Starting phenix.real_space_refine on Fri Aug 7 03:33:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zs2_74675/08_2026/9zs2_74675.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zs2_74675/08_2026/9zs2_74675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zs2_74675/08_2026/9zs2_74675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zs2_74675/08_2026/9zs2_74675.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zs2_74675/08_2026/9zs2_74675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zs2_74675/08_2026/9zs2_74675.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 63 5.16 5 C 11596 2.51 5 N 3353 2.21 5 O 3500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18542 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5343 Classifications: {'peptide': 694} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 650} Chain breaks: 1 Chain: "E" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1883 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "F" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1883 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "G" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1883 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "H" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1883 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "I" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2491 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 291} Chain: "J" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2547 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 24, 'TRANS': 297} Chain breaks: 1 Chain: "K" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 629 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 8, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 11, 'rna3p': 18} Time building chain proxies: 3.88, per 1000 atoms: 0.21 Number of scatterers: 18542 At special positions: 0 Unit cell: (109.98, 111.86, 224.66, 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 63 16.00 P 30 15.00 O 3500 8.00 N 3353 7.00 C 11596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 780.0 milliseconds 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4194 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 23 sheets defined 39.2% alpha, 16.2% beta 0 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 2 through 26 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 55 through 71 Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.802A pdb=" N LEU A 92 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 146 removed outlier: 4.449A pdb=" N ALA A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 182 through 204 removed outlier: 3.682A pdb=" N GLN A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 230 through 236 Processing helix chain 'A' and resid 241 through 272 removed outlier: 6.820A pdb=" N ALA A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 296 through 317 Processing helix chain 'A' and resid 336 through 357 Processing helix chain 'A' and resid 358 through 361 removed outlier: 3.815A pdb=" N LEU A 361 " --> pdb=" O ARG A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 361' Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.658A pdb=" N ILE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 466 through 469 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 578 through 595 Processing helix chain 'A' and resid 595 through 604 Processing helix chain 'A' and resid 605 through 608 removed outlier: 3.503A pdb=" N ALA A 608 " --> pdb=" O PRO A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 605 through 608' Processing helix chain 'A' and resid 625 through 644 Processing helix chain 'A' and resid 664 through 681 removed outlier: 4.123A pdb=" N LEU A 668 " --> pdb=" O PRO A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'E' and resid 49 through 66 removed outlier: 3.598A pdb=" N LEU E 53 " --> pdb=" O PRO E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 87 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 106 through 110 removed outlier: 3.669A pdb=" N ASP E 109 " --> pdb=" O SER E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 132 through 139 Processing helix chain 'E' and resid 188 through 206 removed outlier: 4.348A pdb=" N LEU E 192 " --> pdb=" O SER E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'F' and resid 49 through 66 removed outlier: 4.014A pdb=" N LEU F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 87 removed outlier: 3.618A pdb=" N TYR F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 104 Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.894A pdb=" N ASP F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 119 Processing helix chain 'F' and resid 132 through 139 Processing helix chain 'F' and resid 189 through 206 Processing helix chain 'F' and resid 210 through 214 Processing helix chain 'F' and resid 230 through 237 Processing helix chain 'G' and resid 49 through 66 removed outlier: 3.907A pdb=" N LEU G 53 " --> pdb=" O PRO G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 89 through 104 Processing helix chain 'G' and resid 106 through 110 removed outlier: 3.556A pdb=" N ASP G 109 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS G 110 " --> pdb=" O GLY G 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 106 through 110' Processing helix chain 'G' and resid 112 through 120 Processing helix chain 'G' and resid 132 through 139 Processing helix chain 'G' and resid 189 through 