Starting phenix.real_space_refine on Wed Sep 17 20:05:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co0_45768/09_2025/9co0_45768.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co0_45768/09_2025/9co0_45768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9co0_45768/09_2025/9co0_45768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co0_45768/09_2025/9co0_45768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9co0_45768/09_2025/9co0_45768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co0_45768/09_2025/9co0_45768.map" } resolution = 3.3 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= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 235 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 6801 2.51 5 N 1848 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10766 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5042 Classifications: {'peptide': 634} Link IDs: {'PTRANS': 25, 'TRANS': 608} Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2576 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 11, 'TRANS': 332} Chain breaks: 2 Chain: "C" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 370 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 7, 'TRANS': 45} Chain: "D" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1661 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "E" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 685 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Unusual residues: {'ACY': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'TRANS': 14, None: 1} Not linked: pdbres="ACY F 0 " pdbres="PHE F 1 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Unusual residues: {'ACY': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'TRANS': 14, None: 1} Not linked: pdbres="ACY G 0 " pdbres="PHE G 1 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Unusual residues: {'ACY': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'TRANS': 14, None: 1} Not linked: pdbres="ACY I 0 " pdbres="PHE I 1 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.28, per 1000 atoms: 0.21 Number of scatterers: 10766 At special positions: 0 Unit cell: (103.14, 112.734, 140.318, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 2084 8.00 N 1848 7.00 C 6801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.02 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 399.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 16 sheets defined 22.5% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.112A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 removed outlier: 3.779A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.667A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.793A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.603A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.861A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 691 through 695 Processing helix chain 'A' and resid 726 through 731 removed outlier: 4.309A pdb=" N ASN A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.906A pdb=" N TYR C 65 " --> pdb=" O SER C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'D' and resid 33 through 46 removed outlier: 4.654A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 4.157A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 97 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.528A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 240 Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.527A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 274 removed outlier: 4.694A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 334 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 376 removed outlier: 4.560A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS A 419 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 802 through 805 removed outlier: 3.570A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR A 454 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLY A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE A 426 " --> pdb=" O PHE F 13 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG F 8 " --> pdb=" O HIS F 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.005A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.966A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.959A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.069A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.589A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.514A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.059A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 