Starting phenix.real_space_refine on Sat Jul 4 07:05:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zs2_74675/07_2026/9zs2_74675.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zs2_74675/07_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_74675/07_2026/9zs2_74675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zs2_74675/07_2026/9zs2_74675.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zs2_74675/07_2026/9zs2_74675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zs2_74675/07_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-dev-6108/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: 4.17, per 1000 atoms: 0.22 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: 1.51 Conformation dependent library (CDL) restraints added in 940.7 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: 1.95 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: 3.59 Time building geometry restraints manager: 2.00 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: 25525 2.50 - 5.00: 379 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=" 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 angle pdb=" CB MET G 201 " pdb=" CG MET G 201 " pdb=" SD MET G 201 " ideal model delta sigma weight residual 112.70 125.10 -12.40 3.00e+00 1.11e-01 1.71e+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: 2333 0.051 - 0.103: 461 0.103 - 0.154: 76 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: 7.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.350 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- 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= 0.186 Angle : 0.761 12.496 25948 Z= 0.426 Chirality : 0.042 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 0.00331 / 0.19 (19022) covalent geometry : angle 0.76078 / 0.43 (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 : 0.745 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: 0.1297 time to fit residues: 28.2377 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 : 0.679 ------------------------------------------------------------------------------- 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: 6.9990 chunk 200 optimal weight: 8.9990 overall best weight: 2.8362 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.047035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.028685 restraints weight = 198266.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.029387 restraints weight = 151425.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.029829 restraints weight = 126423.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.030028 restraints weight = 112145.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.030379 restraints weight = 104207.613| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19022 Z= 0.183 Angle : 0.641 12.152 25948 Z= 0.322 Chirality : 0.040 0.182 2877 Planarity : 0.005 0.056 3314 Dihedral : 10.998 95.145 2929 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.85 % Favored : 94.98 % Rotamer: Outliers : 0.05 % Allowed : 2.29 % 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: 0.82 (0.18), residues: 801 sheet: -0.57 (0.25), residues: 371 loop : -0.87 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 298 TYR 0.012 0.002 TYR A 519 PHE 0.019 0.002 PHE A 614 TRP 0.024 0.002 TRP J 318 HIS 0.005 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (19022) covalent geometry : angle 0.64110 / 0.32 (25948) hydrogen bonds : bond 0.04258 / 2.86 ( 768) hydrogen bonds : angle 6.12561 / 4.49 ( 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 121 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.732 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: A 236 PHE cc_start: 0.9655 (t80) cc_final: 0.9295 (t80) REVERT: A 288 LEU cc_start: 0.9752 (tt) cc_final: 0.9371 (mm) REVERT: E 1 MET cc_start: 0.7820 (mmp) cc_final: 0.6913 (mmp) REVERT: E 220 PHE cc_start: 0.8774 (m-80) cc_final: 0.8372 (m-10) REVERT: G 61 LEU cc_start: 0.9316 (mt) cc_final: 0.9008 (mt) REVERT: G 201 MET cc_start: 0.9620 (mpp) cc_final: 0.9009 (mmt) REVERT: H 19 LEU cc_start: 0.9380 (tp) cc_final: 0.8823 (mt) REVERT: I 66 ILE cc_start: 0.9672 (mm) cc_final: 0.9391 (tp) REVERT: I 135 MET cc_start: 0.8179 (tmm) cc_final: 0.7964 (tmm) REVERT: I 157 SER cc_start: 0.9348 (t) cc_final: 0.9070 (p) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.1357 time to fit residues: 25.5413 Evaluate side-chains 95 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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: 6.9990 chunk 228 optimal weight: 0.9990 chunk 179 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 83 optimal weight: 0.0870 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 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** J 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.047982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.029270 restraints weight = 196146.