206 removed outlier: 3.591A pdb=" N GLU G 203 " --> pdb=" O LEU G 199 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU G 204 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 214 Processing helix chain 'G' and resid 230 through 237 Processing helix chain 'H' and resid 49 through 65 removed outlier: 3.661A pdb=" N LEU H 53 " --> pdb=" O PRO H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 89 through 104 removed outlier: 3.629A pdb=" N GLY H 104 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.892A pdb=" N ASP H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 120 removed outlier: 3.606A pdb=" N ALA H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 139 Processing helix chain 'H' and resid 188 through 206 removed outlier: 4.220A pdb=" N LEU H 192 " --> pdb=" O SER H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 237 removed outlier: 3.885A pdb=" N GLN H 236 " --> pdb=" O PRO H 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 54 removed outlier: 7.558A pdb=" N GLU I 47 " --> pdb=" O GLU I 43 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N ALA I 48 " --> pdb=" O SER I 44 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 91 through 101 removed outlier: 4.160A pdb=" N LYS I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN I 97 " --> pdb=" O ARG I 93 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN I 100 " --> pdb=" O LYS I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 109 No H-bonds generated for 'chain 'I' and resid 107 through 109' Processing helix chain 'I' and resid 112 through 120 removed outlier: 4.576A pdb=" N GLY I 117 " --> pdb=" O ALA I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 194 Processing helix chain 'I' and resid 198 through 202 Processing helix chain 'I' and resid 239 through 243 Processing helix chain 'I' and resid 256 through 261 Processing helix chain 'J' and resid 151 through 169 removed outlier: 3.904A pdb=" N LEU J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN J 169 " --> pdb=" O SER J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 194 Processing helix chain 'J' and resid 208 through 215 removed outlier: 3.750A pdb=" N HIS J 211 " --> pdb=" O ARG J 208 " (cutoff:3.500A) Proline residue: J 213 - end of helix Processing helix chain 'J' and resid 287 through 294 Processing helix chain 'J' and resid 296 through 308 Processing helix chain 'J' and resid 308 through 319 removed outlier: 3.558A pdb=" N CYS J 312 " --> pdb=" O THR J 308 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU J 319 " --> pdb=" O GLU J 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 347 removed outlier: 3.581A pdb=" N LEU J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 353 Processing helix chain 'J' and resid 366 through 371 removed outlier: 3.810A pdb=" N SER J 369 " --> pdb=" O GLY J 366 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS J 370 " --> pdb=" O ALA J 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 279 through 283 removed outlier: 5.760A pdb=" N GLN A 279 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL A 290 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 397 through 399 Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 461 removed outlier: 6.349A pdb=" N ARG A 437 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 479 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 611 through 616 removed outlier: 6.813A pdb=" N PHE A 621 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA A 615 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ASP A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 690 Processing sheet with id=AA6, first strand: chain 'E' and resid 124 through 126 removed outlier: 3.589A pdb=" N ALA E 11 " --> pdb=" O PHE E 177 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN E 5 " --> pdb=" O GLN E 183 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR E 12 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA E 222 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL E 14 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE E 220 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 33 through 35 removed outlier: 4.390A pdb=" N ILE E 33 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLU E 167 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER E 35 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HIS E 162 " --> pdb=" O CYS E 152 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS E 152 " --> pdb=" O HIS E 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 124 through 126 removed outlier: 3.723A pdb=" N GLU F 130 " --> pdb=" O ASP F 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 124 through 126 removed outlier: 4.555A pdb=" N THR F 12 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ALA F 222 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL F 14 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N PHE F 220 " --> pdb=" O VAL F 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 146 through 151 Processing sheet with id=AB2, first strand: chain 'G' and resid 124 through 126 removed outlier: 3.575A pdb=" N ALA G 11 " --> pdb=" O PHE G 177 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN G 5 " --> pdb=" O GLN G 183 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR G 12 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ALA G 222 " --> pdb=" O THR G 12 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL G 14 " --> pdb=" O PHE G 220 