Starting phenix.real_space_refine on Sun Jun 15 18:38:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x32_38026/06_2025/8x32_38026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x32_38026/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x32_38026/06_2025/8x32_38026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x32_38026/06_2025/8x32_38026.map" model { file = "/net/cci-nas-00/data/ceres_data/8x32_38026/06_2025/8x32_38026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x32_38026/06_2025/8x32_38026.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.022 sd= 0.415 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1064 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 23 5.16 5 C 9819 2.51 5 N 3043 2.21 5 O 3769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.87, per 1000 atoms: 0.58 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: 4.11 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 7.44 Creating SS restraints... Processing helix chain 'N' and resid 3 through 10 removed outlier: 4.260A pdb=" N LEU N 7 " --> pdb=" O PRO N 3 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN N 9 " --> pdb=" O LEU N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 29 removed outlier: 4.259A pdb=" N LEU N 25 " --> pdb=" O PHE N 21 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLU N 27 " --> pdb=" O TYR N 23 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE N 28 " --> pdb=" O LEU N 24 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 39 removed outlier: 3.772A pdb=" N GLU N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 4.072A pdb=" N LYS N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS N 87 " --> pdb=" O GLN N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 82 through 87' Processing helix chain 'N' and resid 87 through 92 Processing helix chain 'N' and resid 94 through 96 No H-bonds generated for 'chain 'N' and resid 94 through 96' Processing helix chain 'N' and resid 97 through 105 removed outlier: 4.077A pdb=" N LEU N 101 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN N 102 " --> pdb=" O ALA N 98 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 111 removed outlier: 4.029A pdb=" N ALA N 109 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 212 through 217 Processing helix chain 'K' and resid 246 through 259 removed outlier: 4.018A pdb=" N ASN K 250 " --> pdb=" O THR K 246 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU K 251 " --> pdb=" O TRP K 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N CYS K 252 " --> pdb=" O CYS K 248 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU K 253 " --> pdb=" O ARG K 249 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER K 255 " --> pdb=" O LEU K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 318 Processing helix chain 'K' and resid 323 through 332 removed outlier: 3.744A pdb=" N LEU K 327 " --> pdb=" O PHE K 323 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS K 329 " --> pdb=" O TYR K 325 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS K 330 " --> pdb=" O GLU K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 363 removed outlier: 4.863A pdb=" N ALA K 351 " --> pdb=" O LEU K 347 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP K 355 " --> pdb=" O ALA K 351 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR K 356 " --> pdb=" O TYR K 352 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU K 357 " --> pdb=" O TRP K 353 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE K 358 " --> pdb=" O SER K 354 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU K 360 " --> pdb=" O THR K 356 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU K 361 " --> pdb=" O LEU K 357 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU K 363 " --> pdb=" O THR K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 385 Processing helix chain 'K' and resid 388 through 392 Processing helix chain 'K' and resid 414 through 419 Processing helix chain 'M' and resid 153 through 159 Processing helix chain 'M' and resid 165 through 170 removed outlier: 4.009A pdb=" N GLU M 169 " --> pdb=" O ASP M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 196 removed outlier: 3.884A pdb=" N LEU M 192 " --> pdb=" O GLU M 188 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER M 194 " --> pdb=" O GLU M 190 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE M 196 " --> pdb=" O LEU M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 214 removed outlier: 3.864A pdb=" N ILE M 214 " --> pdb=" O PRO M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 219 Processing helix chain 'M' and resid 220 through 225 removed outlier: 3.886A pdb=" N ILE M 225 " --> pdb=" O LYS