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.030029 restraints weight = 148311.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.030536 restraints weight = 123409.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.030751 restraints weight = 108561.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.031113 restraints weight = 100454.897| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 19022 Z= 0.114 Angle : 0.580 11.771 25948 Z= 0.288 Chirality : 0.040 0.176 2877 Planarity : 0.004 0.061 3314 Dihedral : 10.926 96.188 2929 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.41 % Favored : 95.41 % Rotamer: Outliers : 0.05 % Allowed : 1.97 % Favored : 97.97 % 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: -0.18 (0.18), residues: 2290 helix: 1.02 (0.18), residues: 802 sheet: -0.42 (0.26), residues: 361 loop : -0.81 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 376 TYR 0.010 0.001 TYR A 519 PHE 0.018 0.001 PHE F 220 TRP 0.011 0.001 TRP A 311 HIS 0.005 0.001 HIS I 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (19022) covalent geometry : angle 0.57963 / 0.29 (25948) hydrogen bonds : bond 0.03600 / 2.41 ( 768) hydrogen bonds : angle 5.63778 / 4.12 ( 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 125 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.684 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: A 236 PHE cc_start: 0.9659 (t80) cc_final: 0.9299 (t80) REVERT: A 288 LEU cc_start: 0.9753 (tt) cc_final: 0.9398 (mm) REVERT: E 1 MET cc_start: 0.7253 (mmp) cc_final: 0.6780 (mmp) REVERT: E 207 LEU cc_start: 0.9253 (tp) cc_final: 0.8957 (tt) REVERT: E 220 PHE cc_start: 0.8812 (m-80) cc_final: 0.8419 (m-10) REVERT: G 61 LEU cc_start: 0.9312 (mt) cc_final: 0.9024 (pp) REVERT: G 195 LEU cc_start: 0.9812 (tt) cc_final: 0.9560 (mt) REVERT: H 19 LEU cc_start: 0.9360 (tp) cc_final: 0.8821 (mt) REVERT: I 33 LEU cc_start: 0.9799 (mt) cc_final: 0.9587 (mt) REVERT: I 70 MET cc_start: 0.8714 (tpt) cc_final: 0.7974 (tpt) REVERT: I 75 LEU cc_start: 0.9646 (mt) cc_final: 0.9382 (mp) REVERT: I 157 SER cc_start: 0.9304 (t) cc_final: 0.8988 (p) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1316 time to fit residues: 25.7108 Evaluate side-chains 95 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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: 20.0000 chunk 195 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 220 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 457 GLN A 588 GLN A 609 ASN A 630 GLN ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN E 83 GLN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 GLN ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 419 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.044780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.027191 restraints weight = 212351.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.027895 restraints weight = 159488.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.028338 restraints weight = 132565.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.028525 restraints weight = 117237.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.028828 restraints weight = 108632.437| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19022 Z= 0.295 Angle : 0.783 10.609 25948 Z= 0.390 Chirality : 0.041 0.187 2877 Planarity : 0.005 0.059 3314 Dihedral : 11.139 90.078 2929 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.81 % Favored : 94.06 % Rotamer: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % 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: -0.58 (0.17), residues: 2290 helix: 0.51 (0.18), residues: 815 sheet: -0.46 (0.26), residues: 360 loop : -0.98 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 178 TYR 0.021 0.002 TYR A 430 PHE 0.020 0.003 PHE I 319 TRP 0.024 0.003 TRP J 375 HIS 0.010 0.002 HIS I 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.30 (19022) covalent geometry : angle 0.78291 / 0.39 (25948) hydrogen bonds : bond 0.04437 / 2.96 ( 768) hydrogen bonds : angle 5.96018 / 4.34 ( 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 107 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.700 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: A 236 PHE cc_start: 0.9693 (t80) cc_final: 0.9290 (t80) REVERT: E 1 MET cc_start: 0.8007 (mmp) cc_final: 0.7513 (mmt) REVERT: E 220 PHE cc_start: 0.8891 (m-80) cc_final: 0.8401 (m-10) REVERT: G 61 LEU cc_start: 0.9319 (mt) cc_final: 0.9008 (mt) REVERT: G 195 LEU cc_start: 0.9851 (tt) cc_final: 0.9636 (mt) REVERT: H 19 LEU cc_start: 0.9394 (tp) cc_final: 0.8796 (mt) REVERT: H 103 PHE cc_start: 0.9560 (m-80) cc_final: 0.9198 (m-80) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1409 time to fit residues: 22.9732 Evaluate side-chains 77 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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: 7.9990 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 231 optimal weight: 30.0000 chunk 209 optimal weight: 40.0000 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 148 optimal weight: 9.9990 chunk 4 optimal weight: 0.0980 chunk 68 optimal weight: 30.0000 chunk 128 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 HIS ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.046043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.027993 restraints weight = 201760.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.028741 restraints weight = 152179.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.029216 restraints weight = 125289.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.029413 restraints weight = 110190.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.029750 restraints weight = 102196.576| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19022 Z= 0.141 Angle : 0.607 10.418 25948 Z= 0.303 Chirality : 0.040 0.236 2877 Planarity : 0.004 0.058 3314 Dihedral : 11.113 92.760 2929 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: -0.34 (0.17), residues: 2290 helix: 0.81 (0.18), residues: 806 sheet: -0.37 (0.26), residues: 358 loop : -0.90 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 95 TYR 0.011 0.001 TYR I 171 PHE 0.019 0.002 PHE F 240 TRP 0.013 0.001 TRP I 103 HIS 0.008 0.001 HIS I 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (19022) covalent geometry : angle 0.60672 / 0.30 (25948) hydrogen bonds : bond 0.03550 / 2.35 ( 768) hydrogen bonds : angle 5.70219 / 4.14 ( 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 106 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.673 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: A 117 MET cc_start: 0.8275 (tpt) cc_final: 0.8058 (tpt) REVERT: A 236 PHE cc_start: 0.9680 (t80) cc_final: 0.9281 (t80) REVERT: A 389 MET cc_start: 0.7978 (ppp) cc_final: 0.7663 (ppp) REVERT: E 1 MET cc_start: 0.7688 (mmp) cc_final: 0.7106 (mmp) REVERT: E 207 LEU cc_start: 0.9254 (tp) cc_final: 0.8997 (tt) REVERT: E 220 PHE cc_start: 0.8899 (m-80) cc_final: 0.8436 (m-10) REVERT: G 61 LEU cc_start: 0.9326 (mt) cc_final: 0.9018 (pp) REVERT: H 19 LEU cc_start: 0.9412 (tp) cc_final: 0.8802 (mt) REVERT: H 103 PHE cc_start: 0.9528 (m-80) cc_final: 0.9136 (m-80) REVERT: I 70 MET cc_start: 0.8865 (tpt) cc_final: 0.8463 (tpt) REVERT: I 75 LEU cc_start: 0.9697 (mt) cc_final: 0.9472 (mp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1286 time to fit residues: 21.4785 Evaluate side-chains 80 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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: 20.0000 chunk 133 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 38 optimal weight: 0.0010 chunk 196 optimal weight: 0.5980 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 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 = 0.3398 r_free = 0.3398 target = 0.046368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.028254 restraints weight = 199131.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.028980 restraints weight = 152609.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.029480 restraints weight = 125554.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.029697 restraints weight = 109392.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.030030 restraints weight = 100972.527| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19022 Z= 0.123 Angle : 0.569 10.096 25948 Z= 0.284 Chirality : 0.039 0.178 2877 Planarity : 0.004 0.058 3314 Dihedral : 11.052 92.990 2929 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.98 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -0.22 (0.18), residues: 2290 helix: 0.93 (0.18), residues: 806 sheet: -0.33 (0.27), residues: 356 loop : -0.83 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 627 TYR 0.012 0.001 TYR A 340 PHE 0.016 0.001 PHE A 614 TRP 0.013 0.001 TRP A 157 HIS 0.007 0.001 HIS I 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (19022) covalent geometry : angle 0.56884 / 0.28 (25948) hydrogen bonds : bond 0.03367 / 2.23 ( 768) hydrogen bonds : angle 5.51598 / 4.00 ( 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 106 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.656 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: A 117 MET cc_start: 0.8494 (tpt) cc_final: 0.8204 (tpt) REVERT: A 236 PHE cc_start: 0.9686 (t80) cc_final: 0.9291 (t80) REVERT: A 389 MET cc_start: 0.8100 (ppp) cc_final: 0.7856 (ppp) REVERT: E 1 MET cc_start: 0.7559 (mmp) cc_final: 0.7005 (mmp) REVERT: E 207 LEU cc_start: 0.9205 (tp) cc_final: 0.8966 (tt) REVERT: E 220 PHE cc_start: 0.8972 (m-80) cc_final: 0.8453 (m-10) REVERT: G 61 LEU cc_start: 0.9320 (mt) cc_final: 0.9021 (pp) REVERT: H 19 LEU cc_start: 0.9360 (tp) cc_final: 0.8784 (mt) REVERT: H 103 PHE cc_start: 0.9549 (m-80) cc_final: 0.9157 (m-80) REVERT: I 70 MET cc_start: 0.8888 (tpt) cc_final: 0.8484 (tpt) REVERT: I 75 LEU cc_start: 0.9720 (mt) cc_final: 0.9492 (mp) REVERT: J 327 ASP cc_start: 0.7580 (p0) cc_final: 0.7327 (t0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1212 time to fit residues: 20.4957 Evaluate side-chains 81 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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: 0.8980 chunk 128 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 0.0980 chunk 39 optimal weight: 8.9990 chunk 163 optimal weight: 0.0980 chunk 219 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** A 588 GLN A 692 ASN ** H 151 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.046948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.028678 restraints weight = 200930.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.029430 restraints weight = 150335.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.029935 restraints weight = 123810.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.030140 restraints weight = 108442.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.030484 restraints weight = 100185.098| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19022 Z= 0.104 Angle : 0.567 9.884 25948 Z= 0.279 Chirality : 0.039 0.169 2877 Planarity : 0.004 0.058 3314 Dihedral : 10.960 92.704 2929 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer: Outliers : 0.05 % Allowed : 1.17 % 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: -0.12 (0.18), residues: 2290 helix: 0.99 (0.19), residues: 802 sheet: -0.41 (0.27), residues: 350 loop : -0.70 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 627 TYR 0.011 0.001 TYR A 132 PHE 0.019 0.001 PHE A 534 TRP 0.014 0.001 TRP A 157 HIS 0.006 0.001 HIS H 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (19022) covalent geometry : angle 0.56668 / 0.28 (25948) hydrogen bonds : bond 0.03199 / 2.10 ( 768) hydrogen bonds : angle 5.37570 / 3.88 ( 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 104 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.684 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: A 117 MET cc_start: 0.8346 (tpt) cc_final: 0.8104 (tpt) REVERT: A 236 PHE cc_start: 0.9674 (t80) cc_final: 0.9310 (t80) REVERT: A 389 MET cc_start: 0.8119 (ppp) cc_final: 0.7875 (ppp) REVERT: E 1 MET cc_start: 0.7313 (mmp) cc_final: 0.6751 (mmt) REVERT: E 207 LEU cc_start: 0.9213 (tp) cc_final: 0.8968 (tt) REVERT: E 220 PHE cc_start: 0.8897 (m-80) cc_final: 0.8381 (m-10) REVERT: G 61 LEU cc_start: 0.9329 (mt) cc_final: 0.8992 (pp) REVERT: H 19 LEU cc_start: 0.9334 (tp) cc_final: 0.8755 (mt) REVERT: H 103 PHE cc_start: 0.9520 (m-80) cc_final: 0.9107 (m-80) REVERT: I 70 MET cc_start: 0.8785 (tpt) cc_final: 0.8388 (tpt) REVERT: I 75 LEU cc_start: 0.9714 (mt) cc_final: 0.9484 (mp) REVERT: J 327 ASP cc_start: 0.7537 (p0) cc_final: 0.7274 (t0) REVERT: J 358 LEU cc_start: 0.7704 (tp) cc_final: 0.7504 (mm) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.1176 time to fit residues: 19.6769 Evaluate side-chains 84 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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: 8.9990 chunk 160 optimal weight: 0.8980 chunk 143 optimal weight: 30.0000 chunk 166 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 171 optimal weight: 0.4980 chunk 153 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 176 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- 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 588 GLN ** H 151 ASN ** 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 = 0.3394 r_free = 0.3394 target = 0.046321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.028402 restraints weight = 198687.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.029076 restraints weight = 154114.