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE G 220 " --> pdb=" O VAL G 14 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 146 through 153 removed outlier: 4.919A pdb=" N CYS G 152 " --> pdb=" O HIS G 162 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS G 162 " --> pdb=" O CYS G 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 124 through 126 removed outlier: 3.521A pdb=" N ASN H 5 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR H 8 " --> pdb=" O LEU H 225 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU H 225 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG H 10 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU H 223 " --> pdb=" O ARG H 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 153 removed outlier: 4.217A pdb=" N CYS H 152 " --> pdb=" O HIS H 162 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N HIS H 162 " --> pdb=" O CYS H 152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 213 through 214 removed outlier: 8.870A pdb=" N GLY H 214 " --> pdb=" O LEU J 217 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL J 219 " --> pdb=" O GLY H 214 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLN J 273 " --> pdb=" O GLY J 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 64 through 66 removed outlier: 4.236A pdb=" N ARG I 15 " --> pdb=" O GLN I 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 74 through 76 Processing sheet with id=AB9, first strand: chain 'I' and resid 130 through 136 Processing sheet with id=AC1, first strand: chain 'I' and resid 277 through 278 Processing sheet with id=AC2, first strand: chain 'I' and resid 247 through 250 Processing sheet with id=AC3, first strand: chain 'I' and resid 293 through 294 removed outlier: 4.110A pdb=" N LEU I 293 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 260 through 263 Processing sheet with id=AC5, first strand: chain 'J' and resid 378 through 380 770 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5979 1.34 - 1.46: 3167 1.46 - 1.58: 9728 1.58 - 1.70: 59 1.70 - 1.82: 89 Bond restraints: 19022 Sorted by residual: bond pdb=" C GLU J 315 " pdb=" O GLU J 315 " ideal model delta sigma weight residual 1.236 1.272 -0.036 1.19e-02 7.06e+03 9.00e+00 bond pdb=" N ASP A 217 " pdb=" CA ASP A 217 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.69e+00 bond pdb=" N GLY A 216 " pdb=" CA GLY A 216 " ideal model delta sigma weight residual 1.452 1.477 -0.024 9.50e-03 1.11e+04 6.58e+00 bond pdb=" N GLU J 321 " pdb=" CA GLU J 321 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.56e+00 bond pdb=" N LEU A 213 " pdb=" CA LEU A 213 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.10e-02 8.26e+03 5.95e+00 ... (remaining 19017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 25502 2.50 - 5.00: 402 5.00 - 7.50: 39 7.50 - 10.00: 1 10.00 - 12.50: 4 Bond angle restraints: 25948 Sorted by residual: angle pdb=" N LEU A 213 " pdb=" CA LEU A 213 " pdb=" C LEU A 213 " ideal model delta sigma weight residual 112.57 106.10 6.47 1.13e+00 7.83e-01 3.28e+01 angle pdb=" N1 U K 24 " pdb=" C2 U K 24 " pdb=" O2 U K 24 " ideal model delta sigma weight residual 122.80 126.09 -3.29 7.00e-01 2.04e+00 2.21e+01 angle pdb=" O5' U K 2 " pdb=" C5' U K 2 " pdb=" C4' U K 2 " ideal model delta sigma weight residual 109.40 113.01 -3.61 8.00e-01 1.56e+00 2.03e+01 angle pdb=" O2 U K 24 " pdb=" C2 U K 24 " pdb=" N3 U K 24 " ideal model delta sigma weight residual 122.20 119.16 3.04 7.00e-01 2.04e+00 1.88e+01 angle pdb=" CB MET I 70 " pdb=" CG MET I 70 " pdb=" SD MET I 70 " ideal model delta sigma weight residual 112.70 100.20 12.50 3.00e+00 1.11e-01 1.74e+01 ... (remaining 25943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.32: 10504 19.32 - 38.64: 747 38.64 - 57.96: 103 57.96 - 77.28: 34 77.28 - 96.60: 7 Dihedral angle restraints: 11395 sinusoidal: 4859 harmonic: 6536 Sorted by residual: dihedral pdb=" CA ARG J 201 " pdb=" C ARG J 201 " pdb=" N ARG J 202 " pdb=" CA ARG J 202 " ideal model delta harmonic sigma weight residual -180.00 -133.30 -46.70 0 5.00e+00 4.00e-02 8.72e+01 dihedral pdb=" CA THR J 200 " pdb=" C THR J 200 " pdb=" N ARG J 201 " pdb=" CA ARG J 201 " ideal model delta harmonic sigma weight residual 180.00 -147.22 -32.78 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA VAL A 395 " pdb=" C VAL A 395 " pdb=" N GLU A 396 " pdb=" CA GLU A 396 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 11392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2302 0.051 - 0.103: 472 0.103 - 0.154: 96 0.154 - 0.205: 6 0.205 - 0.256: 1 Chirality restraints: 2877 Sorted by residual: chirality pdb=" CA LEU J 316 " pdb=" N LEU J 316 " pdb=" C LEU J 316 " pdb=" CB LEU J 316 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA ASP A 95 " pdb=" N ASP A 95 " pdb=" C ASP A 95 " pdb=" CB ASP A 95 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE H 6 " pdb=" CA ILE H 6 " pdb=" CG1 ILE H 6 " pdb=" CG2 ILE H 6 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.64e-01 ... (remaining 2874 not shown) Planarity restraints: 3314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 528 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C ASN A 528 " 0.047 2.00e-02 2.50e+03 pdb=" O ASN A 528 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY A 529 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS J 314 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C HIS J 314 " 0.036 2.00e-02 2.50e+03 pdb=" O HIS J 314 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU J 315 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 488 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 489 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " -0.027 5.00e-02 4.00e+02 ... (remaining 3311 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6079 2.85 - 3.36: 18438 3.36 - 3.87: 31823 3.87 - 4.39: 36734 4.39 - 4.90: 58305 Nonbonded interactions: 151379 Sorted by model distance: nonbonded pdb=" O SER A 258 " pdb=" OE1 GLU A 262 " model vdw 2.335 3.040 nonbonded pdb=" O ASN A 528 " pdb=" OD1 ASN A 528 " model vdw 2.387 3.040 nonbonded pdb=" O ASP A 639 " pdb=" CB TYR A 643 " model vdw 2.398 2.752 nonbonded pdb=" O GLY A 216 " pdb=" OG SER A 331 " model vdw 2.422 3.040 nonbonded pdb=" O ALA J 317 " pdb=" C TRP J 318 " model vdw 2.444 3.270 ... (remaining 151374 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 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 6.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.670 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 : 0.003 0.046 19022 Z= 0.188 Angle : 0.770 12.496 25948 Z= 0.438 Chirality : 0.044 0.256 2877 Planarity : 0.005 0.061 3314 Dihedral : 13.460 96.596 7201 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.19 % Favored : 95.50 % Rotamer: Outliers : 0.32 % Allowed : 0.32 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2290 helix: 0.41 (0.18), residues: 785 sheet: -0.64 (0.26), residues: 371 loop : -0.79 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 142 TYR 0.016 0.002 TYR A 519 PHE 0.028 0.002 PHE I 34 TRP 0.029 0.002 TRP A 423 HIS 0.008 0.001 HIS J 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.19 (19022) covalent geometry : angle 0.76997 / 0.44 (25948) hydrogen bonds : bond 0.12445 / 8.18 ( 768) hydrogen bonds : angle 7.54103 / 5.54 ( 2142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.698 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: A 217 ASP cc_start: 0.9291 (OUTLIER) cc_final: 0.9016 (m-30) REVERT: A 236 PHE cc_start: 0.9680 (t80) cc_final: 0.9387 (t80) REVERT: E 47 TYR cc_start: 0.9549 (p90) cc_final: 0.9105 (p90) REVERT: E 220 PHE cc_start: 0.8957 (m-80) cc_final: 0.8493 (m-80) REVERT: G 61 LEU cc_start: 0.9342 (mt) cc_final: 0.9027 (pp) REVERT: G 220 PHE cc_start: 0.8372 (m-10) cc_final: 0.7881 (m-10) REVERT: I 66 ILE cc_start: 0.9690 (mm) cc_final: 0.9482 (tp) REVERT: I 75 LEU cc_start: 0.9813 (mt) cc_final: 0.9588 (mp) REVERT: I 135 MET cc_start: 0.8135 (tmm) cc_final: 0.7848 (tmm) outliers start: 6 outliers final: 0 residues processed: 141 average time/residue: 0.1467 time to fit residues: 32.3452 Evaluate side-chains 101 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 overall best weight: 2.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 651 HIS A 671 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN E 242 HIS ** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS I 321 HIS ** J 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.047172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.028818 restraints weight = 197729.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.029515 restraints weight = 151104.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.030001 restraints weight = 126288.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.030192 restraints weight = 111382.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.030510 restraints weight = 103772.290| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19022 Z= 0.176 Angle : 0.642 12.586 25948 Z= 0.321 Chirality : 0.040 0.187 2877 Planarity : 0.005 0.056 3314 Dihedral : 10.925 91.557 2929 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.85 % Favored : 94.98 % Rotamer: Outliers : 0.11 % Allowed : 2.24 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.18), residues: 2290 helix: 0.83 (0.18), residues: 801 sheet: -0.56 (0.25), residues: 371 loop : -0.88 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 298 TYR 0.012 0.001 TYR A 519 PHE 0.019 0.002 PHE A 614 TRP 0.025 0.002 TRP J 318 HIS 0.005 0.001 HIS J 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (19022) covalent geometry : angle 0.64192 / 0.32 (25948) hydrogen bonds : bond 0.04120 / 2.78 ( 768) hydrogen bonds : angle 6.07365 / 4.46 ( 2142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.718 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: A 236 PHE cc_start: 0.9656 (t80) cc_final: 0.9294 (t80) REVERT: A 288 LEU cc_start: 0.9753 (tt) cc_final: 0.9372 (mm) REVERT: E 1 MET cc_start: 0.7694 (mmp) cc_final: 0.6773 (mmp) REVERT: E 220 PHE cc_start: 0.8775 (m-80) cc_final: 0.8365 (m-10) REVERT: G 61 LEU cc_start: 0.9323 (mt) cc_final: 0.9026 (mt) REVERT: G 201 MET cc_start: 0.9621 (mpp) cc_final: 0.9012 (mmt) REVERT: H 19 LEU cc_start: 0.9380 (tp) cc_final: 0.8824 (mt) REVERT: I 66 ILE cc_start: 0.9670 (mm) cc_final: 0.9389 (tp) REVERT: I 135 MET cc_start: 0.8175 (tmm) cc_final: 0.7962 (tmm) REVERT: I 157 SER cc_start: 0.9342 (t) cc_final: 0.9060 (p) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.1451 time to fit residues: 27.8331 Evaluate side-chains 96 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 81 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 159 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 83 optimal weight: 0.0570 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN I 127 HIS ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.047452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.028841 restraints weight = 198820.