Starting phenix.real_space_refine on Sun May 18 23:44:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x32_38026/05_2025/8x32_38026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x32_38026/05_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_38026/05_2025/8x32_38026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x32_38026/05_2025/8x32_38026.map" model { file = "/net/cci-nas-00/data/ceres_data/8x32_38026/05_2025/8x32_38026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x32_38026/05_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-5687/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: 9.15, per 1000 atoms: 0.54 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: 4.00 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: 7.79 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: 7.03 Time building geometry restraints manager: 4.75 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 43.380 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.770 ------------------------------------------------------------------------------- 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 : 1.427 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: 0.3628 time to fit residues: 192.7135 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 : 1.354 ------------------------------------------------------------------------------- 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 = 0.151218 restraints weight = 89196.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.152182 restraints weight = 74438.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.153077 restraints weight = 67532.416| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 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 : 1.432 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: 0.5126 (m-10) cc_final: 0.3987 (m-80) REVERT: K 311 TYR cc_start: 0.2987 (t80) cc_final: 0.2706 (t80) REVERT: K 316 TYR cc_start: 0.4849 (p90) cc_final: 0.4600 (p90) REVERT: K 328 SER cc_start: 0.7715 (m) cc_final: 0.7289 (p) REVERT: K 329 LYS cc_start: 0.7273 (mtmm) cc_final: 0.7005 (mtmm) REVERT: K 391 LEU cc_start: 0.8203 (tp) cc_final: 0.7957 (tp) REVERT: M 72 ASN cc_start: 0.6602 (t0) cc_final: 0.6369 (t0) REVERT: M 289 TYR cc_start: 0.5821 (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: 0.7439 (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: 0.7530 (tp) REVERT: B 68 ASP cc_start: 0.7716 (p0) cc_final: 0.6727 (m-30) REVERT: D 87 ASN cc_start: 0.7942 (p0) cc_final: 0.7709 (p0) REVERT: D 116 GLU cc_start: 0.7284 (pp20) cc_final: 0.6946 (pp20) REVERT: E 85 GLN cc_start: 0.4552 (mm110) cc_final: 0.4158 (mm110) REVERT: E 100 LEU cc_start: 0.7555 (pp) cc_final: 0.7334 (pp) REVERT: E 103 LEU cc_start: 0.7688 (pp) cc_final: 0.7488 (pp) REVERT: E 104 PHE cc_start: 0.7666 (m-80) cc_final: 0.7403 (m-10) REVERT: F 34 ILE cc_start: 0.8808 (tp) cc_final: 0.8387 (tp) REVERT: F 37 LEU cc_start: 0.7971 (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: 0.4503 (tp) REVERT: H 66 ASN cc_start: 0.7223 (t0) cc_final: 0.6868 (t0) REVERT: H 112 HIS cc_start: 0.5675 (t70) cc_final: 0.5436 (t70) outliers start: 6 outliers final: 1 residues processed: 325 average time/residue: 0.3473 time to fit residues: 156.8120 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 : 1.287 ------------------------------------------------------------------------------- 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: 0.6980 chunk 138 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.9424 ------------------------------------------------------------------------------- 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 ** B 75 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.169637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.146803 restraints weight = 88121.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.148119 restraints weight = 70956.