Starting phenix.real_space_refine on Thu Jul 2 23:15:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcs_37108/07_2026/8kcs_37108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcs_37108/07_2026/8kcs_37108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kcs_37108/07_2026/8kcs_37108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcs_37108/07_2026/8kcs_37108.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcs_37108/07_2026/8kcs_37108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcs_37108/07_2026/8kcs_37108.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 40 5.16 5 C 7110 2.51 5 N 1709 2.21 5 O 1976 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10843 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2436 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'PC1': 1, 'Q70': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 2.64, per 1000 atoms: 0.24 Number of scatterers: 10843 At special positions: 0 Unit cell: (110.415, 93.095, 128.817, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 2 15.00 F 6 9.00 O 1976 8.00 N 1709 7.00 C 7110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.63 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.17 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=1, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 387.0 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2470 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 60.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 80 through 87 removed outlier: 3.552A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.775A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.986A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.761A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.567A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.960A pdb=" N GLY A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.512A pdb=" N PHE A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 313 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 435 removed outlier: 4.242A pdb=" N ALA A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 472 through 479 removed outlier: 3.908A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.575A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.547A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 537 through 538 No H-bonds generated for 'chain 'A' and resid 537 through 538' Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.533A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.596A pdb=" N ASP A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.692A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.511A pdb=" N GLU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 82 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 156 removed outlier: 3.527A pdb=" N TYR B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 removed outlier: 3.664A pdb=" N ILE B 162 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 241 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.653A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 402 through 429 removed outlier: 3.591A pdb=" N THR B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 452 removed outlier: 4.437A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 464 removed outlier: 3.543A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 14 through 25 Processing helix chain 'C' and resid 28 through 60 removed outlier: 3.660A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 103 removed outlier: 3.568A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 141 removed outlier: 5.879A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 Processing helix chain 'C' and resid 186 through 204 removed outlier: 3.784A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.527A pdb=" N LYS D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.524A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 82 Processing helix chain 'D' and resid 86 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.666A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 9.169A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.146A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.693A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 601 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1635 1.30 - 1.43: 3095 1.43 - 1.56: 6325 1.56 - 1.69: 7 1.69 - 1.81: 61 Bond restraints: 11123 Sorted by residual: bond pdb=" C27 Q70 B 502 " pdb=" N13 Q70 B 502 " ideal model delta sigma weight residual 1.299 1.446 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C27 Q70 B 502 " pdb=" C28 Q70 B 502 " ideal model delta sigma weight residual 1.484 1.578 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" N ARG A 434 " pdb=" CA ARG A 434 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.06e-02 8.90e+03 1.48e+01 bond pdb=" C21 Q70 B 502 " pdb=" N11 Q70 B 502 " ideal model delta sigma weight residual 1.371 1.446 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C21 Q70 B 502 " pdb=" O08 Q70 B 502 " ideal model delta sigma weight residual 1.238 1.177 0.061 2.00e-02 2.50e+03 9.35e+00 ... (remaining 11118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 14717 1.96 - 3.92: 370 3.92 - 5.88: 61 5.88 - 7.85: 21 7.85 - 9.81: 7 Bond angle restraints: 15176 Sorted by residual: angle pdb=" CA ARG A 434 " pdb=" C ARG A 434 " pdb=" O ARG A 434 " ideal model delta sigma weight residual 119.08 114.82 4.26 1.03e+00 9.43e-01 1.71e+01 angle pdb=" C THR A 209 " pdb=" N PHE A 210 " pdb=" CA PHE A 210 " ideal model delta sigma weight residual 120.26 125.73 -5.47 1.34e+00 5.57e-01 1.67e+01 angle pdb=" C ALA A 433 " pdb=" N ARG A 434 " pdb=" CA ARG A 434 " ideal model delta sigma weight residual 121.18 114.78 6.40 1.64e+00 3.72e-01 1.52e+01 angle pdb=" N TRP A 289 " pdb=" CA TRP A 289 " pdb=" C TRP A 289 " ideal model delta sigma weight residual 110.97 114.76 -3.79 1.09e+00 8.42e-01 1.21e+01 angle pdb=" N GLY C 234 " pdb=" CA GLY C 234 " pdb=" C GLY C 234 " ideal model delta sigma weight residual 113.18 120.99 -7.81 2.37e+00 1.78e-01 1.09e+01 ... (remaining 15171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 6391 23.85 - 47.70: 444 47.70 - 71.54: 68 71.54 - 95.39: 25 95.39 - 119.24: 18 Dihedral angle restraints: 6946 sinusoidal: 3113 harmonic: 3833 Sorted by residual: dihedral