M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 259 removed outlier: 3.873A pdb=" N GLN M 258 " --> pdb=" O PRO M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 272 removed outlier: 3.775A pdb=" N ILE M 268 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS M 270 " --> pdb=" O GLN M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 275 No H-bonds generated for 'chain 'M' and resid 273 through 275' Processing helix chain 'M' and resid 276 through 281 removed outlier: 4.090A pdb=" N GLU M 281 " --> pdb=" O ASP M 277 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 287 Processing helix chain 'M' and resid 328 through 332 removed outlier: 3.659A pdb=" N SER M 331 " --> pdb=" O ILE M 328 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN M 332 " --> pdb=" O LEU M 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 328 through 332' Processing helix chain 'M' and resid 333 through 339 removed outlier: 3.740A pdb=" N ALA M 336 " --> pdb=" O ARG M 333 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS M 338 " --> pdb=" O ARG M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 349 Processing helix chain 'M' and resid 352 through 357 Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.129A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 4.236A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.781A pdb=" N ILE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.975A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 48 through 61 removed outlier: 3.751A pdb=" N ALA C 55 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL C 56 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.668A pdb=" N ALA C 72 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 73 " --> pdb=" O ASN C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 73' Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.937A pdb=" N GLU C 94 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 58 through 87 Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 107 through 127 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.501A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.513A pdb=" N ILE E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.795A pdb=" N ASP F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 19 through 23 Processing helix chain 'G' and resid 28 through 39 Processing helix chain 'G' and resid 47 through 50 Processing helix chain 'G' and resid 51 through 57 removed outlier: 3.596A pdb=" N LEU G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 67 removed outlier: 3.844A pdb=" N LEU G 65 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 74 removed outlier: 4.340A pdb=" N ALA G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 91 removed outlier: 4.003A pdb=" N LEU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 97 removed outlier: 4.413A pdb=" N ASP G 96 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 52 removed outlier: 4.405A pdb=" N ILE H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 84 Processing helix chain 'H' and resid 93 through 104 removed outlier: 4.064A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 123 Processing sheet with id=AA1, first strand: chain 'K' and resid 170 through 172 removed outlier: 6.759A pdb=" N ILE K 171 " --> pdb=" O ILE K 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 226 through 230 removed outlier: 5.433A pdb=" N GLU K 227 " --> pdb=" O GLU K 238 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU K 238 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR K 229 " --> pdb=" O PHE K 236 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR K 274 " --> pdb=" O TYR K 289 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYR K 289 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET K 276 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR K 289 " --> pdb=" O LEU K 306 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU K 306 " --> pdb=" O TYR K 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.420A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 397 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 226 stacking parallelities Total time for adding SS restraints: 6.72 Time building geometry restraints manager: 4.93 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 44.300 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.610 ------------------------------------------------------------------------------- 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 : 15.