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.149325 restraints weight = 61470.710| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17855 Z= 0.271 Angle : 0.908 13.160 25347 Z= 0.506 Chirality : 0.050 0.283 2859 Planarity : 0.008 0.153 2191 Dihedral : 29.928 117.397 4760 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 26.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 0.42 % Allowed : 9.11 % Favored : 90.47 % 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: -3.91 (0.20), residues: 1320 helix: -2.46 (0.17), residues: 620 sheet: -2.33 (1.25), residues: 20 loop : -2.75 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP K 247 HIS 0.014 0.002 HIS G 38 PHE 0.041 0.003 PHE K 404 TYR 0.037 0.004 TYR D 86 ARG 0.013 0.001 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.08596 ( 741) hydrogen bonds : angle 5.72734 ( 1799) covalent geometry : bond 0.00586 (17855) covalent geometry : angle 0.90783 (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 330 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 325 time to evaluate : 1.469 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 268 VAL cc_start: 0.6883 (m) cc_final: 0.6288 (t) REVERT: K 346 LEU cc_start: 0.7771 (mm) cc_final: 0.7273 (mm) REVERT: K 393 ILE cc_start: 0.6950 (tp) cc_final: 0.6546 (tp) REVERT: K 408 ASP cc_start: 0.7126 (p0) cc_final: 0.6554 (p0) REVERT: M 128 MET cc_start: 0.0630 (ptt) cc_final: 0.0114 (ptt) REVERT: A 73 GLU cc_start: 0.8361 (tt0) cc_final: 0.8135 (mt-10) REVERT: A 123 ASP cc_start: 0.6225 (m-30) cc_final: 0.4721 (m-30) REVERT: B 50 ILE cc_start: 0.7795 (tp) cc_final: 0.7433 (tp) REVERT: C 35 LEU cc_start: 0.7907 (pp) cc_final: 0.7531 (pp) REVERT: D 103 LEU cc_start: 0.7773 (tp) cc_final: 0.7478 (tp) REVERT: D 122 THR cc_start: 0.8234 (p) cc_final: 0.8007 (p) REVERT: E 69 ARG cc_start: 0.7984 (ptt90) cc_final: 0.7726 (ptt90) REVERT: E 72 ARG cc_start: 0.6032 (tpt170) cc_final: 0.5829 (tpt170) REVERT: E 84 PHE cc_start: 0.7807 (m-10) cc_final: 0.7472 (m-10) REVERT: E 100 LEU cc_start: 0.7960 (pp) cc_final: 0.7753 (pp) REVERT: E 103 LEU cc_start: 0.7848 (pp) cc_final: 0.7568 (pp) REVERT: E 104 PHE cc_start: 0.7833 (m-80) cc_final: 0.7554 (m-10) REVERT: E 120 GLN cc_start: 0.3767 (OUTLIER) cc_final: 0.2787 (pp30) REVERT: F 51 TYR cc_start: 0.6715 (m-80) cc_final: 0.6503 (m-80) REVERT: H 38 GLU cc_start: 0.7462 (pm20) cc_final: 0.6993 (pm20) REVERT: H 66 ASN cc_start: 0.8050 (t0) cc_final: 0.7474 (t0) REVERT: H 70 ASN cc_start: 0.7908 (m110) cc_final: 0.7680 (m-40) outliers start: 5 outliers final: 1 residues processed: 328 average time/residue: 0.3509 time to fit residues: 160.0813 Evaluate side-chains 283 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 105 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 D 59 GLN D 70 ASN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.171181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.150558 restraints weight = 75217.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.152473 restraints weight = 60655.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.153539 restraints weight = 49846.548| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17855 Z= 0.185 Angle : 0.800 14.083 25347 Z= 0.439 Chirality : 0.045 0.230 2859 Planarity : 0.007 0.112 2191 Dihedral : 29.908 121.653 4760 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % 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: -3.69 (0.20), residues: 1320 helix: -2.17 (0.18), residues: 625 sheet: -1.49 (1.49), residues: 18 loop : -2.78 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP K 247 HIS 0.014 0.001 HIS G 38 PHE 0.033 0.002 PHE K 404 TYR 0.027 0.002 TYR K 349 ARG 0.009 0.001 ARG C 33 Details of bonding type rmsd hydrogen bonds : bond 0.06512 ( 741) hydrogen bonds : angle 5.22108 ( 1799) covalent geometry : bond 0.00395 (17855) covalent geometry : angle 0.79995 (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 311 