290 through 292 removed outlier: 4.056A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.521A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.139A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.281A pdb=" N ASN E 71 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 2 through 4 489 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3463 1.34 - 1.46: 1881 1.46 - 1.57: 5605 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 11010 Sorted by residual: bond pdb=" N ASN A 681 " pdb=" CA ASN A 681 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.48e+00 bond pdb=" C ACY G 0 " pdb=" O ACY G 0 " ideal model delta sigma weight residual 1.248 1.285 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C ACY F 0 " pdb=" O ACY F 0 " ideal model delta sigma weight residual 1.248 1.284 -0.036 2.00e-02 2.50e+03 3.28e+00 bond pdb=" C ACY I 0 " pdb=" O ACY I 0 " ideal model delta sigma weight residual 1.248 1.284 -0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" CB ASP A 582 " pdb=" CG ASP A 582 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.79e+00 ... (remaining 11005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 14470 1.75 - 3.50: 402 3.50 - 5.25: 54 5.25 - 7.00: 21 7.00 - 8.75: 2 Bond angle restraints: 14949 Sorted by residual: angle pdb=" N VAL B 357 " pdb=" CA VAL B 357 " pdb=" C VAL B 357 " ideal model delta sigma weight residual 113.53 109.91 3.62 9.80e-01 1.04e+00 1.37e+01 angle pdb=" C SER A 680 " pdb=" N ASN A 681 " pdb=" CA ASN A 681 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C HIS G 5 " pdb=" N LYS G 6 " pdb=" CA LYS G 6 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 angle pdb=" N GLN D 54 " pdb=" CA GLN D 54 " pdb=" CB GLN D 54 " ideal model delta sigma weight residual 110.16 114.77 -4.61 1.48e+00 4.57e-01 9.68e+00 angle pdb=" CA LYS G 6 " pdb=" CB LYS G 6 " pdb=" CG LYS G 6 " ideal model delta sigma weight residual 114.10 120.31 -6.21 2.00e+00 2.50e-01 9.63e+00 ... (remaining 14944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5970 17.75 - 35.49: 375 35.49 - 53.24: 70 53.24 - 70.99: 22 70.99 - 88.74: 13 Dihedral angle restraints: 6450 sinusoidal: 2526 harmonic: 3924 Sorted by residual: dihedral pdb=" CA CYS A 700 " pdb=" C CYS A 700 " pdb=" N LYS A 701 " pdb=" CA LYS A 701 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA CYS A 690 " pdb=" C CYS A 690 " pdb=" N ALA A 691 " pdb=" CA ALA A 691 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual 93.00 123.52 -30.52 1 1.00e+01 1.00e-02 1.33e+01 ... (remaining 6447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1226 0.052 - 0.105: 303 0.105 - 0.157: 68 0.157 - 0.209: 4 0.209 - 0.261: 1 Chirality restraints: 1602 Sorted by residual: chirality pdb=" CB ILE F 4 " pdb=" CA ILE F 4 " pdb=" CG1 ILE F 4 " pdb=" CG2 ILE F 4 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE G 4 " pdb=" CA ILE G 4 " pdb=" CG1 ILE G 4 " pdb=" CG2 ILE G 4 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CA ASN A 681 " pdb=" N ASN A 681 " pdb=" C ASN A 681 " pdb=" CB ASN A 681 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 1599 not shown) Planarity restraints: 1961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 99 " 0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO D 100 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 408 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO A 409 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 48 " -0.023 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP D 48 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP D 48 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 48 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 48 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 48 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP D 48 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 48 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 48 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 48 " -0.004 2.00e-02 2.50e+03 ... (remaining 1958 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1091 2.76 - 3.29: 10504 3.29 - 3.83: 18022 3.83 - 4.36: 20922 4.36 - 4.90: 37001 Nonbonded interactions: 87540 Sorted by model distance: nonbonded