Starting phenix.real_space_refine on Mon Jun 9 21:33:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co0_45768/06_2025/9co0_45768.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co0_45768/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9co0_45768/06_2025/9co0_45768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co0_45768/06_2025/9co0_45768.map" model { file = "/net/cci-nas-00/data/ceres_data/9co0_45768/06_2025/9co0_45768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co0_45768/06_2025/9co0_45768.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.23, per 1000 atoms: 0.58 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: 2.42 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.18 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: 3.63 Time building geometry restraints manager: 2.89 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.880 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.058 0.002 TRP D 48 HIS 0.004 0.001 HIS I 5 PHE 0.022 0.001 PHE A 802 TYR 0.021 0.002 TYR A 229 ARG 0.013 0.001 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.19756 ( 485) hydrogen bonds : angle 8.01397 ( 1344) SS BOND : bond 0.00981 ( 1) SS BOND : angle 3.61917 ( 2) covalent geometry : bond 0.00314 (11010) covalent geometry : angle 0.69199 (14949) 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 : 1.310 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: 0.8583 (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: 0.7619 (m100) REVERT: I 8 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7310 (mtm180) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2237 time to fit residues: 69.6220 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 : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 0.0270 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 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** A 463 ASN B 62 ASN F 5 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099340 restraints weight = 17721.666| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.82 r_work: 0.3053 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1478 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= 0.147 Angle : 0.567 7.602 14951 Z= 0.307 Chirality : 0.045 0.194 1602 Planarity : 0.005 0.062 1961 Dihedral : 4.407 16.678 1504 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.49 % Allowed : 6.84 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1346 helix: 1.18 (0.31), residues: 264 sheet: 0.05 (0.25), residues: 421 loop : 0.11 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 48 HIS 0.003 0.001 HIS A 533 PHE 0.018 0.001 PHE A 440 TYR 0.032 0.001 TYR A 550 ARG 0.006 0.001 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 485) hydrogen bonds : angle 5.57372 ( 1344) SS BOND : bond 0.00279 ( 1) SS BOND : angle 4.44575 ( 2) covalent geometry : bond 0.00321 (11010) covalent geometry : angle 0.56458 (14949) Misc. bond : bond 0.00023 ( 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 218 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.9551 (mt) cc_final: 0.9223 (mp) REVERT: A 314 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8364 (ttm170) REVERT: A 323 GLN cc_start: 0.7792 (pm20) cc_final: 0.7466 (pm20) REVERT: A 546 TRP cc_start: 0.7337 (m100) cc_final: 0.6558 (m100) REVERT: A 683 ASP cc_start: 0.8418 (t0) cc_final: 0.8180 (t0) REVERT: A 729 TYR cc_start: 0.7606 (m-10) cc_final: 0.7152 (m-10) REVERT: A 777 MET cc_start: 0.8765 (mmm) cc_final: 0.8533 (mmt) REVERT: B 127 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8399 (mm-30) REVERT: B 170 GLN cc_start: 0.6773 (pt0) cc_final: 0.6281 (pm20) REVERT: B 343 GLU cc_start: 0.8147 (tp30) cc_final: 0.7871 (tp30) REVERT: B 368 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8340 (tm-30) REVERT: D 93 ASP cc_start: 0.8866 (t70) cc_final: 0.8576 (t0) REVERT: D 112 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.7851 (ttp-170) REVERT: D 183 GLU cc_start: 0.8494 (tt0) cc_final: 0.8232 (tt0) REVERT: F 12 TRP