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.292 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 205 PHE cc_start: 0.5296 (m-10) cc_final: 0.4168 (m-10) REVERT: K 268 VAL cc_start: 0.7255 (m) cc_final: 0.6721 (t) REVERT: K 408 ASP cc_start: 0.7198 (p0) cc_final: 0.6749 (p0) REVERT: M 128 MET cc_start: 0.1042 (ptt) cc_final: 0.0264 (ptt) REVERT: A 59 GLU cc_start: 0.4857 (pm20) cc_final: 0.4477 (pm20) REVERT: A 62 ILE cc_start: 0.7562 (mm) cc_final: 0.7332 (mm) REVERT: A 73 GLU cc_start: 0.7995 (tt0) cc_final: 0.7703 (tt0) REVERT: A 104 PHE cc_start: 0.7616 (m-80) cc_final: 0.7335 (m-80) REVERT: A 123 ASP cc_start: 0.6610 (m-30) cc_final: 0.5936 (m-30) REVERT: B 68 ASP cc_start: 0.7637 (m-30) cc_final: 0.6770 (m-30) REVERT: B 92 ARG cc_start: 0.6188 (mmp80) cc_final: 0.5961 (mmp80) REVERT: C 34 TYR cc_start: 0.5043 (m-80) cc_final: 0.4412 (m-80) REVERT: D 72 ILE cc_start: 0.8076 (pt) cc_final: 0.7457 (pt) REVERT: D 87 ASN cc_start: 0.8342 (p0) cc_final: 0.8051 (p0) REVERT: E 100 LEU cc_start: 0.7846 (pp) cc_final: 0.7585 (pp) REVERT: E 104 PHE cc_start: 0.7660 (m-80) cc_final: 0.7256 (m-10) REVERT: F 34 ILE cc_start: 0.8350 (tp) cc_final: 0.7957 (tp) REVERT: F 51 TYR cc_start: 0.6626 (m-80) cc_final: 0.6232 (m-10) REVERT: F 58 LEU cc_start: 0.8048 (tp) cc_final: 0.7671 (tp) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.3623 time to fit residues: 156.3870 Evaluate side-chains 273 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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: 0.9980 chunk 7 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN M 252 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.170734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.148699 restraints weight = 75433.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.150774 restraints weight = 60367.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.151522 restraints weight = 51574.225| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17855 Z= 0.191 Angle : 0.800 12.600 25347 Z= 0.440 Chirality : 0.045 0.216 2859 Planarity : 0.006 0.096 2191 Dihedral : 29.645 118.458 4760 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.95 (0.18), residues: 626 sheet: -1.31 (1.50), residues: 18 loop : -2.70 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP K 247 HIS 0.012 0.001 HIS A 113 PHE 0.034 0.002 PHE K 404 TYR 0.045 0.003 TYR B 72 ARG 0.011 0.001 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.06791 ( 741) hydrogen bonds : angle 5.06280 ( 1799) covalent geometry : bond 0.00411 (17855) covalent geometry : angle 0.80020 (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 309 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 23 TYR cc_start: 0.6448 (t80) cc_final: 0.6189 (t80) REVERT: K 268 VAL cc_start: 0.7275 (m) cc_final: 0.6857 (t) REVERT: K 323 PHE cc_start: 0.7643 (m-10) cc_final: 0.7421 (m-10) REVERT: K 358 ILE cc_start: 0.6478 (pt) cc_final: 0.5723 (pt) REVERT: K 393 ILE cc_start: 0.6831 (tp) cc_final: 0.6460 (tp) REVERT: K 408 ASP cc_start: 0.7124 (p0) cc_final: 0.6767 (p0) REVERT: M 128 MET cc_start: 0.0920 (ptt) cc_final: 0.0231 (ptt) REVERT: A 73 GLU cc_start: 0.8039 (tt0) cc_final: 0.7740 (tt0) REVERT: A 104 PHE cc_start: 0.7618 (m-80) cc_final: 0.7412 (m-80) REVERT: A 123 ASP cc_start: 0.6468 (m-30) cc_final: 0.6098 (m-30) REVERT: B 50 ILE cc_start: 0.7995 (tp) cc_final: 0.7775 (tp) REVERT: B 88 TYR cc_start: 0.6109 (m-10) cc_final: 0.5566 (m-10) REVERT: C 102 THR cc_start: 0.7317 (p) cc_final: 0.7078 (t) REVERT: D 72 ILE cc_start: 0.8051 (pt) cc_final: 0.7779 (pt) REVERT: D 76 ILE cc_start: 0.8609 (pt) cc_final: 0.8382 (pt) REVERT: D 87 ASN cc_start: 0.8229 (p0) cc_final: 0.8016 (p0) REVERT: D 119 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7199 (ttp80) REVERT: E 45 THR cc_start: 0.5050 (p) cc_final: 0.4837 (p) REVERT: E 69 ARG cc_start: 0.8071 (ptt90) cc_final: 0.7651 (ptt90) REVERT: E 100 LEU cc_start: 0.7867 (pp) cc_final: 0.7506 (pp) REVERT: E 103 LEU cc_start: 0.7562 (pp) cc_final: 0.7234 (pp) REVERT: E 104 PHE cc_start: 0.7649 (m-80) cc_final: 0.7394 (m-10) REVERT: F 34 ILE cc_start: 0.8213 (tp) cc_final: 0.8011 (tp) REVERT: G 79 ARG cc_start: 0.2639 (tpm170) cc_final: 0.2413 (tpm170) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.3689 time to fit residues: 158.4555 Evaluate side-chains 263 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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: 3.9990 chunk 133 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 6 optimal weight: 0.4980 chunk 95 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** E 93 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.175069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.152740 restraints weight = 90097.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.153548 restraints weight = 76844.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.154296 restraints weight = 69574.740| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17855 Z= 0.171 Angle : 0.788 13.694 25347 Z= 0.428 Chirality : 0.045 0.276 2859 Planarity : 0.006 0.088 2191 Dihedral : 29.490 116.071 4760 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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: -1.95 (0.18), residues: 650 sheet: -1.35 (1.55), residues: 18 loop : -2.70 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP K 247 HIS 0.007 0.001 HIS A 113 PHE 0.037 0.002 PHE K 205 TYR 0.037 0.002 TYR B 72 ARG 0.010 0.001 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.06153 ( 741) hydrogen bonds : angle 4.87094 ( 1799) covalent geometry : bond 0.00364 (17855) covalent geometry : angle 0.78790 (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 302 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.305 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: K 268 VAL cc_start: 0.7350 (m) cc_final: 0.6942 (t) REVERT: K 333 LYS cc_start: 0.6980 (mmmt) cc_final: 0.6424 (mmmt) REVERT: K 346 LEU cc_start: 0.8209 (mm) cc_final: 0.7785 (mm) REVERT: M 128 MET cc_start: 0.0723 (ptt) cc_final: 0.0431 (ptt) REVERT: A 73 GLU cc_start: 0.8110 (tt0) cc_final: 0.7809 (tt0) REVERT: A 104 PHE cc_start: 0.7758 (m-80) cc_final: 0.7429 (m-80) REVERT: A 118 THR cc_start: 0.7054 (m) cc_final: 0.6804 (m) REVERT: A 119 ILE cc_start: 0.7293 (pt) cc_final: 0.7044 (pt) REVERT: C 97 SER cc_start: 0.7439 (t) cc_final: 0.7163 (p) REVERT: C 102 THR cc_start: 0.7221 (p) cc_final: 0.6112 (p) REVERT: D 64 ILE cc_start: 0.7153 (tt) cc_final: 0.6899 (pt) REVERT: D 68 PHE cc_start: 0.5398 (t80) cc_final: 0.4183 (t80) REVERT: D 72 ILE cc_start: 0.8089 (pt) cc_final: 0.7610 (pt) REVERT: D 119 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7192 (ttp80) REVERT: E 45 THR cc_start: 0.5405 (p) cc_final: 0.5094 (p) REVERT: E 72 ARG cc_start: 0.6324 (tpt170) cc_final: 0.5717 (tpt170) REVERT: E 84 PHE cc_start: 0.7358 (m-10) cc_final: 0.7020 (m-10) REVERT: E 100 LEU cc_start: 0.7738 (pp) cc_final: 0.7488 (pp) REVERT: E 104 PHE cc_start: 0.7750 (m-80) cc_final: 0.7335 (m-10) REVERT: F 34 ILE cc_start: 0.8415 (tp) cc_final: 0.8115 (tp) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.3667 time to fit residues: 150.9235 Evaluate side-chains 260 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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: 4.9990 chunk 49 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 144 optimal weight: 0.0270 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 A 55 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** 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 = 0.4648 r_free = 0.4648 target = 0.173519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.151853 restraints weight = 73377.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.154047 restraints weight = 58568.