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.037 0.006 TRP K 353 HIS 0.025 0.004 HIS G 84 PHE 0.060 0.005 PHE K 404 TYR 0.057 0.005 TYR H 124 ARG 0.031 0.002 ARG G 21 Details of bonding type rmsd hydrogen bonds : bond 0.22712 ( 741) hydrogen bonds : angle 7.83661 ( 1799) covalent geometry : bond 0.01250 (17855) covalent geometry : angle 1.47132 (25347) *********************** 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 : 1.261 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: 0.8828 (tp) REVERT: M 67 LYS cc_start: 0.6024 (tmmt) cc_final: 0.4812 (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: 0.2290 (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: 0.6988 (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: 0.7049 (ptp-170) REVERT: B 68 ASP cc_start: 0.7633 (p0) cc_final: 0.7332 (m-30) REVERT: C 52 TYR cc_start: 0.8085 (t80) cc_final: 0.7756 (t80) REVERT: C 102 THR cc_start: 0.7453 (p) cc_final: 0.7187 (t) REVERT: D 39 THR cc_start: 0.6777 (t) cc_final: 0.6141 (t) REVERT: D 64 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6636 (mt) REVERT: D 68 PHE cc_start: 0.6132 (t80) cc_final: 0.5683 (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: 0.8523 (tp) REVERT: F 37 LEU cc_start: 0.8114 (mt) cc_final: 0.7716 (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: 0.7981 (tp) REVERT: F 61 PHE cc_start: 0.7992 (t80) cc_final: 0.7768 (t80) REVERT: G 35 LEU cc_start: 0.5049 (mp) cc_final: 0.4710 (tp) REVERT: G 87 LEU cc_start: 0.8127 (pp) cc_final: 0.7800 (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: 0.3700 time to fit residues: 195.5441 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 : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.8980 chunk 118 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 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 9 GLN N 16 ASN ** K 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.172710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.151214 restraints weight = 89196.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.152179 restraints weight = 74440.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.153059 restraints weight = 67607.753| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.3252 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= 0.210 Angle : 0.873 13.578 25347 Z= 0.483 Chirality : 0.047 0.262 2859 Planarity : 0.007 0.095 2191 Dihedral : 30.169 119.565 4760 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.50 % Allowed : 7.78 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.19), residues: 1320 helix: -2.73 (0.17), residues: 602 sheet: -1.11 (1.40), residues: 19 loop : -2.83 (0.21), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP K 353 HIS 0.015 0.001 HIS G 38 PHE 0.044 0.003 PHE K 404 TYR 0.032 0.003 TYR D 45 ARG 0.008 0.001 ARG D 119 Details of bonding type rmsd hydrogen bonds : bond 0.07357 ( 741) hydrogen bonds : angle 5.83034 ( 1799) covalent geometry : bond 0.00436 (17855) covalent geometry : angle 0.87325 (25347) *********************** 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 326 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 320 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 205 PHE cc_start: 0.5119 (m-10) cc_final: 0.3987 (m-80) REVERT: K 311 TYR cc_start: 0.2990 (t80) cc_final: 0.2707 (t80) REVERT: K 316 TYR cc_start: 0.4853 (p90) cc_final: 0.4603 (p90) REVERT: K 328 SER cc_start: 0.7712 (m) cc_final: 0.7286 (p) REVERT: K 329 LYS cc_start: 0.7272 (mtmm) cc_final: 0.7005 (mtmm) REVERT: K 391 LEU cc_start: 0.8202 (tp) cc_final: 0.7956 (tp) REVERT: M 72 ASN cc_start: 0.6601 (t0) cc_final: 0.6370 (t0) REVERT: M 289 TYR cc_start: 0.5822 (m-80) cc_final: 0.5518 (m-80) REVERT: A 52 ARG cc_start: 0.7619 (tpp80) cc_final: 0.7412 (tpp80) REVERT: A 62 ILE cc_start: 0.7438 (mm) cc_final: 0.7101 (mm) REVERT: A 118 THR cc_start: 0.6764 (m) cc_final: 0.6421 (m) REVERT: B 50 ILE cc_start: 0.7731 (tp) cc_final: 0.7529 (tp) REVERT: B 68 ASP cc_start: 0.7716 (p0) cc_final: 0.6729 (m-30) REVERT: D 87 ASN cc_start: 0.7941 (p0) cc_final: 0.7707 (p0) REVERT: D 116 GLU cc_start: 0.7283 (pp20) cc_final: 0.6948 (pp20) REVERT: E 85 GLN cc_start: 0.4554 (mm110) cc_final: 0.4159 (mm110) REVERT: E 100 LEU cc_start: 0.7556 (pp) cc_final: 0.7334 (pp) REVERT: E 104 PHE cc_start: 0.7666 (m-80) cc_final: 0.7402 (m-10) REVERT: F 34 ILE cc_start: 0.8808 (tp) cc_final: 0.8387 (tp) REVERT: F 37 LEU cc_start: 0.7969 (mt) cc_final: 0.7747 (mt) REVERT: F 66 ILE cc_start: 0.7178 (pt) cc_final: 0.6965 (pt) REVERT: G 35 LEU cc_start: 0.4794 (mp) cc_final: 0.4501 (tp) REVERT: H 66 ASN cc_start: 0.7221 (t0) cc_final: 0.6863 (t0) REVERT: H 112 HIS cc_start: 0.5677 (t70) cc_final: 0.5437 (t70) outliers start: 6 outliers final: 1 residues processed: 325 average time/residue: 0.3598 time to fit residues: 162.9202 Evaluate side-chains 269 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 54 optimal weight: 0.0170 chunk 140 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- 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 168 ASN K 285 HIS K 401 HIS M 252 GLN A 55 GLN A 85 GLN ** A 113 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.170046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.147045 restraints weight = 88060.