cc_start: 0.8164 (m-90) cc_final: 0.7812 (m100) REVERT: I 7 ARG cc_start: 0.8026 (tpp-160) cc_final: 0.7650 (mmm-85) outliers start: 17 outliers final: 13 residues processed: 208 average time/residue: 0.2497 time to fit residues: 73.8633 Evaluate side-chains 197 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** B 62 ASN E 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099406 restraints weight = 17913.260| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.83 r_work: 0.3060 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11020 Z= 0.129 Angle : 0.543 7.610 14951 Z= 0.291 Chirality : 0.044 0.185 1602 Planarity : 0.004 0.052 1961 Dihedral : 4.258 15.086 1504 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.49 % Allowed : 10.34 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1346 helix: 1.33 (0.32), residues: 264 sheet: 0.15 (0.25), residues: 422 loop : 0.15 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 48 HIS 0.003 0.001 HIS A 533 PHE 0.028 0.001 PHE A 238 TYR 0.023 0.001 TYR D 184 ARG 0.005 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 485) hydrogen bonds : angle 5.21941 ( 1344) SS BOND : bond 0.00205 ( 1) SS BOND : angle 2.33279 ( 2) covalent geometry : bond 0.00281 (11010) covalent geometry : angle 0.54248 (14949) Misc. bond : bond 0.00012 ( 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 219 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 GLN cc_start: 0.7654 (pm20) cc_final: 0.7288 (mp10) REVERT: A 729 TYR cc_start: 0.7635 (m-10) cc_final: 0.7324 (m-10) REVERT: B 170 GLN cc_start: 0.6898 (pt0) cc_final: 0.6288 (pm20) REVERT: B 176 GLU cc_start: 0.7899 (pt0) cc_final: 0.7587 (pt0) REVERT: B 343 GLU cc_start: 0.8168 (tp30) cc_final: 0.7819 (tp30) REVERT: B 368 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8326 (tm-30) REVERT: D 93 ASP cc_start: 0.8841 (t70) cc_final: 0.8538 (t0) REVERT: D 98 LEU cc_start: 0.9302 (tp) cc_final: 0.9065 (tt) REVERT: F 12 TRP cc_start: 0.8182 (m-90) cc_final: 0.7939 (m100) REVERT: I 7 ARG cc_start: 0.8067 (tpp-160) cc_final: 0.7686 (mmm-85) outliers start: 17 outliers final: 13 residues processed: 211 average time/residue: 0.2485 time to fit residues: 75.0734 Evaluate side-chains 196 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 558 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 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 48 VAL Chi-restraints excluded: chain E residue 55 VAL 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 5 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 105 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 112 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** E 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098537 restraints weight = 17820.559| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.82 r_work: 0.3041 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11020 Z= 0.141 Angle : 0.541 7.448 14951 Z= 0.289 Chirality : 0.044 0.188 1602 Planarity : 0.004 0.046 1961 Dihedral : 4.234 16.735 1504 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.93 % Allowed : 12.36 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.23), residues: 1346 helix: 1.43 (0.32), residues: 264 sheet: 0.10 (0.25), residues: 422 loop : 0.18 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 48 HIS 0.003 0.001 HIS A 533 PHE 0.026 0.001 PHE A 238 TYR 0.022 0.001 TYR D 184 ARG 0.006 0.000 ARG F 8 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 485) hydrogen bonds : angle 5.05826 ( 1344) SS BOND : bond 0.00542 ( 1) SS BOND : angle 4.87559 ( 2) covalent geometry : bond 0.00310 (11010) covalent geometry : angle 0.53800 (14949) Misc. bond : bond 0.00015 ( 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 212 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.167 Fit side-chains REVERT: A 247 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8388 (pt) REVERT: A 323 GLN cc_start: 0.7655 (pm20) cc_final: 0.7229 (mp10) REVERT: A 325 MET cc_start: 0.7824 (tmm) cc_final: 0.7613 (tmm) REVERT: A 338 ARG cc_start: 0.8458 (mtp-110) cc_final: 0.8205 (mtp-110) REVERT: A 546 TRP cc_start: 0.7998 (m100) cc_final: 0.7597 (m-10) REVERT: A 729 TYR cc_start: 0.7677 (m-10) cc_final: 0.7375 (m-10) REVERT: B 127 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7685 (mm-30) REVERT: B 170 GLN cc_start: 0.6986 (pt0) cc_final: 0.6609 (pm20) REVERT: B 176 GLU cc_start: 0.7984 (pt0) cc_final: 0.7642 (pt0) REVERT: B 343 GLU cc_start: 0.8212 (tp30) cc_final: 0.8004 (tp30) REVERT: B 352 GLU cc_start: 0.7595 (tp30) cc_final: 0.7355 (tp30) REVERT: B 368 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8335 (tm-30) REVERT: D 48 TRP cc_start: 0.8250 (m-10) cc_final: 0.8048 (m-10) REVERT: D 93 ASP cc_start: 0.8866 (t70) cc_final: 0.8581 (t0) REVERT: D 98 LEU cc_start: 0.9279 (tp) cc_final: 0.9040 (tt) REVERT: F 12 TRP cc_start: 0.8180 (m-90) cc_final: 0.7928 (m100) REVERT: I 7 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7764 (mmm-85) outliers start: 22 outliers final: 14 residues processed: 201 average time/residue: 0.2360 time to fit residues: 68.3955 Evaluate side-chains 190 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 463 ASN 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 124 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 42 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 49 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.134604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.094805 restraints weight = 17761.769| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.66 r_work: 0.3023 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11020 Z= 0.224 Angle : 0.578 6.876 14951 Z= 0.310 Chirality : 0.045 0.185 1602 Planarity : 0.004 0.057 1961 Dihedral : 4.397 17.202 1504 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.54 % Allowed : 12.53 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1346 helix: 1.40 (0.32), residues: 264 sheet: -0.00 (0.25), residues: 420 loop : 0.09 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 48 HIS 0.003 0.001 HIS A 533 PHE 0.031 0.002 PHE A 238 TYR 0.022 0.001 TYR D 184 ARG 0.006 0.000 ARG F 8 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 485) hydrogen bonds : angle 5.20006 ( 1344) SS BOND : bond 0.00607 ( 1) SS BOND : angle 4.60992 ( 2) covalent geometry : bond 0.00497 (11010) covalent geometry : angle 0.57562 (14949) Misc. bond : bond 0.00039 ( 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 211 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.155 Fit side-chains REVERT: A 247 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8451 (pt) REVERT: A 323 GLN cc_start: 0.7717 (pm20) cc_final: 0.7260 (mp10) REVERT: A 325 MET cc_start: 0.7815 (tmm) cc_final: 0.7327 (tmm) REVERT: A 338 ARG cc_start: 0.8462 (mtp-110) cc_final: 0.7962 (mtm110) REVERT: A 413 ASP cc_start: 0.7834 (m-30) cc_final: 0.7602 (m-30) REVERT: A 552 MET cc_start: 0.9006 (mmm) cc_final: 0.8711 (mmm) REVERT: A 729 TYR cc_start: 0.7781 (m-10) cc_final: 0.7529 (m-10) REVERT: A 805 ASN cc_start: 0.8586 (t0) cc_final: 0.8303 (t0) REVERT: B 170 GLN cc_start: 0.7327 (pt0) cc_final: 0.6899 (pm20) REVERT: B 222 GLU cc_start: 0.7594 (tp30) cc_final: 0.7390 (tp30) REVERT: B 352 GLU cc_start: 0.7593 (tp30) cc_final: 0.7275 (tp30) REVERT: B 368 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8378 (tm-30) REVERT: D 93 ASP cc_start: 0.8781 (t70) cc_final: 0.8493 (t0) REVERT: D 98 LEU cc_start: 0.9234 (tp) cc_final: 0.8991 (tt) REVERT: F 12 TRP cc_start: 0.8196 (m-90) cc_final: 0.7867 (m100) REVERT: I 7 ARG cc_start: 0.8106 (tpp-160) cc_final: 0.7810 (mpt-90) outliers start: 29 outliers final: 17 residues processed: 197 average time/residue: 0.2158 time to fit residues: 61.0135 Evaluate side-chains 197 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 463 ASN 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 122 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 126 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 0.0870 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- 