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.154914 restraints weight = 48439.795| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5573 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17855 Z= 0.168 Angle : 0.783 13.486 25347 Z= 0.424 Chirality : 0.044 0.225 2859 Planarity : 0.005 0.087 2191 Dihedral : 29.345 111.101 4760 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -3.32 (0.21), residues: 1320 helix: -1.87 (0.18), residues: 641 sheet: -1.24 (1.57), residues: 18 loop : -2.59 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP K 247 HIS 0.007 0.001 HIS E 113 PHE 0.030 0.002 PHE K 404 TYR 0.028 0.002 TYR B 72 ARG 0.009 0.001 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.06083 ( 741) hydrogen bonds : angle 4.75817 ( 1799) covalent geometry : bond 0.00356 (17855) covalent geometry : angle 0.78287 (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 299 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.446 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: K 175 TYR cc_start: 0.6595 (t80) cc_final: 0.6191 (t80) REVERT: K 268 VAL cc_start: 0.7358 (m) cc_final: 0.6963 (t) REVERT: K 333 LYS cc_start: 0.6778 (mmmt) cc_final: 0.6276 (mmmt) REVERT: K 346 LEU cc_start: 0.8112 (mm) cc_final: 0.7826 (mm) REVERT: M 128 MET cc_start: 0.1226 (ptt) cc_final: 0.0862 (ptt) REVERT: A 62 ILE cc_start: 0.7691 (mm) cc_final: 0.7472 (mm) REVERT: A 73 GLU cc_start: 0.7964 (tt0) cc_final: 0.7692 (tt0) REVERT: D 64 ILE cc_start: 0.7104 (tt) cc_final: 0.6796 (pt) REVERT: D 72 ILE cc_start: 0.8079 (pt) cc_final: 0.7678 (pt) REVERT: D 87 ASN cc_start: 0.8330 (p0) cc_final: 0.8084 (p0) REVERT: D 119 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7494 (ttp80) REVERT: E 45 THR cc_start: 0.5273 (p) cc_final: 0.5033 (p) REVERT: E 70 LEU cc_start: 0.4977 (mt) cc_final: 0.4754 (mt) REVERT: E 72 ARG cc_start: 0.6011 (tpt170) cc_final: 0.5471 (tpt170) REVERT: E 100 LEU cc_start: 0.7772 (pp) cc_final: 0.7392 (pp) REVERT: E 103 LEU cc_start: 0.7313 (pp) cc_final: 0.6854 (pp) REVERT: F 34 ILE cc_start: 0.8308 (tp) cc_final: 0.8073 (tp) REVERT: F 91 LYS cc_start: 0.6471 (pttp) cc_final: 0.4945 (pttm) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3740 time to fit residues: 153.8843 Evaluate side-chains 260 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 22 optimal weight: 0.0770 chunk 17 optimal weight: 4.9990 chunk 59 optimal weight: 100.0000 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN ** M 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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** H 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.165149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.141942 restraints weight = 72583.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.144304 restraints weight = 57288.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.145574 restraints weight = 46788.256| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5816 moved from start: 0.7571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17855 Z= 0.232 Angle : 0.872 13.696 25347 Z= 0.476 Chirality : 0.049 0.291 2859 Planarity : 0.007 0.110 2191 Dihedral : 29.325 109.139 4760 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 26.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -3.51 (0.21), residues: 1320 helix: -1.97 (0.18), residues: 632 sheet: -1.72 (1.51), residues: 18 loop : -2.73 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP K 247 HIS 0.009 0.002 HIS G 38 PHE 0.037 0.003 PHE E 104 TYR 0.035 0.003 TYR K 311 ARG 0.015 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.07761 ( 741) hydrogen bonds : angle 5.09957 ( 1799) covalent geometry : bond 0.00502 (17855) covalent geometry : angle 0.87194 (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 308 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.427 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 257 LEU cc_start: 0.4406 (tp) cc_final: 0.4153 (tp) REVERT: K 333 LYS cc_start: 0.7212 (mmmt) cc_final: 0.6671 (mmmt) REVERT: K 346 LEU cc_start: 