pdb=" OG1 THR A 615 " pdb=" OG1 THR A 633 " model vdw 2.219 3.040 nonbonded pdb=" NE2 GLN D 40 " pdb=" OD2 ASP D 74 " model vdw 2.279 3.120 nonbonded pdb=" OG SER A 778 " pdb=" O GLY A 781 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR B 166 " pdb=" OD1 ASN B 168 " model vdw 2.298 3.040 nonbonded pdb=" OD1 ASN A 463 " pdb=" OH TYR I 11 " model vdw 2.304 3.040 ... (remaining 87535 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 'F' selection = chain 'G' selection = chain 'I' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.004 0.102 11020 Z= 0.227 Angle : 0.693 8.746 14951 Z= 0.377 Chirality : 0.047 0.261 1602 Planarity : 0.006 0.096 1961 Dihedral : 13.259 88.735 3957 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.21 (0.23), residues: 1346 helix: 0.92 (0.31), residues: 260 sheet: 0.11 (0.26), residues: 394 loop : -0.02 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 314 TYR 0.021 0.002 TYR A 229 PHE 0.022 0.001 PHE A 802 TRP 0.058 0.002 TRP D 48 HIS 0.004 0.001 HIS I 5 Details of bonding type rmsd covalent geometry : bond 0.00314 (11010) covalent geometry : angle 0.69199 (14949) SS BOND : bond 0.00981 ( 1) SS BOND : angle 3.61917 ( 2) hydrogen bonds : bond 0.19756 ( 485) hydrogen bonds : angle 8.01397 ( 1344) Misc. bond : bond 0.05848 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.9482 (mt) cc_final: 0.9254 (mp) REVERT: A 229 TYR cc_start: 0.8975 (t80) cc_final: 0.8744 (t80) REVERT: A 325 MET cc_start: 0.7825 (ppp) cc_final: 0.7484 (tmm) REVERT: A 583 ARG cc_start: 0.7973 (ttp-170) cc_final: 0.7721 (ttp80) REVERT: A 729 TYR cc_start: 0.7177 (m-10) cc_final: 0.6755 (m-10) REVERT: B 273 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7591 (mtm110) REVERT: B 290 ILE cc_start: 0.8883 (tp) cc_final: 0.8582 (tp) REVERT: B 368 GLN cc_start: 0.8300 (tm-30) cc_final: 0.8002 (tm-30) REVERT: D 93 ASP cc_start: 0.8562 (t70) cc_final: 0.8259 (t0) REVERT: D 109 MET cc_start: 0.8310 (mmt) cc_final: 0.7842 (mmt) REVERT: F 12 TRP cc_start: 0.7914 (m-90) cc_final: 0.7618 (m100) REVERT: I 8 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7312 (mtm180) REVERT: I 9 PHE cc_start: 0.8153 (p90) cc_final: 0.7931 (p90) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.0937 time to fit residues: 28.9833 Evaluate side-chains 182 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.0270 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 495 GLN B 62 ASN F 5 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.094894 restraints weight = 17874.083| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.89 r_work: 0.2968 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 11020 Z= 0.281 Angle : 0.641 7.922 14951 Z= 0.348 Chirality : 0.048 0.184 1602 Planarity : 0.005 0.082 1961 Dihedral : 4.759 20.314 1504 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.84 % Allowed : 7.01 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.25 (0.23), residues: 1346 helix: 1.04 (0.31), residues: 261 sheet: 0.01 (0.25), residues: 414 loop : 0.05 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 203 TYR 0.029 0.002 TYR A 550 PHE 0.017 0.002 PHE A 802 TRP 0.051 0.002 TRP D 48 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00622 (11010) covalent geometry : angle 0.63909 (14949) SS BOND : bond 0.00195 ( 1) SS BOND : angle 4.68405 ( 2) hydrogen bonds : bond 0.04573 ( 485) hydrogen bonds : angle 5.76249 ( 1344) Misc. bond : bond 0.00060 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 323 GLN cc_start: 0.7813 (pm20) cc_final: 0.7497 (pm20) REVERT: A 729 TYR cc_start: 0.7825 (m-10) cc_final: 0.7539 (m-10) REVERT: A 777 MET cc_start: 0.8814 (mmm) cc_final: 0.8573 (mmt) REVERT: B 170 GLN cc_start: 0.7385 (pt0) cc_final: 0.7084 (pt0) REVERT: B 176 GLU cc_start: 0.8057 (pt0) cc_final: 0.7707 (pt0) REVERT: B 343 GLU cc_start: 0.8275 (tp30) cc_final: 0.7997 (tp30) REVERT: B 388 TYR cc_start: 0.9066 (m-80) cc_final: 0.8842 (m-80) REVERT: D 93 ASP cc_start: 0.8897 (t70) cc_final: 0.8615 (t0) REVERT: D 183 GLU cc_start: 0.8599 (tt0) cc_final: 0.8363 (tt0) REVERT: F 12 TRP cc_start: 0.8216 (m-90) cc_final: 0.7840 (m100) outliers start: 21 outliers final: 17 residues processed: 208 average time/residue: 0.0915 time to fit residues: 27.1414 Evaluate side-chains 200 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 15 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN C 51 HIS E 