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 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099855 restraints weight = 17820.585| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.73 r_work: 0.3059 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11020 Z= 0.120 Angle : 0.535 9.262 14951 Z= 0.284 Chirality : 0.044 0.212 1602 Planarity : 0.004 0.040 1961 Dihedral : 4.172 15.200 1504 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.10 % Allowed : 13.58 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1346 helix: 1.51 (0.32), residues: 264 sheet: 0.02 (0.25), residues: 423 loop : 0.17 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 48 HIS 0.002 0.000 HIS A 533 PHE 0.031 0.001 PHE A 238 TYR 0.023 0.001 TYR D 184 ARG 0.004 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 485) hydrogen bonds : angle 4.98446 ( 1344) SS BOND : bond 0.00095 ( 1) SS BOND : angle 3.04947 ( 2) covalent geometry : bond 0.00265 (11010) covalent geometry : angle 0.53415 (14949) Misc. bond : bond 0.00012 ( 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 207 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8369 (pt) REVERT: A 323 GLN cc_start: 0.7612 (pm20) cc_final: 0.7166 (mp10) REVERT: A 325 MET cc_start: 0.7803 (tmm) cc_final: 0.7442 (tmm) REVERT: A 338 ARG cc_start: 0.8458 (mtp-110) cc_final: 0.8103 (mtp-110) REVERT: A 413 ASP cc_start: 0.7886 (m-30) cc_final: 0.7616 (m-30) REVERT: A 552 MET cc_start: 0.9045 (mmm) cc_final: 0.8779 (mmm) REVERT: A 729 TYR cc_start: 0.7542 (m-10) cc_final: 0.7314 (m-10) REVERT: A 805 ASN cc_start: 0.8572 (t0) cc_final: 0.8263 (t0) REVERT: B 170 GLN cc_start: 0.7054 (pt0) cc_final: 0.6682 (pm20) REVERT: B 176 GLU cc_start: 0.8082 (pt0) cc_final: 0.7653 (pt0) REVERT: B 273 ARG cc_start: 0.8254 (mtm180) cc_final: 0.7977 (mtm110) REVERT: B 352 GLU cc_start: 0.7611 (tp30) cc_final: 0.7268 (tp30) REVERT: B 368 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8319 (tm-30) REVERT: D 93 ASP cc_start: 0.8826 (t70) cc_final: 0.8545 (t0) REVERT: D 98 LEU cc_start: 0.9230 (tp) cc_final: 0.8980 (tt) REVERT: F 12 TRP cc_start: 0.8158 (m-90) cc_final: 0.7824 (m100) REVERT: I 7 ARG cc_start: 0.8110 (tpp-160) cc_final: 0.7809 (mpt-90) outliers start: 24 outliers final: 16 residues processed: 195 average time/residue: 0.2202 time to fit residues: 62.3703 Evaluate side-chains 193 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 124 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 132 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 111 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** E 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.134615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095902 restraints weight = 18173.546| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.78 r_work: 0.2996 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11020 Z= 0.242 Angle : 0.603 9.718 14951 Z= 0.320 Chirality : 0.046 0.232 1602 Planarity : 0.004 0.056 1961 Dihedral : 4.448 18.874 1504 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.07 % Allowed : 13.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1346 helix: 1.41 (0.32), residues: 264 sheet: -0.12 (0.25), residues: 437 loop : 0.12 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 48 HIS 0.003 0.001 HIS B 64 PHE 0.034 0.002 PHE A 238 TYR 0.022 0.002 TYR D 184 ARG 0.005 0.000 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 485) hydrogen bonds : angle 5.19926 ( 1344) SS BOND : bond 0.00153 ( 1) SS BOND : angle 8.02462 ( 2) covalent geometry : bond 0.00540 (11010) covalent geometry : angle 0.59621 (14949) Misc. bond : bond 0.00042 ( 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 218 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8452 (pt) REVERT: A 323 GLN cc_start: 0.7683 (pm20) cc_final: 0.7328 (pm20) REVERT: A 325 MET cc_start: 0.7803 (tmm) cc_final: 0.7115 (tmm) REVERT: A 338 ARG cc_start: 0.8471 (mtp-110) cc_final: 0.7977 (mtm110) REVERT: A 358 ASP cc_start: 0.8105 (m-30) cc_final: 0.7809 (t0) REVERT: A 536 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8884 (mp) REVERT: A 552 MET cc_start: 0.8979 (mmm) cc_final: 0.8664 (mmm) REVERT: A 729 TYR cc_start: 0.7727 (m-10) cc_final: 0.7514 (m-10) REVERT: A 805 ASN cc_start: 0.8615 (t0) cc_final: 0.8388 (t0) REVERT: B 170 GLN cc_start: 0.7401 (pt0) cc_final: 0.7135 (pm20) REVERT: B 368 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8403 (tm-30) REVERT: D 93 ASP cc_start: 0.8816 (t70) cc_final: 0.8542 (t0) REVERT: D 98 LEU cc_start: 0.9215 (tp) cc_final: 0.8963 (tt) REVERT: D 205 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8517 (m-80) REVERT: D 232 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8103 (mm-30) REVERT: F 12 TRP cc_start: 0.8208 (m-90) cc_final: 0.7856 (m100) REVERT: I 7 ARG cc_start: 0.8131 (tpp-160) cc_final: 0.7715 (mmm-85) outliers start: 35 outliers final: 23 residues processed: 201 average time/residue: 0.2148 time to fit residues: 62.1284 Evaluate side-chains 212 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 768 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 318 THR 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 205 TYR 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 Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 109 optimal weight: 0.2980 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096900 restraints weight = 17784.411| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.70 r_work: 0.3019 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11020 Z= 0.174 Angle : 0.597 9.837 14951 Z= 0.314 Chirality : 0.045 0.233 1602 Planarity : 0.004 0.050 1961 Dihedral : 4.395 17.449 1504 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.63 % Allowed : 14.64 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1346 helix: 1.46 (0.32), residues: 264 sheet: -0.17 (0.25), residues: 437 loop : 0.16 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 48 HIS 0.002 0.000 HIS B 64 PHE 0.036 0.001 PHE A 238 TYR 0.023 0.001 TYR D 184 ARG 0.006 0.000 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 485) hydrogen bonds : angle 5.11931 ( 1344) SS BOND : bond 0.00311 ( 1) SS BOND : angle 7.18647 ( 2) covalent geometry : bond 0.00389 (11010) covalent geometry : angle 0.59074 (14949) Misc. bond : bond 0.00021 ( 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 216 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8374 (pt) REVERT: A 323 GLN cc_start: 0.7638 (pm20) cc_final: 0.7284 (pm20) REVERT: A 325 MET cc_start: 0.7784 (tmm) cc_final: 0.7057 (tmm) REVERT: A 338 ARG cc_start: 0.8462 (mtp-110) cc_final: 0.7944 (mtm110) REVERT: A 358 ASP cc_start: 0.8118 (m-30) cc_final: 0.7808 (t0) REVERT: A 536 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8864 (mp) REVERT: A 552 MET cc_start: 0.8986 (mmm) cc_final: 0.8703 (mmm) REVERT: A 729 TYR cc_start: 0.7683 (m-10) cc_final: 0.7465 (m-10) REVERT: A 805 ASN cc_start: 0.8615 (t0) cc_final: 0.8372 (t0) REVERT: B 127 GLU cc_start: 0.8727 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 170 GLN cc_start: 0.7207 (pt0) cc_final: 0.6817 (pm20) REVERT: B 176 GLU cc_start: 0.8200 (pt0) cc_final: 0.7695 (pt0) REVERT: B 273 ARG cc_start: 0.8284 (mtm180) cc_final: 0.8043 (mtm110) REVERT: B 333 TYR cc_start: 0.8463 (t80) cc_final: 0.8041 (t80) REVERT: B 343 GLU cc_start: 0.8389 (tp30) cc_final: 0.7962 (tp30) REVERT: B 352 GLU cc_start: 0.7624 (tp30) cc_final: 0.7281 (tp30) REVERT: B 368 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8371 (tm-30) REVERT: D 93 ASP cc_start: 0.8851 (t70) cc_final: 0.8575 (t0) REVERT: D 98 LEU cc_start: 0.9228 (tp) cc_final: 0.8971 (tt) REVERT: D 205 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: E 50 MET cc_start: 0.7752 (ttt) cc_final: 0.7460 (ptm) REVERT: F 12 TRP cc_start: 0.8166 (m-90) cc_final: 0.7823 (m100) REVERT: I 7 ARG cc_start: 0.8101 (tpp-160) cc_final: 0.7741 (mpt-90) outliers start: 30 outliers final: 22 residues processed: 201 average time/residue: 0.2447 time to fit residues: 