0.7991 (mm) cc_final: 0.7629 (mm) REVERT: K 368 ILE cc_start: 0.2750 (tp) cc_final: 0.2505 (tp) REVERT: K 386 HIS cc_start: 0.7801 (t70) cc_final: 0.7452 (t70) REVERT: K 391 LEU cc_start: 0.8382 (tp) cc_final: 0.8169 (tp) REVERT: K 408 ASP cc_start: 0.8256 (p0) cc_final: 0.7830 (p0) REVERT: M 128 MET cc_start: 0.0734 (ptt) cc_final: 0.0192 (ptt) REVERT: M 164 MET cc_start: 0.3651 (ttp) cc_final: 0.3010 (ttt) REVERT: A 73 GLU cc_start: 0.7995 (tt0) cc_final: 0.7674 (tt0) REVERT: A 89 ILE cc_start: 0.5275 (tt) cc_final: 0.4373 (tt) REVERT: A 93 GLN cc_start: 0.6468 (mt0) cc_final: 0.6107 (tt0) REVERT: B 65 VAL cc_start: 0.8615 (p) cc_final: 0.8407 (p) REVERT: D 64 ILE cc_start: 0.7231 (tt) cc_final: 0.6995 (pt) REVERT: D 68 PHE cc_start: 0.5948 (t80) cc_final: 0.5412 (t80) REVERT: D 72 ILE cc_start: 0.7968 (pt) cc_final: 0.7376 (pt) REVERT: D 87 ASN cc_start: 0.8408 (p0) cc_final: 0.8205 (p0) REVERT: D 119 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7314 (ttp80) REVERT: E 104 PHE cc_start: 0.7427 (m-10) cc_final: 0.7148 (m-10) REVERT: F 34 ILE cc_start: 0.8500 (tp) cc_final: 0.8268 (tp) REVERT: H 63 SER cc_start: 0.7853 (t) cc_final: 0.7509 (p) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.3812 time to fit residues: 160.4824 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 : 1.332 ------------------------------------------------------------------------------- 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: 6.9990 chunk 136 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.172353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.150691 restraints weight = 73446.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.152847 restraints weight = 58609.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.154322 restraints weight = 47053.173| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17855 Z= 0.181 Angle : 0.819 12.673 25347 Z= 0.444 Chirality : 0.047 0.282 2859 Planarity : 0.006 0.107 2191 Dihedral : 29.337 110.533 4760 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -3.41 (0.21), residues: 1320 helix: -1.93 (0.18), residues: 637 sheet: -1.51 (1.56), residues: 18 loop : -2.64 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 353 HIS 0.007 0.001 HIS E 113 PHE 0.037 0.002 PHE A 104 TYR 0.047 0.003 TYR D 45 ARG 0.015 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.06279 ( 741) hydrogen bonds : angle 4.87458 ( 1799) covalent geometry : bond 0.00389 (17855) covalent geometry : angle 0.81869 (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 288 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 172 MET cc_start: 0.5002 (ppp) cc_final: 0.3752 (pmm) REVERT: K 189 LEU cc_start: 0.6508 (pp) cc_final: 0.6089 (pt) REVERT: K 214 TYR cc_start: 0.6325 (m-10) cc_final: 0.6028 (m-10) REVERT: K 386 HIS cc_start: 0.7623 (t70) cc_final: 0.7399 (t70) REVERT: K 393 ILE cc_start: 0.6947 (tp) cc_final: 0.6718 (tp) REVERT: K 408 ASP cc_start: 0.8135 (p0) cc_final: 0.7868 (p0) REVERT: M 128 MET cc_start: 0.1166 (ptt) cc_final: 0.0643 (ptt) REVERT: A 73 GLU cc_start: 0.7900 (tt0) cc_final: 0.7669 (tt0) REVERT: A 100 LEU cc_start: 0.8130 (pp) cc_final: 0.7851 (pp) REVERT: C 38 HIS cc_start: 0.7251 (t70) cc_final: 0.7042 (t70) REVERT: C 63 GLU cc_start: 0.3794 (pm20) cc_final: 0.3524 (pm20) REVERT: D 64 ILE cc_start: 0.7227 (tt) cc_final: 0.6945 (pt) REVERT: D 72 ILE cc_start: 0.7982 (pt) cc_final: 0.7434 (pt) REVERT: D 119 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7299 (ttp80) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.3861 time to fit residues: 151.3493 Evaluate side-chains 255 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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: 0.7980 chunk 140 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 16 ASN M 173 ASN ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 363 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 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 = 0.4560 r_free = 0.4560 target = 0.163738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.141403 restraints weight = 72510.