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.029539 restraints weight = 128737.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.029924 restraints weight = 113108.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.030059 restraints weight = 102914.044| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19022 Z= 0.143 Angle : 0.580 9.591 25948 Z= 0.290 Chirality : 0.038 0.180 2877 Planarity : 0.004 0.059 3314 Dihedral : 10.945 90.541 2929 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.12 (0.18), residues: 2290 helix: 1.01 (0.19), residues: 802 sheet: -0.44 (0.27), residues: 357 loop : -0.70 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 627 TYR 0.012 0.001 TYR A 340 PHE 0.035 0.001 PHE A 534 TRP 0.013 0.001 TRP I 116 HIS 0.006 0.001 HIS I 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (19022) covalent geometry : angle 0.57959 / 0.29 (25948) hydrogen bonds : bond 0.03335 / 2.20 ( 768) hydrogen bonds : angle 5.44246 / 3.91 ( 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 103 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.635 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: A 117 MET cc_start: 0.8378 (tpt) cc_final: 0.8142 (tpt) REVERT: A 236 PHE cc_start: 0.9684 (t80) cc_final: 0.9312 (t80) REVERT: E 1 MET cc_start: 0.7513 (mmp) cc_final: 0.6943 (mmt) REVERT: E 207 LEU cc_start: 0.9254 (tp) cc_final: 0.8978 (tt) REVERT: G 61 LEU cc_start: 0.9292 (mt) cc_final: 0.8970 (pp) REVERT: H 103 PHE cc_start: 0.9518 (m-80) cc_final: 0.9115 (m-80) REVERT: I 70 MET cc_start: 0.8748 (tpt) cc_final: 0.8381 (tpt) REVERT: I 75 LEU cc_start: 0.9705 (mt) cc_final: 0.9483 (mp) REVERT: J 327 ASP cc_start: 0.7588 (p0) cc_final: 0.7338 (t0) REVERT: J 358 LEU cc_start: 0.7765 (tp) cc_final: 0.7548 (mm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1178 time to fit residues: 19.4391 Evaluate side-chains 78 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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: 0.6980 chunk 177 optimal weight: 8.9990 chunk 205 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 225 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 133 optimal weight: 0.0040 chunk 111 optimal weight: 7.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- 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** A 588 GLN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.047081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.028745 restraints weight = 199608.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.029502 restraints weight = 150567.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.029988 restraints weight = 122885.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.030395 restraints weight = 107292.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.030539 restraints weight = 97379.498| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19022 Z= 0.099 Angle : 0.564 9.217 25948 Z= 0.276 Chirality : 0.039 0.175 2877 Planarity : 0.004 0.058 3314 Dihedral : 10.886 92.966 2929 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -0.04 (0.18), residues: 2290 helix: 1.03 (0.19), residues: 805 sheet: -0.39 (0.27), residues: 355 loop : -0.62 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 627 TYR 0.010 0.001 TYR A 643 PHE 0.013 0.001 PHE A 614 TRP 0.016 0.001 TRP A 311 HIS 0.006 0.001 HIS H 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (19022) covalent geometry : angle 0.56356 / 0.28 (25948) hydrogen bonds : bond 0.03080 / 2.01 ( 768) hydrogen bonds : angle 5.28336 / 3.79 ( 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 : 0.535 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: A 117 MET cc_start: 0.8344 (tpt) cc_final: 0.8074 (tpt) REVERT: A 236 PHE cc_start: 0.9665 (t80) cc_final: 0.9293 (t80) REVERT: A 389 MET cc_start: 0.7849 (ppp) cc_final: 0.7599 (ppp) REVERT: A 434 LEU cc_start: 0.9465 (mt) cc_final: 0.9256 (mm) REVERT: E 1 MET cc_start: 0.7227 (mmp) cc_final: 0.6408 (mmt) REVERT: E 207 LEU cc_start: 0.9207 (tp) cc_final: 0.8985 (tt) REVERT: E 220 PHE cc_start: 0.8810 (m-80) cc_final: 0.7998 (m-10) REVERT: G 61 LEU cc_start: 0.9311 (mt) cc_final: 0.8971 (pp) REVERT: H 103 PHE cc_start: 0.9526 (m-80) cc_final: 0.9117 (m-80) REVERT: I 70 MET cc_start: 0.8811 (tpt) cc_final: 0.8456 (tpt) REVERT: I 75 LEU cc_start: 0.9707 (mt) cc_final: 0.9489 (mp) REVERT: I 213 MET cc_start: 0.8763 (mmt) cc_final: 0.8127 (mmt) REVERT: J 327 ASP cc_start: 0.7599 (p0) cc_final: 0.7349 (t0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1260 time to fit residues: 21.6428 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 : 0.623 ------------------------------------------------------------------------------- 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: 0.7980 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 63 optimal weight: 0.0770 chunk 105 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- 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** A 588 GLN A 692 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.046943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.028884 restraints weight = 194609.