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098361 restraints weight = 17792.829| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.83 r_work: 0.3028 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11020 Z= 0.145 Angle : 0.557 7.408 14951 Z= 0.300 Chirality : 0.044 0.185 1602 Planarity : 0.004 0.052 1961 Dihedral : 4.439 15.866 1504 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.93 % Allowed : 11.04 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.36 (0.23), residues: 1346 helix: 1.25 (0.32), residues: 263 sheet: 0.02 (0.25), residues: 420 loop : 0.11 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 314 TYR 0.023 0.001 TYR D 184 PHE 0.026 0.001 PHE A 238 TRP 0.044 0.002 TRP D 48 HIS 0.006 0.001 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00316 (11010) covalent geometry : angle 0.55682 (14949) SS BOND : bond 0.00779 ( 1) SS BOND : angle 2.32463 ( 2) hydrogen bonds : bond 0.03775 ( 485) hydrogen bonds : angle 5.30779 ( 1344) Misc. bond : bond 0.00017 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 323 GLN cc_start: 0.7794 (pm20) cc_final: 0.7363 (pm20) REVERT: A 369 MET cc_start: 0.9109 (mmm) cc_final: 0.8825 (mmm) REVERT: A 512 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: A 729 TYR cc_start: 0.7717 (m-10) cc_final: 0.7435 (m-10) REVERT: A 777 MET cc_start: 0.8753 (mmm) cc_final: 0.8511 (mmt) REVERT: A 789 GLN cc_start: 0.8049 (tt0) cc_final: 0.7706 (tp40) REVERT: B 127 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 170 GLN cc_start: 0.7055 (pt0) cc_final: 0.6635 (pm20) REVERT: B 176 GLU cc_start: 0.8009 (pt0) cc_final: 0.7641 (pt0) REVERT: B 343 GLU cc_start: 0.8262 (tp30) cc_final: 0.7932 (tp30) REVERT: B 352 GLU cc_start: 0.7601 (tp30) cc_final: 0.7326 (tp30) REVERT: B 368 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8378 (tm-30) REVERT: D 93 ASP cc_start: 0.8909 (t70) cc_final: 0.8610 (t0) REVERT: D 98 LEU cc_start: 0.9286 (tp) cc_final: 0.9051 (tt) REVERT: D 183 GLU cc_start: 0.8514 (tt0) cc_final: 0.8263 (tt0) REVERT: F 12 TRP cc_start: 0.8198 (m-90) cc_final: 0.7868 (m100) REVERT: I 7 ARG cc_start: 0.8169 (tpp-160) cc_final: 0.7665 (mmm-85) outliers start: 22 outliers final: 13 residues processed: 201 average time/residue: 0.0917 time to fit residues: 27.0033 Evaluate side-chains 194 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 63 optimal weight: 0.0000 chunk 89 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 0.0030 chunk 41 optimal weight: 0.3980 chunk 104 optimal weight: 10.0000 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098513 restraints weight = 17946.724| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.67 r_work: 0.3079 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11020 Z= 0.115 Angle : 0.533 7.408 14951 Z= 0.285 Chirality : 0.044 0.190 1602 Planarity : 0.004 0.046 1961 Dihedral : 4.272 16.786 1504 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.93 % Allowed : 11.57 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.44 (0.23), residues: 1346 helix: 1.40 (0.32), residues: 263 sheet: 0.04 (0.25), residues: 420 loop : 0.15 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 8 TYR 0.023 0.001 TYR D 184 PHE 0.026 0.001 PHE A 238 TRP 0.050 0.002 TRP D 48 HIS 0.004 0.000 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00250 (11010) covalent geometry : angle 0.52916 (14949) SS BOND : bond 0.00993 ( 1) SS BOND : angle 5.68105 ( 2) hydrogen bonds : bond 0.03379 ( 485) hydrogen bonds : angle 5.07091 ( 1344) Misc. bond : bond 0.00011 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9341 (mp) REVERT: A 323 GLN cc_start: 0.7724 (pm20) cc_final: 0.7291 (mp10) REVERT: A 325 MET cc_start: 0.7834 (tmm) cc_final: 0.7143 (tmm) REVERT: A 338 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.7837 (mtm110) REVERT: A 369 MET cc_start: 0.9071 (mmm) cc_final: 0.8866 (mmm) REVERT: A 512 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: A 729 TYR cc_start: 0.7664 (m-10) cc_final: 0.7380 (m-10) REVERT: B 127 GLU cc_start: 0.8548 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 170 GLN cc_start: 0.7003 (pt0) cc_final: 0.6670 (pm20) REVERT: B 176 GLU cc_start: 0.8025 (pt0) cc_final: 0.7679 (pt0) REVERT: B 343 GLU cc_start: 0.8186 (tp30) cc_final: 0.7817 (tp30) REVERT: B 352 GLU cc_start: 0.7572 (tp30) cc_final: 0.7237 (tp30) REVERT: B 368 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8344 (tm-30) REVERT: D 93 ASP cc_start: 0.8774 (t70) cc_final: 0.8498 (t0) REVERT: D 98 LEU cc_start: 0.9226 (tp) cc_final: 0.8980 (tt) REVERT: F 12 TRP cc_start: 0.8158 (m-90) cc_final: 0.7911 (m100) REVERT: I 7 ARG cc_start: 0.8140 (tpp-160) cc_final: 0.7686 (mmm-85) outliers start: 22 outliers final: 13 residues processed: 198 average time/residue: 0.0925 time to fit residues: 26.5777 Evaluate side-chains 193 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 130 optimal weight: 0.0000 chunk 7 optimal weight: 2.9990 chunk 131 optimal weight: 50.0000 chunk 10 optimal weight: 3.