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.148674 restraints weight = 70722.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.149640 restraints weight = 59906.843| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17855 Z= 0.253 Angle : 0.887 12.864 25347 Z= 0.492 Chirality : 0.049 0.279 2859 Planarity : 0.008 0.148 2191 Dihedral : 29.909 116.308 4760 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.42 % Allowed : 8.78 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.20), residues: 1320 helix: -2.51 (0.17), residues: 638 sheet: -2.37 (1.23), residues: 20 loop : -2.73 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP K 247 HIS 0.014 0.002 HIS G 38 PHE 0.041 0.003 PHE K 404 TYR 0.037 0.003 TYR D 86 ARG 0.013 0.001 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.08176 ( 741) hydrogen bonds : angle 5.64959 ( 1799) covalent geometry : bond 0.00554 (17855) covalent geometry : angle 0.88703 (25347) *********************** 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 324 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 319 time to evaluate : 1.314 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 268 VAL cc_start: 0.6795 (m) cc_final: 0.6153 (t) REVERT: K 346 LEU cc_start: 0.7847 (mm) cc_final: 0.7507 (mm) REVERT: K 393 ILE cc_start: 0.6913 (tp) cc_final: 0.6494 (tp) REVERT: K 408 ASP cc_start: 0.7097 (p0) cc_final: 0.6477 (p0) REVERT: M 128 MET cc_start: 0.0647 (ptt) cc_final: 0.0153 (ptt) REVERT: A 118 THR cc_start: 0.7106 (m) cc_final: 0.6874 (m) REVERT: A 123 ASP cc_start: 0.6324 (m-30) cc_final: 0.4832 (m-30) REVERT: B 50 ILE cc_start: 0.7748 (tp) cc_final: 0.7378 (tp) REVERT: D 103 LEU cc_start: 0.7715 (tp) cc_final: 0.7420 (tp) REVERT: D 122 THR cc_start: 0.8264 (p) cc_final: 0.8049 (p) REVERT: E 69 ARG cc_start: 0.7994 (ptt90) cc_final: 0.7734 (ptt90) REVERT: E 72 ARG cc_start: 0.6051 (tpt170) cc_final: 0.5824 (tpt170) REVERT: E 84 PHE cc_start: 0.7841 (m-10) cc_final: 0.7492 (m-10) REVERT: E 104 PHE cc_start: 0.7711 (m-80) cc_final: 0.7343 (m-10) REVERT: E 120 GLN cc_start: 0.3744 (OUTLIER) cc_final: 0.2805 (pp30) REVERT: F 34 ILE cc_start: 0.8604 (tp) cc_final: 0.8353 (tp) REVERT: F 37 LEU cc_start: 0.8004 (mt) cc_final: 0.7740 (mt) REVERT: F 58 LEU cc_start: 0.8350 (tp) cc_final: 0.7669 (tp) REVERT: H 38 GLU cc_start: 0.7448 (pm20) cc_final: 0.6994 (pm20) REVERT: H 66 ASN cc_start: 0.8048 (t0) cc_final: 0.7562 (t0) REVERT: H 70 ASN cc_start: 0.7933 (m110) cc_final: 0.7675 (m-40) outliers start: 5 outliers final: 1 residues processed: 322 average time/residue: 0.3630 time to fit residues: 162.4898 Evaluate side-chains 277 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 275 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 128 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 105 optimal weight: 0.0010 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN M 163 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.170309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.148884 restraints weight = 75838.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.151018 restraints weight = 58920.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.152282 restraints weight = 49043.707| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17855 Z= 0.198 Angle : 0.814 15.412 25347 Z= 0.447 Chirality : 0.046 0.231 2859 Planarity : 0.007 0.120 2191 Dihedral : 29.879 120.842 4760 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.20), residues: 1320 helix: -2.17 (0.18), residues: 615 sheet: -1.66 (1.46), residues: 18 loop : -2.76 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP K 247 HIS 0.015 0.001 HIS G 38 PHE 0.034 0.002 PHE K 404 TYR 0.036 0.003 TYR K 349 ARG 0.007 0.001 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.06848 ( 741) hydrogen bonds : angle 5.30316 ( 1799) covalent geometry : bond 0.00427 (17855) covalent geometry : angle 0.81439 (25347) *********************** 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 315 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.355 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: K 205 PHE cc_start: 0.4968 (m-10) cc_final: 0.2174 (m-80) REVERT: K 268 VAL cc_start: 0.7004 (m) cc_final: 0.6481 (t) REVERT: M 128 MET cc_start: 0.0851 (ptt) cc_final: 0.0102 (ptt) REVERT: A 59 GLU cc_start: 0.4899 (pm20) cc_final: 0.4483 (pm20) REVERT: A 62 ILE cc_start: 0.7405 (mm) cc_final: 0.7027 (mm) REVERT: A 104 PHE