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.029593 restraints weight = 152117.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.030074 restraints weight = 125889.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.030450 restraints weight = 111156.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.030597 restraints weight = 101568.673| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19022 Z= 0.130 Angle : 0.585 11.896 25948 Z= 0.293 Chirality : 0.039 0.174 2877 Planarity : 0.004 0.058 3314 Dihedral : 10.873 92.119 2929 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.72 % Favored : 95.11 % Rotamer: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 2290 helix: 0.99 (0.18), residues: 804 sheet: -0.47 (0.25), residues: 365 loop : -0.82 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 376 TYR 0.011 0.001 TYR A 519 PHE 0.017 0.001 PHE A 614 TRP 0.011 0.001 TRP J 216 HIS 0.007 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (19022) covalent geometry : angle 0.58492 / 0.29 (25948) hydrogen bonds : bond 0.03724 / 2.49 ( 768) hydrogen bonds : angle 5.72975 / 4.19 ( 2142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.704 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: A 117 MET cc_start: 0.7468 (tpt) cc_final: 0.6896 (tpt) REVERT: A 236 PHE cc_start: 0.9662 (t80) cc_final: 0.9294 (t80) REVERT: A 288 LEU cc_start: 0.9746 (tt) cc_final: 0.9389 (mm) REVERT: E 1 MET cc_start: 0.7367 (mmp) cc_final: 0.6885 (mmp) REVERT: E 207 LEU cc_start: 0.9253 (tp) cc_final: 0.8944 (tt) REVERT: E 220 PHE cc_start: 0.8791 (m-80) cc_final: 0.8383 (m-10) REVERT: G 61 LEU cc_start: 0.9328 (mt) cc_final: 0.9024 (pp) REVERT: G 195 LEU cc_start: 0.9813 (tt) cc_final: 0.9562 (mt) REVERT: H 19 LEU cc_start: 0.9361 (tp) cc_final: 0.8826 (mt) REVERT: I 157 SER cc_start: 0.9325 (t) cc_final: 0.9030 (p) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1368 time to fit residues: 26.6778 Evaluate side-chains 89 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 119 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 609 ASN A 630 GLN E 45 GLN E 83 GLN ** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.046584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.028447 restraints weight = 204433.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.029195 restraints weight = 154306.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.029689 restraints weight = 126954.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.029988 restraints weight = 111244.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.030179 restraints weight = 102676.910| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19022 Z= 0.161 Angle : 0.596 9.978 25948 Z= 0.299 Chirality : 0.039 0.175 2877 Planarity : 0.004 0.058 3314 Dihedral : 10.858 90.480 2929 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.98 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2290 helix: 0.92 (0.18), residues: 816 sheet: -0.42 (0.25), residues: 363 loop : -0.83 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 178 TYR 0.009 0.001 TYR I 171 PHE 0.016 0.002 PHE A 614 TRP 0.019 0.002 TRP J 375 HIS 0.012 0.001 HIS I 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (19022) covalent geometry : angle 0.59645 / 0.30 (25948) hydrogen bonds : bond 0.03606 / 2.40 ( 768) hydrogen bonds : angle 5.63643 / 4.11 ( 2142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.583 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: A 236 PHE cc_start: 0.9695 (t80) cc_final: 0.9320 (t80) REVERT: E 1 MET cc_start: 0.7532 (mmp) cc_final: 0.7111 (mmt) REVERT: E 207 LEU cc_start: 0.9154 (tp) cc_final: 0.8883 (tt) REVERT: E 220 PHE cc_start: 0.8899 (m-80) cc_final: 0.8419 (m-10) REVERT: G 61 LEU cc_start: 0.9334 (mt) cc_final: 0.9049 (pp) REVERT: G 195 LEU cc_start: 0.9844 (tt) cc_final: 0.9604 (mt) REVERT: H 19 LEU cc_start: 0.9367 (tp) cc_final: 0.8833 (mt) REVERT: H 103 PHE cc_start: 0.9527 (m-80) cc_final: 0.9119 (m-80) REVERT: I 66 ILE cc_start: 0.9701 (mm) cc_final: 0.9351 (tp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1277 time to fit residues: 21.9822 Evaluate side-chains 84 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 140 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 231 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 10 optimal weight: 0.0770 chunk 38 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 4 optimal weight: 0.0020 chunk 68 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 HIS ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.047041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.028762 restraints weight = 199370.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.029470 restraints weight = 151689.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.029980 restraints weight = 125838.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.030186 restraints weight = 110391.