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.029613 restraints weight = 148234.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.030086 restraints weight = 123131.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.030333 restraints weight = 108625.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.030683 restraints weight = 98561.921| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2643 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= 0.108 Angle : 0.559 9.728 25948 Z= 0.274 Chirality : 0.038 0.167 2877 Planarity : 0.004 0.058 3314 Dihedral : 10.840 91.200 2929 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 0.05 % Allowed : 0.48 % 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: 0.01 (0.18), residues: 2290 helix: 1.09 (0.19), residues: 807 sheet: -0.35 (0.27), residues: 355 loop : -0.61 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 345 TYR 0.010 0.001 TYR A 340 PHE 0.014 0.001 PHE A 614 TRP 0.015 0.001 TRP A 311 HIS 0.006 0.001 HIS H 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (19022) covalent geometry : angle 0.55865 / 0.27 (25948) hydrogen bonds : bond 0.03084 / 2.02 ( 768) hydrogen bonds : angle 5.26723 / 3.78 ( 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 105 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.563 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: A 117 MET cc_start: 0.8398 (tpt) cc_final: 0.8139 (tpt) REVERT: A 236 PHE cc_start: 0.9657 (t80) cc_final: 0.9291 (t80) REVERT: A 351 MET cc_start: 0.9568 (mmp) cc_final: 0.9366 (mmp) REVERT: A 389 MET cc_start: 0.7842 (ppp) cc_final: 0.7600 (ppp) REVERT: A 434 LEU cc_start: 0.9471 (mt) cc_final: 0.9263 (mm) REVERT: E 1 MET cc_start: 0.7050 (mmp) cc_final: 0.6425 (mmt) REVERT: E 207 LEU cc_start: 0.9265 (tp) cc_final: 0.9014 (tt) REVERT: E 220 PHE cc_start: 0.8765 (m-80) cc_final: 0.7956 (m-10) REVERT: F 201 MET cc_start: 0.9727 (mpp) cc_final: 0.9352 (mpp) REVERT: G 61 LEU cc_start: 0.9287 (mt) cc_final: 0.8964 (pp) REVERT: H 103 PHE cc_start: 0.9512 (m-80) cc_final: 0.9107 (m-80) REVERT: I 70 MET cc_start: 0.8753 (tpt) cc_final: 0.8414 (tpt) REVERT: I 75 LEU cc_start: 0.9706 (mt) cc_final: 0.9485 (mp) REVERT: I 213 MET cc_start: 0.8720 (mmt) cc_final: 0.8143 (mmt) REVERT: J 327 ASP cc_start: 0.7621 (p0) cc_final: 0.7373 (t0) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.1196 time to fit residues: 19.9183 Evaluate side-chains 82 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 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 165 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 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 = 0.3405 r_free = 0.3405 target = 0.046756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.028775 restraints weight = 195800.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.029504 restraints weight = 149479.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.029801 restraints weight = 123531.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.030290 restraints weight = 110358.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.030414 restraints weight = 100822.796| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2735 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= 0.112 Angle : 0.562 10.453 25948 Z= 0.275 Chirality : 0.038 0.174 2877 Planarity : 0.004 0.059 3314 Dihedral : 10.823 90.791 2929 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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: 0.04 (0.18), residues: 2290 helix: 1.12 (0.19), residues: 806 sheet: -0.29 (0.27), residues: 355 loop : -0.62 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 345 TYR 0.010 0.001 TYR A 340 PHE 0.014 0.001 PHE A 614 TRP 0.015 0.001 TRP I 116 HIS 0.006 0.001 HIS H 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (19022) covalent geometry : angle 0.56226 / 0.28 (25948) hydrogen bonds : bond 0.03094 / 2.02 ( 768) hydrogen bonds : angle 5.26783 / 3.77 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3130.78 seconds wall clock time: 55 minutes 1.78 seconds (3301.78 seconds total)