cc_start: 0.7690 (m-80) cc_final: 0.7290 (m-80) REVERT: A 123 ASP cc_start: 0.6767 (m-30) cc_final: 0.6109 (m-30) REVERT: B 50 ILE cc_start: 0.7718 (tp) cc_final: 0.7433 (tp) REVERT: B 68 ASP cc_start: 0.7771 (m-30) cc_final: 0.6916 (m-30) REVERT: D 72 ILE cc_start: 0.8094 (pt) cc_final: 0.7512 (pt) REVERT: D 87 ASN cc_start: 0.8383 (p0) cc_final: 0.8117 (p0) REVERT: D 114 VAL cc_start: 0.8128 (p) cc_final: 0.7873 (p) REVERT: E 84 PHE cc_start: 0.7321 (m-10) cc_final: 0.6342 (m-10) REVERT: E 86 SER cc_start: 0.7534 (m) cc_final: 0.7150 (m) REVERT: E 100 LEU cc_start: 0.7895 (pp) cc_final: 0.7680 (pp) REVERT: E 104 PHE cc_start: 0.7701 (m-80) cc_final: 0.7322 (m-10) REVERT: F 34 ILE cc_start: 0.8389 (tp) cc_final: 0.8071 (tp) REVERT: F 58 LEU cc_start: 0.8147 (tp) cc_final: 0.7596 (tp) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.3760 time to fit residues: 165.0077 Evaluate side-chains 275 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 0.0570 chunk 111 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 21 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.172243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.150168 restraints weight = 75937.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.152173 restraints weight = 59450.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.153601 restraints weight = 49062.711| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17855 Z= 0.177 Angle : 0.780 12.162 25347 Z= 0.429 Chirality : 0.045 0.213 2859 Planarity : 0.006 0.086 2191 Dihedral : 29.594 118.906 4760 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.20), residues: 1320 helix: -2.05 (0.18), residues: 639 sheet: -1.19 (1.53), residues: 18 loop : -2.70 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 247 HIS 0.013 0.001 HIS G 38 PHE 0.032 0.002 PHE K 404 TYR 0.050 0.002 TYR B 72 ARG 0.010 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.06366 ( 741) hydrogen bonds : angle 5.00673 ( 1799) covalent geometry : bond 0.00378 (17855) covalent geometry : angle 0.78049 (25347) *********************** 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 314 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 1.498 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: N 23 TYR cc_start: 0.6391 (t80) cc_final: 0.6126 (t80) REVERT: K 205 PHE cc_start: 0.5115 (m-10) cc_final: 0.4719 (m-10) REVERT: K 268 VAL cc_start: 0.7268 (m) cc_final: 0.6837 (t) REVERT: K 323 PHE cc_start: 0.7603 (m-10) cc_final: 0.7349 (m-10) REVERT: K 333 LYS cc_start: 0.6960 (mmmt) cc_final: 0.6417 (mmmt) REVERT: K 393 ILE cc_start: 0.6926 (tp) cc_final: 0.6540 (tp) REVERT: K 408 ASP cc_start: 0.7296 (p0) cc_final: 0.7002 (p0) REVERT: M 128 MET cc_start: 0.0764 (ptt) cc_final: 0.0464 (ptt) REVERT: A 123 ASP cc_start: 0.6501 (m-30) cc_final: 0.5973 (m-30) REVERT: B 88 TYR cc_start: 0.5916 (m-10) cc_final: 0.5216 (m-10) REVERT: C 102 THR cc_start: 0.7148 (p) cc_final: 0.6892 (t) REVERT: D 64 ILE cc_start: 0.7210 (tt) cc_final: 0.6858 (pt) REVERT: D 72 ILE cc_start: 0.8054 (pt) cc_final: 0.7708 (pt) REVERT: D 76 ILE cc_start: 0.8567 (pt) cc_final: 0.8294 (pt) REVERT: D 119 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7193 (ttp80) REVERT: E 45 THR cc_start: 0.5027 (p) cc_final: 0.4814 (p) REVERT: E 100 LEU cc_start: 0.7822 (pp) cc_final: 0.7597 (pp) REVERT: E 104 PHE cc_start: 0.7587 (m-80) cc_final: 0.7185 (m-10) REVERT: F 34 ILE cc_start: 0.8345 (tp) cc_final: 0.8096 (tp) REVERT: G 109 LEU cc_start: 0.6361 (mt) cc_final: 0.6151 (mt) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.3759 time to fit residues: 164.4451 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 : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 87 optimal weight: 20.0000 chunk 133 optimal weight: 0.7980 chunk 42 optimal weight: 0.0060 chunk 6 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN A 55 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.174863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.153181 restraints weight = 90077.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.153992 restraints weight = 74916.