69.6789 Evaluate side-chains 204 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 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 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 A residue 768 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 318 THR 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 180 SER Chi-restraints excluded: chain D residue 205 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.0170 chunk 55 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 2 optimal weight: 0.0870 chunk 92 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.137608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099991 restraints weight = 17826.594| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.75 r_work: 0.3064 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2668 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= 0.121 Angle : 0.568 10.154 14951 Z= 0.299 Chirality : 0.044 0.240 1602 Planarity : 0.004 0.039 1961 Dihedral : 4.259 17.115 1504 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.10 % Allowed : 15.51 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1346 helix: 1.55 (0.32), residues: 265 sheet: -0.30 (0.24), residues: 449 loop : 0.25 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 48 HIS 0.002 0.000 HIS F 5 PHE 0.034 0.001 PHE A 238 TYR 0.023 0.001 TYR D 184 ARG 0.007 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 485) hydrogen bonds : angle 4.94759 ( 1344) SS BOND : bond 0.01364 ( 1) SS BOND : angle 6.26780 ( 2) covalent geometry : bond 0.00267 (11010) covalent geometry : angle 0.56302 (14949) Misc. bond : bond 0.00009 ( 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 209 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ASP cc_start: 0.9061 (t0) cc_final: 0.8651 (p0) REVERT: A 323 GLN cc_start: 0.7573 (pm20) cc_final: 0.7222 (pm20) REVERT: A 325 MET cc_start: 0.7734 (tmm) cc_final: 0.7442 (tmm) REVERT: A 338 ARG cc_start: 0.8443 (mtp-110) cc_final: 0.8165 (ttm-80) REVERT: A 358 ASP cc_start: 0.8107 (m-30) cc_final: 0.7789 (t0) REVERT: A 536 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8803 (mp) REVERT: A 552 MET cc_start: 0.9028 (mmm) cc_final: 0.8748 (mmm) REVERT: A 583 ARG cc_start: 0.8260 (ttp80) cc_final: 0.8006 (ttp-170) REVERT: A 729 TYR cc_start: 0.7531 (m-10) cc_final: 0.7324 (m-10) REVERT: A 805 ASN cc_start: 0.8618 (t0) cc_final: 0.8357 (t0) REVERT: B 127 GLU cc_start: 0.8637 (mm-30) cc_final: 0.7775 (mm-30) REVERT: B 170 GLN cc_start: 0.7057 (pt0) cc_final: 0.6637 (pm20) REVERT: B 176 GLU cc_start: 0.8151 (pt0) cc_final: 0.7656 (pt0) REVERT: B 223 GLN cc_start: 0.8109 (mp10) cc_final: 0.7857 (mp10) REVERT: B 273 ARG cc_start: 0.8262 (mtm180) cc_final: 0.8008 (mtm110) REVERT: B 333 TYR cc_start: 0.8430 (t80) cc_final: 0.8074 (t80) REVERT: B 343 GLU cc_start: 0.8331 (tp30) cc_final: 0.7900 (tp30) REVERT: B 352 GLU cc_start: 0.7648 (tp30) cc_final: 0.7311 (tp30) REVERT: B 368 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8294 (tm-30) REVERT: D 93 ASP cc_start: 0.8793 (t70) cc_final: 0.8504 (t0) REVERT: D 98 LEU cc_start: 0.9195 (tp) cc_final: 0.8932 (tt) REVERT: D 205 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: D 207 ASP cc_start: 0.8397 (p0) cc_final: 0.8077 (p0) REVERT: E 50 MET cc_start: 0.7809 (ttt) cc_final: 0.7604 (ptm) REVERT: F 12 TRP cc_start: 0.8181 (m-90) cc_final: 0.7821 (m100) REVERT: I 7 ARG cc_start: 0.8073 (tpp-160) cc_final: 0.7735 (mpt-90) outliers start: 24 outliers final: 19 residues processed: 197 average time/residue: 0.2255 time to fit residues: 63.6553 Evaluate side-chains 206 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 463 ASN 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 124 ILE Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 318 THR 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 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 0.0060 chunk 74 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099788 restraints weight = 17795.038| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.70 