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.143490 restraints weight = 57321.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.144245 restraints weight = 48442.441| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.8411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17855 Z= 0.266 Angle : 0.922 13.914 25347 Z= 0.505 Chirality : 0.052 0.314 2859 Planarity : 0.008 0.106 2191 Dihedral : 29.339 110.034 4760 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 31.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -2.03 (0.18), residues: 608 sheet: -1.71 (1.55), residues: 18 loop : -2.60 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP K 353 HIS 0.011 0.002 HIS G 84 PHE 0.036 0.003 PHE A 104 TYR 0.043 0.003 TYR B 98 ARG 0.015 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.08595 ( 741) hydrogen bonds : angle 5.30235 ( 1799) covalent geometry : bond 0.00578 (17855) covalent geometry : angle 0.92178 (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 289 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.352 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: K 370 ILE cc_start: 0.5761 (pt) cc_final: 0.5233 (pt) REVERT: K 386 HIS cc_start: 0.7657 (t70) cc_final: 0.7383 (t70) REVERT: K 391 LEU cc_start: 0.8315 (tp) cc_final: 0.8070 (tp) REVERT: K 408 ASP cc_start: 0.8373 (p0) cc_final: 0.7941 (p0) REVERT: M 128 MET cc_start: 0.1235 (ptt) cc_final: 0.0623 (ptt) REVERT: A 73 GLU cc_start: 0.8020 (tt0) cc_final: 0.7738 (tt0) REVERT: A 89 ILE cc_start: 0.5437 (tt) cc_final: 0.4412 (tt) REVERT: A 93 GLN cc_start: 0.6649 (mt0) cc_final: 0.6340 (tt0) REVERT: A 100 LEU cc_start: 0.8230 (pp) cc_final: 0.7943 (pp) REVERT: A 104 PHE cc_start: 0.7998 (m-80) cc_final: 0.7626 (m-80) REVERT: D 64 ILE cc_start: 0.7319 (tt) cc_final: 0.7055 (pt) REVERT: D 68 PHE cc_start: 0.5921 (t80) cc_final: 0.5011 (t80) REVERT: D 72 ILE cc_start: 0.7822 (pt) cc_final: 0.7203 (pt) REVERT: D 122 THR cc_start: 0.7981 (p) cc_final: 0.7643 (p) REVERT: E 45 THR cc_start: 0.5105 (p) cc_final: 0.4835 (p) REVERT: E 74 ILE cc_start: 0.6830 (pt) cc_final: 0.6316 (pt) REVERT: E 106 ASP cc_start: 0.8869 (m-30) cc_final: 0.8589 (m-30) REVERT: H 75 ARG cc_start: 0.7494 (ppt170) cc_final: 0.7094 (ppt170) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.3744 time to fit residues: 147.5938 Evaluate side-chains 263 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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: 0.0370 chunk 45 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 139 optimal weight: 0.0870 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.172333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.150113 restraints weight = 72300.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.152730 restraints weight = 57272.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.154965 restraints weight = 43185.780| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.8755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17855 Z= 0.185 Angle : 0.834 11.679 25347 Z= 0.454 Chirality : 0.047 0.256 2859 Planarity : 0.006 0.084 2191 Dihedral : 29.328 113.230 4760 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -3.33 (0.21), residues: 1320 helix: -1.86 (0.18), residues: 619 sheet: -4.57 (1.34), residues: 12 loop : -2.52 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP K 353 HIS 0.006 0.001 HIS G 38 PHE 0.033 0.002 PHE A 104 TYR 0.038 0.003 TYR B 72 ARG 0.022 0.001 ARG K 278 Details of bonding type rmsd hydrogen bonds : bond 0.06390 ( 741) hydrogen bonds : angle 4.99379 ( 1799) covalent geometry : bond 0.00397 (17855) covalent geometry : angle 0.83369 (25347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5501.67 seconds wall clock time: 97 minutes 23.22 seconds (5843.22 seconds total)