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.030551 restraints weight = 102084.844| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19022 Z= 0.117 Angle : 0.566 10.264 25948 Z= 0.282 Chirality : 0.039 0.173 2877 Planarity : 0.004 0.057 3314 Dihedral : 10.845 90.972 2929 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.67 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2290 helix: 1.00 (0.18), residues: 808 sheet: -0.33 (0.26), residues: 364 loop : -0.78 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG I 95 TYR 0.012 0.001 TYR A 132 PHE 0.015 0.001 PHE A 614 TRP 0.012 0.001 TRP A 311 HIS 0.009 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (19022) covalent geometry : angle 0.56635 / 0.28 (25948) hydrogen bonds : bond 0.03321 / 2.21 ( 768) hydrogen bonds : angle 5.51104 / 4.01 ( 2142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.967 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: A 236 PHE cc_start: 0.9689 (t80) cc_final: 0.9317 (t80) REVERT: A 389 MET cc_start: 0.7995 (ppp) cc_final: 0.7702 (ppp) REVERT: E 1 MET cc_start: 0.7383 (mmp) cc_final: 0.7011 (mmp) REVERT: E 207 LEU cc_start: 0.9137 (tp) cc_final: 0.8889 (tt) REVERT: E 220 PHE cc_start: 0.8922 (m-80) cc_final: 0.8410 (m-10) REVERT: G 61 LEU cc_start: 0.9343 (mt) cc_final: 0.9040 (pp) REVERT: G 195 LEU cc_start: 0.9852 (tt) cc_final: 0.9611 (mt) REVERT: H 19 LEU cc_start: 0.9356 (tp) cc_final: 0.8816 (mt) REVERT: H 103 PHE cc_start: 0.9509 (m-80) cc_final: 0.9099 (m-80) REVERT: I 66 ILE cc_start: 0.9683 (mm) cc_final: 0.9338 (tp) REVERT: I 75 LEU cc_start: 0.9706 (mt) cc_final: 0.9500 (mp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1378 time to fit residues: 24.4813 Evaluate side-chains 88 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 95 optimal weight: 0.0670 chunk 133 optimal weight: 0.1980 chunk 205 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 123 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 38 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.759 > 50:) chunk 196 optimal weight: 8.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN H 95 GLN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.048080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.029432 restraints weight = 192090.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.029990 restraints weight = 144217.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.030710 restraints weight = 119156.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.030933 restraints weight = 104047.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.031311 restraints weight = 95849.914| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19022 Z= 0.100 Angle : 0.553 9.793 25948 Z= 0.272 Chirality : 0.039 0.186 2877 Planarity : 0.004 0.057 3314 Dihedral : 10.740 90.973 2929 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 0.05 % Allowed : 1.33 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.18), residues: 2290 helix: 1.06 (0.19), residues: 805 sheet: -0.35 (0.26), residues: 368 loop : -0.66 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 95 TYR 0.016 0.001 TYR A 430 PHE 0.014 0.001 PHE F 240 TRP 0.014 0.001 TRP A 311 HIS 0.006 0.001 HIS I 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (19022) covalent geometry : angle 0.55282 / 0.27 (25948) hydrogen bonds : bond 0.03110 / 2.06 ( 768) hydrogen bonds : angle 5.24351 / 3.80 ( 2142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.733 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: A 117 MET cc_start: 0.8247 (tpt) cc_final: 0.8013 (tpt) REVERT: A 236 PHE cc_start: 0.9672 (t80) cc_final: 0.9308 (t80) REVERT: A 334 PHE cc_start: 0.9389 (t80) cc_final: 0.9183 (t80) REVERT: A 389 MET cc_start: 0.8115 (ppp) cc_final: 0.7856 (ppp) REVERT: E 1 MET cc_start: 0.7130 (mmp) cc_final: 0.6837 (mmp) REVERT: E 47 TYR cc_start: 0.9513 (p90) cc_final: 0.8947 (p90) REVERT: E 207 LEU cc_start: 0.9187 (tp) cc_final: 0.8939 (tt) REVERT: E 220 PHE cc_start: 0.8933 (m-80) cc_final: 0.8329 (m-10) REVERT: F 19 LEU cc_start: 0.9074 (tt) cc_final: 0.8165 (mp) REVERT: G 61 LEU cc_start: 0.9326 (mt) cc_final: 0.8986 (pp) REVERT: G 195 LEU cc_start: 0.9852 (tt) cc_final: 0.9617 (mt) REVERT: G 220 PHE cc_start: 0.7996 (m-10) cc_final: 0.7614 (m-10) REVERT: H 19 LEU cc_start: 0.9382 (tp) cc_final: 0.8846 (mt) REVERT: H 103 PHE cc_start: 0.9518 (m-80) cc_final: 0.9115 (m-80) REVERT: I 70 MET cc_start: 0.8775 (tpt) cc_final: 0.8468 (tpt) REVERT: I 75 LEU cc_start: 0.9680 (mt) cc_final: 0.9455 (mp) outliers start: 1 outliers final: 1 residues processed: 120 average time/residue: 0.1407 time to fit residues: 26.6915 Evaluate side-chains 90 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 80 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 163 optimal weight: 0.0030 chunk 219 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 220 optimal weight: 20.0000 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.047134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.028757 restraints weight = 201608.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.029485 restraints weight = 152127.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.029983 restraints weight = 125952.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.030202 restraints weight = 110580.