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095941 restraints weight = 17853.009| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.69 r_work: 0.3033 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11020 Z= 0.191 Angle : 0.564 8.280 14951 Z= 0.300 Chirality : 0.045 0.185 1602 Planarity : 0.004 0.049 1961 Dihedral : 4.334 16.090 1504 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.98 % Allowed : 12.01 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.41 (0.23), residues: 1346 helix: 1.40 (0.32), residues: 264 sheet: -0.02 (0.25), residues: 420 loop : 0.14 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 8 TYR 0.022 0.001 TYR D 184 PHE 0.029 0.002 PHE A 238 TRP 0.056 0.002 TRP D 48 HIS 0.003 0.001 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00425 (11010) covalent geometry : angle 0.56210 (14949) SS BOND : bond 0.00702 ( 1) SS BOND : angle 4.31135 ( 2) hydrogen bonds : bond 0.03596 ( 485) hydrogen bonds : angle 5.14300 ( 1344) Misc. bond : bond 0.00025 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.462 Fit side-chains REVERT: A 193 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9375 (mp) REVERT: A 247 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8392 (pt) REVERT: A 323 GLN cc_start: 0.7747 (pm20) cc_final: 0.7420 (pm20) REVERT: A 325 MET cc_start: 0.7808 (tmm) cc_final: 0.6902 (tmm) REVERT: A 338 ARG cc_start: 0.8460 (mtp-110) cc_final: 0.7696 (mtm110) REVERT: A 512 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: A 729 TYR cc_start: 0.7586 (m-10) cc_final: 0.7341 (m-10) REVERT: A 805 ASN cc_start: 0.8551 (t0) cc_final: 0.8305 (t0) REVERT: B 127 GLU cc_start: 0.8675 (mm-30) cc_final: 0.7688 (mm-30) REVERT: B 170 GLN cc_start: 0.7255 (pt0) cc_final: 0.6790 (pm20) REVERT: B 176 GLU cc_start: 0.8156 (pt0) cc_final: 0.7642 (pt0) REVERT: B 273 ARG cc_start: 0.8288 (mtm180) cc_final: 0.7923 (mtm110) REVERT: B 343 GLU cc_start: 0.8249 (tp30) cc_final: 0.7830 (tp30) REVERT: B 352 GLU cc_start: 0.7602 (tp30) cc_final: 0.7210 (tp30) REVERT: B 368 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8404 (tm-30) REVERT: D 93 ASP cc_start: 0.8802 (t70) cc_final: 0.8530 (t0) REVERT: D 98 LEU cc_start: 0.9232 (tp) cc_final: 0.8983 (tt) REVERT: E 42 ASP cc_start: 0.7522 (m-30) cc_final: 0.7299 (m-30) REVERT: F 12 TRP cc_start: 0.8184 (m-90) cc_final: 0.7866 (m100) REVERT: I 7 ARG cc_start: 0.8181 (tpp-160) cc_final: 0.7934 (mpt-90) outliers start: 34 outliers final: 24 residues processed: 202 average time/residue: 0.0975 time to fit residues: 28.5937 Evaluate side-chains 207 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 114 optimal weight: 0.9980 chunk 91 optimal weight: 0.0060 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099078 restraints weight = 17863.029| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.75 r_work: 0.3048 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11020 Z= 0.124 Angle : 0.539 7.343 14951 Z= 0.285 Chirality : 0.044 0.205 1602 Planarity : 0.004 0.039 1961 Dihedral : 4.203 15.311 1504 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.63 % Allowed : 13.32 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.44 (0.23), residues: 1346 helix: 1.52 (0.32), residues: 264 sheet: -0.06 (0.25), residues: 424 loop : 0.17 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.023 0.001 TYR D 184 PHE 0.031 0.001 PHE A 238 TRP 0.038 0.002 TRP D 48 HIS 0.003 0.000 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00274 (11010) covalent geometry : angle 0.53813 (14949) SS BOND : bond 0.00205 ( 1) SS BOND : angle 3.11445 ( 2) hydrogen bonds : bond 0.03283 ( 485) hydrogen bonds : angle 4.96750 ( 1344) Misc. bond : bond 0.00013 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.340 Fit side-chains REVERT: A 193 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9358 (mp) REVERT: A 323 GLN cc_start: 0.7691 (pm20) cc_final: 0.7355 (pm20) REVERT: A 325 MET cc_start: 0.7772 (tmm) cc_final: 0.7421 (tmm) REVERT: A 338 ARG cc_start: 0.8441 (mtp-110) cc_final: 0.8102 (mtp-110) REVERT: A 512 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8073 (m-30) REVERT: A 536 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8827 (mp) REVERT: A 729 TYR cc_start: 0.7561 (m-10) cc_final: 0.7333 (m-10) REVERT: A 805 ASN cc_start: 0.8558 (t0) cc_final: 0.8292 (t0) REVERT: B 170 GLN cc_start: 0.7088 (pt0) cc_final: 0.6687 (pm20) REVERT: B 176 GLU cc_start: 0.8093 (pt0) cc_final: 0.7573 (pt0) REVERT: B 343 GLU cc_start: 0.8238 (tp30) cc_final: 0.7808 (tp30) REVERT: B 352 GLU cc_start: 0.7645 (tp30) cc_final: 0.7241 (tp30) REVERT: B 368 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8381 (tm-30) REVERT: D 93 ASP cc_start: 0.8844 (t70) cc_final: 0.8544 (t0) REVERT: D 98 LEU cc_start: 0.9252 (tp) cc_final: 0.8995 (tt) REVERT: F 12 TRP cc_start: 0.8148 (m-90) cc_final: 0.7819 (m100) REVERT: I 7 ARG cc_start: 0.8191 (tpp-160) cc_final: 0.7928 (mpt-90) outliers start: 30 outliers final: 21 residues processed: 208 average time/residue: 0.0959 time to fit residues: 28.8310 Evaluate side-chains 204 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 2 optimal weight: 10.0000 chunk 111 optimal weight: 0.0370 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 95 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS E 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099671 restraints weight = 17728.317| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.71 r_work: 0.3065 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11020 Z= 0.124 Angle : 0.548 8.244 14951 Z= 0.288 Chirality : 0.043 0.187 1602 Planarity : 0.004 0.037 1961 Dihedral : 4.156 18.589 1504 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.72 % Allowed : 14.11 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.48 (0.23), residues: 1346 helix: 1.59 (0.32), residues: 264 sheet: -0.05 (0.25), residues: 426 loop : 0.19 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 29 TYR 0.023 0.001 TYR D 184 PHE 0.031 0.001 PHE A 238 TRP 0.029 0.001 TRP D 48 HIS 0.003 0.000 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00276 (11010) covalent geometry : angle 0.54266 (14949) SS BOND : bond 0.00201 ( 1) SS BOND : angle 6.59140 ( 2) hydrogen bonds : bond 0.03165 ( 485) hydrogen bonds : angle 4.87448 ( 1344) Misc. bond : bond 0.00014 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9353 (mp) REVERT: A 323 GLN cc_start: 0.7707 (pm20) cc_final: 0.7370 (pm20) REVERT: A 325 MET cc_start: 0.7764 (tmm) cc_final: 0.7378 (tmm) REVERT: A 338 ARG cc_start: 0.8437 (mtp-110) cc_final: 0.8042 (mtp-110) REVERT: A 512 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: A 536 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8825 (mp) REVERT: A 583 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7960 (ttp-170) REVERT: A 729 TYR cc_start: 0.7511 (m-10) cc_final: 0.7290 (m-10) REVERT: A 805 ASN cc_start: 0.8615 (t0) cc_final: 0.8386 (t0) REVERT: B 170 GLN cc_start: 0.7084 (pt0) cc_final: 0.6695 (pm20) REVERT: B 176 GLU cc_start: 0.8089 (pt0) cc_final: 0.7569 (pt0) REVERT: B 273 ARG cc_start: 0.8235 (mtm180) cc_final: 0.7973 (mtm110) REVERT: B 343 GLU cc_start: 0.8200 (tp30) cc_final: 0.7735 (tp30) REVERT: B 352 GLU cc_start: 0.7659 (tp30) cc_final: 0.7257 (tp30) REVERT: B 368 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 93 ASP cc_start: 0.8827 (t70) cc_final: 0.8544 (t0) REVERT: D 98 LEU cc_start: 0.9205 (tp) cc_final: 0.8944 (tt) REVERT: F 12 TRP cc_start: 0.8137 (m-90) cc_final: 0.7795 (m100) REVERT: I 7 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7724 (mmm-85) outliers start: 31 outliers final: 20 residues processed: 205 average time/residue: 0.0953 time to fit residues: 28.5381 Evaluate side-chains 198 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 126 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 99 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.095441 restraints weight = 17734.842| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.68 r_work: 0.3028 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11020 Z= 0.186 Angle : 0.578 8.799 14951 Z= 0.306 Chirality : 0.045 0.192 1602 Planarity : 0.004 0.046 1961 Dihedral : 4.284 17.983 1504 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.89 % Allowed : 13.85 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.38 (0.23), residues: 1346 helix: 1.53 (0.32), residues: 264 sheet: -0.15 (0.25), residues: 440 loop : 0.16 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 29 TYR 0.022 0.001 TYR D 184 PHE 0.034 0.001 PHE A 238 TRP 0.040 0.002 TRP D 48 HIS 0.003 0.001 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00417 (11010) covalent geometry : angle 0.57206 (14949) SS BOND : bond 0.00187 ( 1) SS BOND : angle 7.32517 ( 2) hydrogen bonds : bond 0.03419 ( 485) hydrogen bonds : angle 5.02704 ( 1344) Misc. bond : bond 0.00028 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9356 (mp) REVERT: A 323 GLN cc_start: 0.7737 (pm20) cc_final: 0.7402 (pm20) REVERT: A 325 MET cc_start: 0.7802 (tmm) cc_final: 0.7383 (tmm) REVERT: A 338 ARG cc_start: 0.8450 (mtp-110) cc_final: 0.7989 (mtp-110) REVERT: A 512 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: A 536 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8865 (mp) REVERT: A 583 ARG cc_start: 0.8423 (ttp80) cc_final: 0.8172 (ttp-170) REVERT: A 729 TYR cc_start: 0.7657 (m-10) cc_final: 0.7443 (m-10) REVERT: A 805 ASN cc_start: 0.8640 (t0) cc_final: 0.8423 (t0) REVERT: B 170 GLN cc_start: 0.7240 (pt0) cc_final: 0.6904 (pm20) REVERT: B 176 GLU cc_start: 0.8216 (pt0) cc_final: 0.7686 (pt0) REVERT: B 343 GLU cc_start: 0.8290 (tp30) cc_final: 0.7841 (tp30) REVERT: B 352 GLU cc_start: 0.7693 (tp30) cc_final: 0.7300 (tp30) REVERT: B 368 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8398 (tm-30) REVERT: D 93 ASP cc_start: 0.8810 (t70) cc_final: 0.8531 (t0) REVERT: D 98 LEU cc_start: 0.9200 (tp) cc_final: 0.8940 (tt) REVERT: D 207 ASP cc_start: 0.8399 (p0) cc_final: 0.8133 (p0) REVERT: E 53 GLN cc_start: 0.8365 (tp-100) cc_final: 0.7938 (tm-30) REVERT: F 12 TRP cc_start: 0.8186 (m-90) cc_final: 0.7822 (m100) REVERT: I 7 ARG cc_start: 0.8180 (tpp-160) cc_final: 0.7692 (mmm-85) outliers start: 33 outliers final: 24 residues processed: 199 average time/residue: 0.0969 time to fit residues: 27.8333 Evaluate side-chains 204 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097507 restraints weight = 17670.598| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.66 r_work: 0.3056 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11020 Z= 0.134 Angle : 0.563 8.718 14951 Z= 0.297 Chirality : 0.044 0.186 1602 Planarity : 0.004 0.039 1961 Dihedral : 4.191 16.694 1504 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.89 % Allowed : 13.67 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.42 (0.23), residues: 1346 helix: 1.57 (0.32), residues: 264 sheet: -0.12 (0.25), residues: 434 loop : 0.17 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 29 TYR 0.023 0.001 TYR D 184 PHE 0.036 0.001 PHE A 238 TRP 0.042 0.002 TRP D 48 HIS 0.003 0.000 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00298 (11010) covalent geometry : angle 0.55889 (14949) SS BOND : bond 0.00302 ( 1) SS BOND : angle 6.06170 ( 2) hydrogen bonds : bond 0.03207 ( 485) hydrogen bonds : angle 4.92303 ( 1344) Misc. bond : bond 0.00015 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9320 (mp) REVERT: A 252 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8037 (tppt) REVERT: A 323 GLN cc_start: 0.7706 (pm20) cc_final: 0.7363 (pm20) REVERT: A 325 MET cc_start: 0.7780 (tmm) cc_final: 0.7388 (tmm) REVERT: A 338 ARG cc_start: 0.8429 (mtp-110) cc_final: 0.8014 (mtp-110) REVERT: A 512 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8169 (m-30) REVERT: A 536 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8837 (mp) REVERT: A 583 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8100 (ttp-170) REVERT: A 729 TYR cc_start: 0.7558 (m-10) cc_final: 0.7349 (m-10) REVERT: A 805 ASN cc_start: 0.8615 (t0) cc_final: 0.8404 (t0) REVERT: B 170 GLN cc_start: 0.7090 (pt0) cc_final: 0.6677 (pm20) REVERT: B 176 GLU cc_start: 0.8127 (pt0) cc_final: 0.7622 (pt0) REVERT: B 273 ARG cc_start: 0.8243 (mtm180) cc_final: 0.7999 (mtm110) REVERT: B 343 GLU cc_start: 0.8293 (tp30) cc_final: 0.7998 (tp30) REVERT: B 352 GLU cc_start: 0.7693 (tp30) cc_final: 0.7352 (tp30) REVERT: B 368 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8333 (tm-30) REVERT: D 93 ASP cc_start: 0.8780 (t70) cc_final: 0.8500 (t0) REVERT: D 98 LEU cc_start: 0.9184 (tp) cc_final: 0.8920 (tt) REVERT: D 207 ASP cc_start: 0.8381 (p0) cc_final: 0.8049 (p0) REVERT: F 7 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6047 (mmm160) REVERT: F 12 TRP cc_start: 0.8154 (m-90) cc_final: 0.7801 (m100) REVERT: I 7 ARG cc_start: 0.8162 (tpp-160) cc_final: 0.7704 (mmm-85) outliers start: 33 outliers final: 25 residues processed: 206 average time/residue: 0.1004 time to fit residues: 29.6647 Evaluate side-chains 208 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 7 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 15 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.096744 restraints weight = 17774.858| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.69 r_work: 0.3043 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11020 Z= 0.156 Angle : 0.581 9.084 14951 Z= 0.307 Chirality : 0.045 0.183 1602 Planarity : 0.004 0.041 1961 Dihedral : 4.278 19.160 1504 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.72 % Allowed : 14.37 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.40 (0.23), residues: 1346 helix: 1.60 (0.32), residues: 263 sheet: -0.14 (0.25), residues: 429 loop : 0.15 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 29 TYR 0.023 0.001 TYR D 184 PHE 0.035 0.001 PHE A 238 TRP 0.042 0.002 TRP D 48 HIS 0.003 0.000 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00347 (11010) covalent geometry : angle 0.57752 (14949) SS BOND : bond 0.00344 ( 1) SS BOND : angle 5.85920 ( 2) hydrogen bonds : bond 0.03258 ( 485) hydrogen bonds : angle 4.95456 ( 1344) Misc. bond : bond 0.00020 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9325 (mp) REVERT: A 307 ASP cc_start: 0.9017 (t0) cc_final: 0.8780 (p0) REVERT: A 323 GLN cc_start: 0.7707 (pm20) cc_final: 0.7349 (pm20) REVERT: A 325 MET cc_start: 0.7769 (tmm) cc_final: 0.7326 (tmm) REVERT: A 338 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.7959 (mtp-110) REVERT: A 358 ASP cc_start: 0.8098 (m-30) cc_final: 0.7757 (t0) REVERT: A 512 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8210 (m-30) REVERT: A 536 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8850 (mp) REVERT: A 583 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8147 (ttp-170) REVERT: A 729 TYR cc_start: 0.7565 (m-10) cc_final: 0.7363 (m-10) REVERT: A 805 ASN cc_start: 0.8629 (t0) cc_final: 0.8418 (t0) REVERT: B 170 GLN cc_start: 0.7151 (pt0) cc_final: 0.6815 (pm20) REVERT: B 176 GLU cc_start: 0.8167 (pt0) cc_final: 0.7651 (pt0) REVERT: B 273 ARG cc_start: 0.8236 (mtm180) cc_final: 0.8024 (mtm110) REVERT: B 343 GLU cc_start: 0.8330 (tp30) cc_final: 0.8028 (tp30) REVERT: B 352 GLU cc_start: 0.7681 (tp30) cc_final: 0.7276 (tp30) REVERT: B 368 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8357 (tm-30) REVERT: D 93 ASP cc_start: 0.8759 (t70) cc_final: 0.8481 (t0) REVERT: D 98 LEU cc_start: 0.9171 (tp) cc_final: 0.8905 (tt) REVERT: D 207 ASP cc_start: 0.8403 (p0) cc_final: 0.8080 (p0) REVERT: F 7 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6060 (mmm160) REVERT: F 12 TRP cc_start: 0.8171 (m-90) cc_final: 0.7812 (m100) REVERT: I 7 ARG cc_start: 0.8181 (tpp-160) cc_final: 0.7731 (mmm-85) outliers start: 31 outliers final: 26 residues processed: 199 average time/residue: 0.0994 time to fit residues: 28.8029 Evaluate side-chains 210 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 7 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.093530 restraints weight = 17924.899| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.67 r_work: 0.2988 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11020 Z= 0.288 Angle : 0.657 9.893 14951 Z= 0.349 Chirality : 0.048 0.178 1602 Planarity : 0.005 0.066 1961 Dihedral : 4.630 19.258 1504 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.37 % Allowed : 14.64 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.24 (0.23), residues: 1346 helix: 1.44 (0.32), residues: 262 sheet: -0.30 (0.24), residues: 439 loop : 0.11 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 29 TYR 0.020 0.002 TYR D 184 PHE 0.038 0.002 PHE A 238 TRP 0.047 0.002 TRP D 48 HIS 0.004 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00646 (11010) covalent geometry : angle 0.65169 (14949) SS BOND : bond 0.00097 ( 1) SS BOND : angle 7.50644 ( 2) hydrogen bonds : bond 0.03827 ( 485) hydrogen bonds : angle 5.29090 ( 1344) Misc. bond : bond 0.00038 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2450.49 seconds wall clock time: 42 minutes 48.82 seconds (2568.82 seconds total)