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.154516 restraints weight = 70699.248| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17855 Z= 0.170 Angle : 0.774 12.461 25347 Z= 0.423 Chirality : 0.044 0.305 2859 Planarity : 0.005 0.067 2191 Dihedral : 29.422 114.310 4760 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.21), residues: 1320 helix: -1.89 (0.18), residues: 639 sheet: -1.43 (1.55), residues: 18 loop : -2.76 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP K 247 HIS 0.011 0.001 HIS A 113 PHE 0.034 0.002 PHE A 104 TYR 0.034 0.002 TYR B 72 ARG 0.007 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.06177 ( 741) hydrogen bonds : angle 4.93339 ( 1799) covalent geometry : bond 0.00362 (17855) covalent geometry : angle 0.77436 (25347) *********************** 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 303 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.309 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: N 23 TYR cc_start: 0.6468 (t80) cc_final: 0.6212 (t80) REVERT: K 203 GLN cc_start: 0.3359 (pm20) cc_final: 0.3041 (mp10) REVERT: K 268 VAL cc_start: 0.7446 (m) cc_final: 0.7000 (t) REVERT: K 333 LYS cc_start: 0.7025 (mmmt) cc_final: 0.6422 (mmmt) REVERT: K 346 LEU cc_start: 0.8178 (mm) cc_final: 0.7738 (mm) REVERT: K 358 ILE cc_start: 0.6156 (pt) cc_final: 0.5313 (pt) REVERT: M 289 TYR cc_start: 0.6403 (m-10) cc_final: 0.6172 (m-10) REVERT: B 50 ILE cc_start: 0.8101 (tp) cc_final: 0.7694 (mm) REVERT: B 68 ASP cc_start: 0.7705 (m-30) cc_final: 0.7007 (m-30) REVERT: B 88 TYR cc_start: 0.5393 (m-10) cc_final: 0.5178 (m-10) REVERT: C 102 THR cc_start: 0.6992 (p) cc_final: 0.5850 (t) REVERT: D 64 ILE cc_start: 0.7146 (tt) cc_final: 0.6921 (pt) REVERT: D 68 PHE cc_start: 0.5070 (t80) cc_final: 0.4741 (t80) REVERT: D 72 ILE cc_start: 0.7987 (pt) cc_final: 0.7445 (pt) REVERT: D 119 ARG cc_start: 0.7519 (ttp80) cc_final: 0.7181 (ttp80) REVERT: E 45 THR cc_start: 0.5045 (p) cc_final: 0.4772 (p) REVERT: E 69 ARG cc_start: 0.8035 (ptt180) cc_final: 0.7711 (ptt90) REVERT: E 104 PHE cc_start: 0.7533 (m-80) cc_final: 0.7176 (m-10) REVERT: F 29 ILE cc_start: 0.8092 (mp) cc_final: 0.7889 (mp) REVERT: F 34 ILE cc_start: 0.8416 (tp) cc_final: 0.8156 (tp) REVERT: F 55 ARG cc_start: 0.6946 (mpp80) cc_final: 0.6168 (ptp90) REVERT: H 108 GLU cc_start: 0.7420 (pp20) cc_final: 0.6926 (pm20) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.3779 time to fit residues: 157.9186 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 : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 89 optimal weight: 0.4980 chunk 49 optimal weight: 0.0370 chunk 79 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN K 401 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN E 120 GLN ** G 38 HIS ** 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 = 0.4643 r_free = 0.4643 target = 0.173080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.151802 restraints weight = 72975.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.153867 restraints weight = 58687.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.155234 restraints weight = 47013.775| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5561 moved from start: 0.7095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17855 Z= 0.168 Angle : 0.778 13.068 25347 Z= 0.424 Chirality : 0.044 0.232 2859 Planarity : 0.005 0.065 2191 Dihedral : 29.297 109.679 4760 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 0.08 % Allowed : 2.59 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.21), residues: 1320 helix: -1.80 (0.18), residues: 633 sheet: -1.35 (1.56), residues: 18 loop : -2.60 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP K 247 HIS 0.006 0.001 HIS A 113 PHE 0.033 0.002 PHE A 104 TYR 0.029 0.002 TYR B 72 ARG 0.008 0.001 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.06168 ( 741) hydrogen bonds : angle 4.84709 ( 1799) covalent geometry : bond 0.00359 (17855) covalent geometry : angle 0.77810 (25347) *********************** 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 302 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 1.549 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: N 23 TYR cc_start: 0.6395 (t80) cc_final: 0.6178 (t80) REVERT: K 203 GLN cc_start: 0.3626 (pm20) cc_final: 0.3169 (mp10) REVERT: K 268 VAL cc_start: 0.7327 (m) cc_final: 0.7070 (t) REVERT: K 333 LYS cc_start: 0.6923 (mmmt) cc_final: 0.6375 (mmmt) REVERT: M 128 MET cc_start: 0.0678 (ptt) cc_final: 0.0322 (ptt) REVERT: A 118 THR cc_start: 0.7140 (m) cc_final: 0.6827 (m) REVERT: B 88 TYR cc_start: 0.5731 (m-10) cc_final: 0.5336 (m-10) REVERT: C 97 SER cc_start: 0.6946 (p) cc_final: 0.6465 (p) REVERT: D 64 ILE cc_start: 0.7023 (tt) cc_final: 0.6802 (pt) REVERT: D 72 ILE cc_start: 0.8045 (pt) cc_final: 0.7592 (pt) REVERT: D 119 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7262 (ttp80) REVERT: E 45 THR cc_start: 0.5122 (p) cc_final: 0.4869 (p) REVERT: E 100 LEU cc_start: 0.7841 (pp) cc_final: 0.7426 (pp) REVERT: E 103 LEU cc_start: 0.7387 (pp) cc_final: 0.7070 (pp) REVERT: E 104 PHE cc_start: 0.7496 (m-80) cc_final: 0.7176 (m-10) REVERT: F 91 LYS cc_start: 0.6548 (pttp) cc_final: 0.5074 (pttp) REVERT: H 108 GLU cc_start: 0.7156 (pp20) cc_final: 0.6552 (pm20) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.3841 time to fit residues: 158.2373 Evaluate side-chains 265 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 53 optimal weight: 0.0870 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 118 optimal weight: 0.0470 chunk 73 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 chunk 59 optimal weight: 100.0000 overall best weight: 0.8858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.174500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.156932 restraints weight = 86393.