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.030517 restraints weight = 102633.184| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19022 Z= 0.129 Angle : 0.558 9.448 25948 Z= 0.276 Chirality : 0.038 0.171 2877 Planarity : 0.004 0.059 3314 Dihedral : 10.707 88.472 2929 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2290 helix: 1.09 (0.19), residues: 813 sheet: -0.34 (0.27), residues: 348 loop : -0.65 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 602 TYR 0.011 0.001 TYR A 132 PHE 0.016 0.001 PHE H 220 TRP 0.015 0.001 TRP I 116 HIS 0.006 0.001 HIS I 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (19022) covalent geometry : angle 0.55780 / 0.28 (25948) hydrogen bonds : bond 0.03211 / 2.12 ( 768) hydrogen bonds : angle 5.26412 / 3.82 ( 2142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.735 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: A 117 MET cc_start: 0.8327 (tpt) cc_final: 0.8094 (tpt) REVERT: A 236 PHE cc_start: 0.9666 (t80) cc_final: 0.9312 (t80) REVERT: A 334 PHE cc_start: 0.9453 (t80) cc_final: 0.9228 (t80) REVERT: E 1 MET cc_start: 0.7310 (mmp) cc_final: 0.6990 (mmp) REVERT: E 47 TYR cc_start: 0.9618 (p90) cc_final: 0.9029 (p90) REVERT: E 207 LEU cc_start: 0.9195 (tp) cc_final: 0.8927 (tt) REVERT: E 220 PHE cc_start: 0.8929 (m-80) cc_final: 0.8328 (m-10) REVERT: G 61 LEU cc_start: 0.9309 (mt) cc_final: 0.8983 (pp) REVERT: G 195 LEU cc_start: 0.9865 (tt) cc_final: 0.9633 (mt) REVERT: G 220 PHE cc_start: 0.7992 (m-10) cc_final: 0.7594 (m-10) REVERT: H 19 LEU cc_start: 0.9374 (tp) cc_final: 0.8807 (mt) REVERT: H 103 PHE cc_start: 0.9523 (m-80) cc_final: 0.9132 (m-80) REVERT: I 70 MET cc_start: 0.8800 (tpt) cc_final: 0.8344 (tpt) REVERT: I 75 LEU cc_start: 0.9693 (mt) cc_final: 0.9446 (mp) REVERT: J 327 ASP cc_start: 0.7437 (p0) cc_final: 0.7188 (t0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1372 time to fit residues: 24.8794 Evaluate side-chains 82 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 198 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 143 optimal weight: 30.0000 chunk 166 optimal weight: 0.0770 chunk 123 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 153 optimal weight: 0.0050 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 HIS ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.047566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.029114 restraints weight = 197893.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.029883 restraints weight = 146782.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.030399 restraints weight = 120117.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.030605 restraints weight = 105063.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.030968 restraints weight = 97153.836| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19022 Z= 0.100 Angle : 0.554 9.274 25948 Z= 0.270 Chirality : 0.038 0.172 2877 Planarity : 0.004 0.058 3314 Dihedral : 10.689 89.386 2929 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.18), residues: 2290 helix: 1.13 (0.19), residues: 806 sheet: -0.26 (0.27), residues: 347 loop : -0.61 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 353 TYR 0.014 0.001 TYR A 132 PHE 0.013 0.001 PHE A 614 TRP 0.029 0.001 TRP I 11 HIS 0.005 0.001 HIS I 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (19022) covalent geometry : angle 0.55379 / 0.27 (25948) hydrogen bonds : bond 0.03046 / 2.00 ( 768) hydrogen bonds : angle 5.18859 / 3.75 ( 2142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.599 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: A 117 MET cc_start: 0.8366 (tpt) cc_final: 0.8068 (tpt) REVERT: A 236 PHE cc_start: 0.9659 (t80) cc_final: 0.9274 (t80) REVERT: A 334 PHE cc_start: 0.9438 (t80) cc_final: 0.9213 (t80) REVERT: A 389 MET cc_start: 0.7744 (ppp) cc_final: 0.7510 (ppp) REVERT: E 1 MET cc_start: 0.7220 (mmp) cc_final: 0.6895 (mmp) REVERT: E 47 TYR cc_start: 0.9561 (p90) cc_final: 0.8970 (p90) REVERT: E 207 LEU cc_start: 0.9220 (tp) cc_final: 0.8975 (tt) REVERT: E 220 PHE cc_start: 0.8901 (m-80) cc_final: 0.8287 (m-10) REVERT: G 61 LEU cc_start: 0.9308 (mt) cc_final: 0.8970 (pp) REVERT: G 195 LEU cc_start: 0.9864 (tt) cc_final: 0.9630 (mt) REVERT: G 220 PHE cc_start: 0.7965 (m-10) cc_final: 0.7620 (m-10) REVERT: H 19 LEU cc_start: 0.9378 (tp) cc_final: 0.8816 (mt) REVERT: H 103 PHE cc_start: 0.9513 (m-80) cc_final: 0.9112 (m-80) REVERT: I 70 MET cc_start: 0.8814 (tpt) cc_final: 0.8410 (tpt) REVERT: I 75 LEU cc_start: 0.9672 (mt) cc_final: 0.9442 (mp) REVERT: I 213 MET cc_start: 0.8776 (mmt) cc_final: 0.8307 (mmt) REVERT: J 327 ASP cc_start: 0.7470 (p0) cc_final: 0.7233 (t0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1318 time to fit residues: 24.8150 Evaluate side-chains 84 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 37 optimal weight: 0.5980 chunk 177 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 chunk 47 optimal weight: 0.2980 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.047042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.028740 restraints weight = 200568.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.029233 restraints weight = 151527.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.029921 restraints weight = 126180.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.030129 restraints weight = 110633.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.030472 restraints weight = 102426.383| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19022 Z= 0.119 Angle : 0.560 9.099 25948 Z= 0.274 Chirality : 0.038 0.169 2877 Planarity : 0.004 0.058 3314 Dihedral : 10.674 88.500 2929 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2290 helix: 1.16 (0.19), residues: 806 sheet: -0.22 (0.27), residues: 352 loop : -0.60 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 25 TYR 0.009 0.001 TYR A 340 PHE 0.017 0.001 PHE A 534 TRP 0.027 0.001 TRP I 11 HIS 0.005 0.001 HIS I 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (19022) covalent geometry : angle 0.55989 / 0.27 (25948) hydrogen bonds : bond 0.03119 / 2.05 ( 768) hydrogen bonds : angle 5.23602 / 3.78 ( 2142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.712 