r_work: 0.3073 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11020 Z= 0.124 Angle : 0.564 9.178 14951 Z= 0.297 Chirality : 0.044 0.183 1602 Planarity : 0.004 0.037 1961 Dihedral : 4.176 16.547 1504 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.19 % Allowed : 15.34 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1346 helix: 1.64 (0.32), residues: 265 sheet: -0.29 (0.24), residues: 449 loop : 0.25 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 48 HIS 0.002 0.000 HIS A 533 PHE 0.034 0.001 PHE A 238 TYR 0.023 0.001 TYR D 184 ARG 0.008 0.000 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 485) hydrogen bonds : angle 4.88947 ( 1344) SS BOND : bond 0.00283 ( 1) SS BOND : angle 5.82169 ( 2) covalent geometry : bond 0.00277 (11010) covalent geometry : angle 0.56035 (14949) Misc. bond : bond 0.00010 ( 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 210 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 307 ASP cc_start: 0.8968 (t0) cc_final: 0.8690 (p0) REVERT: A 323 GLN cc_start: 0.7577 (pm20) cc_final: 0.7239 (pm20) REVERT: A 325 MET cc_start: 0.7742 (tmm) cc_final: 0.7325 (tmm) REVERT: A 338 ARG cc_start: 0.8432 (mtp-110) cc_final: 0.8157 (mtp-110) REVERT: A 536 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8805 (mp) REVERT: A 552 MET cc_start: 0.9012 (mmm) cc_final: 0.8746 (mmm) REVERT: A 583 ARG cc_start: 0.8263 (ttp80) cc_final: 0.8018 (ttp-170) REVERT: A 805 ASN cc_start: 0.8627 (t0) cc_final: 0.8367 (t0) REVERT: B 127 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 170 GLN cc_start: 0.7064 (pt0) cc_final: 0.6662 (pm20) REVERT: B 176 GLU cc_start: 0.8158 (pt0) cc_final: 0.7672 (pt0) REVERT: B 223 GLN cc_start: 0.8087 (mp10) cc_final: 0.7840 (mp10) REVERT: B 273 ARG cc_start: 0.8176 (mtm180) cc_final: 0.7918 (mtm110) REVERT: B 343 GLU cc_start: 0.8337 (tp30) cc_final: 0.7903 (tp30) REVERT: B 352 GLU cc_start: 0.7635 (tp30) cc_final: 0.7298 (tp30) REVERT: B 368 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8305 (tm-30) REVERT: D 93 ASP cc_start: 0.8739 (t70) cc_final: 0.8457 (t0) REVERT: D 98 LEU cc_start: 0.9162 (tp) cc_final: 0.8896 (tt) REVERT: F 12 TRP cc_start: 0.8160 (m-90) cc_final: 0.7804 (m100) REVERT: I 7 ARG cc_start: 0.8063 (tpp-160) cc_final: 0.7711 (mpt-90) outliers start: 25 outliers final: 20 residues processed: 197 average time/residue: 0.2265 time to fit residues: 64.0966 Evaluate side-chains 201 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 463 ASN 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 124 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 42 LEU 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 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 34 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 HIS ** 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 = 0.3748 r_free = 0.3748 target = 0.136343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096941 restraints weight = 17734.623| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.65 r_work: 0.3039 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11020 Z= 0.169 Angle : 0.579 9.290 14951 Z= 0.306 Chirality : 0.045 0.179 1602 Planarity : 0.004 0.046 1961 Dihedral : 4.265 16.557 1504 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.02 % Allowed : 15.25 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1346 helix: 1.62 (0.32), residues: 265 sheet: -0.20 (0.25), residues: 439 loop : 0.20 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 48 HIS 0.002 0.000 HIS A 533 PHE 0.036 0.001 PHE A 238 TYR 0.022 0.001 TYR D 184 ARG 0.008 0.000 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 485) hydrogen bonds : angle 4.98495 ( 1344) SS BOND : bond 0.00360 ( 1) SS BOND : angle 5.94640 ( 2) covalent geometry : bond 0.00378 (11010) covalent geometry : angle 0.57468 (14949) Misc. bond : bond 0.00024 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5237.95 seconds wall clock time: 91 minutes 1.40 seconds (5461.40 seconds total)