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.156400 restraints weight = 86402.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.156561 restraints weight = 87575.463| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17855 Z= 0.179 Angle : 0.804 14.918 25347 Z= 0.438 Chirality : 0.045 0.211 2859 Planarity : 0.006 0.095 2191 Dihedral : 29.228 107.169 4760 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.21), residues: 1320 helix: -1.82 (0.18), residues: 620 sheet: -2.09 (1.36), residues: 18 loop : -2.58 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP K 247 HIS 0.009 0.001 HIS G 38 PHE 0.032 0.002 PHE A 104 TYR 0.050 0.003 TYR D 45 ARG 0.021 0.001 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.06308 ( 741) hydrogen bonds : angle 4.85539 ( 1799) covalent geometry : bond 0.00383 (17855) covalent geometry : angle 0.80386 (25347) *********************** 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 303 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.322 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 172 MET cc_start: 0.4790 (ppp) cc_final: 0.4083 (pmm) REVERT: K 205 PHE cc_start: 0.5208 (m-10) cc_final: 0.5003 (m-80) REVERT: K 268 VAL cc_start: 0.7347 (m) cc_final: 0.7033 (t) REVERT: K 333 LYS cc_start: 0.7037 (mmmt) cc_final: 0.6460 (mmmt) REVERT: M 128 MET cc_start: 0.0280 (ptt) cc_final: -0.0124 (ptt) REVERT: A 100 LEU cc_start: 0.8105 (pp) cc_final: 0.7730 (pp) REVERT: B 87 VAL cc_start: 0.7273 (p) cc_final: 0.7038 (p) REVERT: B 88 TYR cc_start: 0.5733 (m-10) cc_final: 0.5363 (m-10) REVERT: C 33 ARG cc_start: 0.7283 (tmm160) cc_final: 0.6976 (tmm160) REVERT: C 97 SER cc_start: 0.7094 (p) cc_final: 0.6661 (p) REVERT: D 64 ILE cc_start: 0.7164 (tt) cc_final: 0.6922 (pt) REVERT: D 72 ILE cc_start: 0.7997 (pt) cc_final: 0.7619 (pt) REVERT: D 119 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7397 (ttp80) REVERT: E 45 THR cc_start: 0.4961 (p) cc_final: 0.4753 (p) REVERT: E 50 GLU cc_start: 0.5088 (tp30) cc_final: 0.4528 (tp30) REVERT: E 100 LEU cc_start: 0.7739 (pp) cc_final: 0.7428 (pp) REVERT: E 104 PHE cc_start: 0.7621 (m-80) cc_final: 0.7375 (m-10) REVERT: F 34 ILE cc_start: 0.8511 (tp) cc_final: 0.8307 (tp) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.4422 time to fit residues: 183.1511 Evaluate side-chains 262 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 1 optimal weight: 0.4980 chunk 136 optimal weight: 0.0000 chunk 13 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 8 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.174617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.153569 restraints weight = 72437.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.155919 restraints weight = 57579.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.156729 restraints weight = 46007.417| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5512 moved from start: 0.7738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17855 Z= 0.164 Angle : 0.793 12.448 25347 Z= 0.428 Chirality : 0.045 0.275 2859 Planarity : 0.006 0.052 2191 Dihedral : 29.173 103.350 4760 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.21), residues: 1320 helix: -1.79 (0.18), residues: 614 sheet: -1.45 (1.40), residues: 18 loop : -2.47 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 353 HIS 0.008 0.001 HIS A 113 PHE 0.031 0.002 PHE A 104 TYR 0.040 0.002 TYR D 45 ARG 0.012 0.001 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.05859 ( 741) hydrogen bonds : angle 4.68830 ( 1799) covalent geometry : bond 0.00346 (17855) covalent geometry : angle 0.79321 (25347) *********************** 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 295 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 166 ASN cc_start: 0.6481 (t0) cc_final: 0.6265 (t0) REVERT: K 346 LEU cc_start: 0.7982 (mm) cc_final: 0.7781 (mm) REVERT: K 386 HIS cc_start: 0.7743 (t70) cc_final: 0.7536 (t70) REVERT: K 402 ILE cc_start: 0.4174 (mp) cc_final: 0.3322 (mt) REVERT: K 408 ASP cc_start: 0.8215 (p0) cc_final: 0.7654 (p0) REVERT: M 128 MET cc_start: 0.1276 (ptt) cc_final: 0.0757 (ptt) REVERT: A 100 LEU cc_start: 0.8106 (pp) cc_final: 0.7739 (pp) REVERT: B 61 PHE cc_start: 0.7611 (t80) cc_final: 0.7073 (t80) REVERT: B 88 TYR cc_start: 0.6151 (m-10) cc_final: 