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: A 117 MET cc_start: 0.8338 (tpt) cc_final: 0.8044 (tpt) REVERT: A 236 PHE cc_start: 0.9655 (t80) cc_final: 0.9276 (t80) REVERT: A 334 PHE cc_start: 0.9451 (t80) cc_final: 0.9223 (t80) REVERT: A 351 MET cc_start: 0.9637 (mmp) cc_final: 0.9427 (mmm) REVERT: A 389 MET cc_start: 0.7774 (ppp) cc_final: 0.7543 (ppp) REVERT: E 1 MET cc_start: 0.7287 (mmp) cc_final: 0.6949 (mmp) REVERT: E 47 TYR cc_start: 0.9578 (p90) cc_final: 0.8994 (p90) REVERT: E 207 LEU cc_start: 0.9248 (tp) cc_final: 0.8983 (tt) REVERT: E 220 PHE cc_start: 0.8851 (m-80) cc_final: 0.8182 (m-10) REVERT: G 61 LEU cc_start: 0.9303 (mt) cc_final: 0.8975 (pp) REVERT: G 195 LEU cc_start: 0.9867 (tt) cc_final: 0.9644 (mt) REVERT: G 220 PHE cc_start: 0.7903 (m-10) cc_final: 0.7578 (m-10) REVERT: H 19 LEU cc_start: 0.9388 (tp) cc_final: 0.8809 (mt) REVERT: H 103 PHE cc_start: 0.9499 (m-80) cc_final: 0.9094 (m-80) REVERT: I 32 THR cc_start: 0.9453 (m) cc_final: 0.9252 (p) REVERT: I 33 LEU cc_start: 0.9838 (mt) cc_final: 0.9614 (mt) REVERT: I 70 MET cc_start: 0.8778 (tpt) cc_final: 0.8418 (tpt) REVERT: I 75 LEU cc_start: 0.9686 (mt) cc_final: 0.9449 (mp) REVERT: I 213 MET cc_start: 0.8770 (mmt) cc_final: 0.8371 (mmt) REVERT: J 327 ASP cc_start: 0.7575 (p0) cc_final: 0.7321 (t0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1288 time to fit residues: 23.0406 Evaluate side-chains 85 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 74 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.047498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.029016 restraints weight = 198118.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.029792 restraints weight = 149203.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.030356 restraints weight = 121602.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.030554 restraints weight = 105263.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.030782 restraints weight = 97511.731| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19022 Z= 0.100 Angle : 0.562 8.948 25948 Z= 0.274 Chirality : 0.039 0.218 2877 Planarity : 0.004 0.058 3314 Dihedral : 10.644 88.929 2929 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2290 helix: 1.11 (0.19), residues: 806 sheet: -0.17 (0.27), residues: 350 loop : -0.57 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 627 TYR 0.017 0.001 TYR A 184 PHE 0.012 0.001 PHE A 614 TRP 0.025 0.001 TRP I 11 HIS 0.005 0.001 HIS H 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (19022) covalent geometry : angle 0.56215 / 0.27 (25948) hydrogen bonds : bond 0.03024 / 1.99 ( 768) hydrogen bonds : angle 5.19135 / 3.74 ( 2142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.520 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: A 117 MET cc_start: 0.8401 (tpt) cc_final: 0.8135 (tpt) REVERT: A 236 PHE cc_start: 0.9635 (t80) cc_final: 0.9307 (t80) REVERT: A 334 PHE cc_start: 0.9454 (t80) cc_final: 0.9217 (t80) REVERT: A 351 MET cc_start: 0.9649 (mmp) cc_final: 0.9447 (mmm) REVERT: A 389 MET cc_start: 0.7768 (ppp) cc_final: 0.7538 (ppp) REVERT: E 1 MET cc_start: 0.7205 (mmp) cc_final: 0.6875 (mmp) REVERT: E 47 TYR cc_start: 0.9577 (p90) cc_final: 0.8983 (p90) REVERT: E 207 LEU cc_start: 0.9209 (tp) cc_final: 0.8982 (tt) REVERT: E 220 PHE cc_start: 0.8864 (m-80) cc_final: 0.8275 (m-10) REVERT: G 61 LEU cc_start: 0.9299 (mt) cc_final: 0.8953 (pp) REVERT: G 195 LEU cc_start: 0.9869 (tt) cc_final: 0.9645 (mt) REVERT: G 220 PHE cc_start: 0.7869 (m-10) cc_final: 0.7551 (m-10) REVERT: H 19 LEU cc_start: 0.9399 (tp) cc_final: 0.8800 (mt) REVERT: H 103 PHE cc_start: 0.9510 (m-80) cc_final: 0.9091 (m-80) REVERT: I 70 MET cc_start: 0.8777 (tpt) cc_final: 0.8428 (tpt) REVERT: I 75 LEU cc_start: 0.9685 (mt) cc_final: 0.9457 (mp) REVERT: I 213 MET cc_start: 0.8743 (mmt) cc_final: 0.8474 (mmt) REVERT: J 327 ASP cc_start: 0.7593 (p0) cc_final: 0.7362 (t0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1188 time to fit residues: 21.6272 Evaluate side-chains 86 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 165 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 194 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.047520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.029021 restraints weight = 198437.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.029805 restraints weight = 149199.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.030346 restraints weight = 121678.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.030540 restraints weight = 106073.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.030879 restraints weight = 98083.523| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19022 Z= 0.099 Angle : 0.557 8.877 25948 Z= 0.270 Chirality : 0.038 0.167 2877 Planarity : 0.004 0.058 3314 Dihedral : 10.602 88.546 2929 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2290 helix: 1.13 (0.19), residues: 807 sheet: -0.17 (0.27), residues: 352 loop : -0.53 (0.20), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 25 TYR 0.015 0.001 TYR A 184 PHE 0.013 0.001 PHE A 614 TRP 0.025 0.001 TRP I 11 HIS 0.005 0.001 HIS H 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (19022) covalent geometry : angle 0.55676 / 0.27 (25948) hydrogen bonds : bond 0.03039 / 1.99 ( 768) hydrogen bonds : angle 5.14685 / 3.71 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.97 seconds wall clock time: 59 minutes 54.55 seconds (3594.55 seconds total)