.36), residues: 18 loop : -2.43 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 72 TYR 0.035 0.002 TYR D 45 PHE 0.028 0.002 PHE K 404 TRP 0.046 0.004 TRP K 247 HIS 0.007 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00366 (17855) covalent geometry : angle 0.79670 (25347) hydrogen bonds : bond 0.05811 ( 741) hydrogen bonds : angle 4.53351 ( 1799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3045.80 seconds wall clock time: 53 minutes 40.35 seconds (3220.35 seconds total)