0.5363 (m-10) REVERT: C 32 LYS cc_start: 0.6975 (tptt) cc_final: 0.6686 (tptt) REVERT: C 35 LEU cc_start: 0.7615 (pp) cc_final: 0.7412 (pp) REVERT: D 64 ILE cc_start: 0.7201 (tt) cc_final: 0.6907 (pt) REVERT: D 72 ILE cc_start: 0.8028 (pt) cc_final: 0.7647 (pt) REVERT: D 119 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7535 (ttp80) REVERT: E 100 LEU cc_start: 0.7658 (pp) cc_final: 0.7322 (pp) REVERT: E 103 LEU cc_start: 0.7660 (pp) cc_final: 0.7245 (pp) REVERT: E 104 PHE cc_start: 0.7379 (m-80) cc_final: 0.7141 (m-10) REVERT: F 34 ILE cc_start: 0.8328 (tp) cc_final: 0.8069 (tp) REVERT: G 44 ARG cc_start: 0.4954 (mpt180) cc_final: 0.3038 (mpt180) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.4551 time to fit residues: 187.7987 Evaluate side-chains 266 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 127 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.172978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.151978 restraints weight = 72626.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.153983 restraints weight = 58048.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.156050 restraints weight = 46171.997| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 0.8036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17855 Z= 0.184 Angle : 0.813 14.212 25347 Z= 0.439 Chirality : 0.046 0.285 2859 Planarity : 0.006 0.062 2191 Dihedral : 29.055 98.043 4760 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.21), residues: 1320 helix: -1.77 (0.19), residues: 608 sheet: -1.59 (1.45), residues: 18 loop : -2.53 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 353 HIS 0.007 0.001 HIS E 113 PHE 0.032 0.002 PHE A 104 TYR 0.034 0.003 TYR D 45 ARG 0.013 0.001 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.06389 ( 741) hydrogen bonds : angle 4.79246 ( 1799) covalent geometry : bond 0.00394 (17855) covalent geometry : angle 0.81268 (25347) ********************** 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 287 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.601 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 166 ASN cc_start: 0.6653 (t0) cc_final: 0.6423 (t0) REVERT: M 128 MET cc_start: 0.0879 (ptt) cc_final: 0.0388 (ptt) REVERT: A 100 LEU cc_start: 0.8083 (pp) cc_final: 0.7722 (pp) REVERT: B 88 TYR cc_start: 0.6237 (m-10) cc_final: 0.5335 (m-80) REVERT: C 44 ARG cc_start: 0.6295 (mmp80) cc_final: 0.5965 (mmp80) REVERT: C 97 SER cc_start: 0.7043 (p) cc_final: 0.6726 (p) REVERT: C 102 THR cc_start: 0.6157 (p) cc_final: 0.5853 (t) REVERT: D 72 ILE cc_start: 0.7933 (pt) cc_final: 0.7366 (pt) REVERT: D 86 TYR cc_start: 0.5975 (m-10) cc_final: 0.5396 (m-80) REVERT: D 119 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7502 (ttp80) REVERT: E 100 LEU cc_start: 0.7644 (pp) cc_final: 0.7106 (pp) REVERT: E 103 LEU cc_start: 0.7619 (pp) cc_final: 0.6958 (pp) REVERT: F 34 ILE cc_start: 0.8395 (tp) cc_final: 0.8005 (tp) REVERT: F 37 LEU cc_start: 0.7706 (mt) cc_final: 0.7469 (mt) REVERT: H 73 PHE cc_start: 0.6195 (t80) cc_final: 0.5829 (t80) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.4709 time to fit residues: 185.6465 Evaluate side-chains 264 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.0000 chunk 155 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 139 optimal weight: 0.0170 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 94 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 overall best weight: 0.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN ** K 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.174940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.153849 restraints weight = 72061.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.156129 restraints weight = 55841.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.157985 restraints weight = 43930.153| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5501 moved from start: 0.8332 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= 0.166 Angle : 0.796 14.387 25347 Z= 0.427 Chirality : 0.045 0.277 2859 Planarity : 0.005 0.064 2191 Dihedral : 29.032 94.876 4760 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.21), residues: 1320 helix: -1.68 (0.19), residues: 610 sheet: -1.89 (1.13), residues: 28 loop : -2.51 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 353 HIS 0.007 0.001 HIS G 84 PHE 0.041 0.002 PHE K 205 TYR 0.028 0.002 TYR E 99 ARG 0.012 0.001 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.05812 ( 741) hydrogen bonds : angle 4.63906 ( 1799) covalent geometry : bond 0.00351 (17855) covalent geometry : angle 0.79585 (25347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6915.83 seconds wall clock time: 124 minutes 31.84 seconds (7471.84 seconds total)