pdb=" CA LEU C 206 " pdb=" C LEU C 206 " pdb=" N ASN C 207 " pdb=" CA ASN C 207 " ideal model delta harmonic sigma weight residual -180.00 -148.07 -31.93 0 5.00e+00 4.00e-02 4.08e+01 dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 143.96 -50.96 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CA ASN A 91 " pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta harmonic sigma weight residual -180.00 -154.03 -25.97 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 6943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1775 0.119 - 0.239: 28 0.239 - 0.358: 6 0.358 - 0.478: 0 0.478 - 0.597: 1 Chirality restraints: 1810 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 562 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.92e+00 chirality pdb=" C22 Q70 B 502 " pdb=" C25 Q70 B 502 " pdb=" N10 Q70 B 502 " pdb=" N13 Q70 B 502 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1807 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 562 " 0.040 2.00e-02 2.50e+03 3.99e-02 1.99e+01 pdb=" CG ASN A 562 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 562 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 562 " -0.059 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 283 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO B 284 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 302 " -0.014 2.00e-02 2.50e+03 1.24e-02 2.69e+00 pdb=" CG PHE A 302 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 302 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 302 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 302 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 302 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 302 " -0.002 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 134 2.64 - 3.21: 9772 3.21 - 3.77: 16816 3.77 - 4.34: 24418 4.34 - 4.90: 38923 Nonbonded interactions: 90063 Sorted by model distance: nonbonded pdb=" CD2 TYR A 545 " pdb=" OD1 ASN A 562 " model vdw 2.080 3.340 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.097 3.040 nonbonded pdb=" O GLN B 464 " pdb=" ND2 ASN C 207 " model vdw 2.152 3.120 nonbonded pdb=" OD1 ASP B 194 " pdb=" CG2 THR B 197 " model vdw 2.172 3.460 nonbonded pdb=" OD1 ASN A 530 " pdb=" NE2 GLN A 535 " model vdw 2.205 3.120 ... (remaining 90058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.310 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.008 0.599 11148 Z= 0.415 Angle : 0.910 39.480 15244 Z= 0.455 Chirality : 0.051 0.597 1810 Planarity : 0.004 0.043 1831 Dihedral : 17.669 119.238 4464 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.32 % Rotamer: Outliers : 3.02 % Allowed : 11.99 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.21), residues: 1303 helix: -0.12 (0.18), residues: 708 sheet: -1.36 (0.42), residues: 128 loop : -2.48 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 109 TYR 0.019 0.002 TYR A 173 PHE 0.029 0.002 PHE A 302 TRP 0.010 0.001 TRP B 203 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.29 (11123) covalent geometry : angle 0.78651 / 0.41 (15176) SS BOND : bond 0.30799 / 16.17 ( 4) SS BOND : angle 17.66123 / 7.86 ( 8) hydrogen bonds : bond 0.16637 / 11.35 ( 601) hydrogen bonds : angle 6.17787 / 4.34 ( 1728) Misc. bond : bond 0.04192 / 2.21 ( 1) link_BETA1-3 : bond 0.00132 / 0.07 ( 1) link_BETA1-3 : angle 1.25423 / 1.05 ( 3) link_BETA1-4 : bond 0.00330 / 0.17 ( 7) link_BETA1-4 : angle 2.14781 / 1.66 ( 21) link_BETA1-6 : bond 0.00621 / 0.33 ( 1) link_BETA1-6 : angle 1.10092 / 0.72 ( 3) link_NAG-ASN : bond 0.01990 / 1.47 ( 11) link_NAG-ASN : angle 4.41665 / 2.54 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7679 (tp30) cc_final: 0.7321 (tp30) REVERT: A 393 GLN cc_start: 0.7973 (mt0) cc_final: 0.7764 (mt0) REVERT: A 516 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7737 (mm-40) REVERT: A 601 GLU cc_start: 0.7985 (tp30) cc_final: 0.7674 (mm-30) REVERT: B 112 GLN cc_start: 0.8694 (tt0) cc_final: 0.8311 (tt0) REVERT: B 133 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8384 (mp) REVERT: B 269 ARG cc_start: 0.8374 (ttt-90) cc_final: 0.8121 (ttt180) REVERT: B 458 ASP cc_start: 0.7999 (p0) cc_final: 0.7798 (p0) REVERT: C 66 ARG cc_start: 0.6976 (mtp85) cc_final: 0.6012 (mmp-170) REVERT: D 11 LYS cc_start: 0.8241 (mtmt) cc_final: 0.8015 (mtmm) REVERT: D 39 ARG cc_start: 0.6662 (ttm-80) cc_final: 0.6449 (ttm170) outliers start: 34 outliers final: 15 residues processed: 206 average time/residue: 0.5952 time to fit residues: 131.8958 Evaluate side-chains 145 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 65 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 GLN A 587 GLN B 222 GLN C 116 GLN C 197 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.115095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.088658 restraints weight = 13337.281| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.91 r_work: 0.2933 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11148 Z= 0.144 Angle : 0.657 9.472 15244 Z= 0.325 Chirality : 0.044 0.237 1810 Planarity : 0.004 0.034 1831 Dihedral : 12.424 117.190 2180 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 2.49 % Allowed : 15.81 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.23), residues: 1303 helix: 1.41 (0.19), residues: 726 sheet: -0.96 (0.44), residues: 132 loop : -1.88 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 59 TYR 0.016 0.002 TYR A 173 PHE 0.032 0.001 PHE A 302 TRP 0.010 0.001 TRP A 533 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (11123) covalent geometry : angle 0.64281 / 0.32 (15176) SS BOND : bond 0.01102 / 0.56 ( 4) SS BOND : angle 0.86160 / 0.45 ( 8) hydrogen bonds : bond 0.05348 / 3.48 ( 601) hydrogen bonds : angle 4.45245 / 3.19 ( 1728) Misc. bond : bond 0.00006 / 0.00 ( 1) link_BETA1-3 : bond 0.01018 / 0.54 ( 1) link_BETA1-3 : angle 1.63861 / 1.16 ( 3) link_BETA1-4 : bond 0.00331 / 0.17 ( 7) link_BETA1-4 : angle 1.63042 / 1.22 ( 21) link_BETA1-6 : bond 0.01694 / 0.89 ( 1) link_BETA1-6 : angle 1.91296 / 1.22 ( 3) link_NAG-ASN : bond 0.00418 / 0.20 ( 11) link_NAG-ASN : angle 2.68219 / 1.68 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: A 388 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: A 393 GLN cc_start: 0.8125 (mt0) cc_final: 0.7807 (mt0) REVERT: A 516 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7942 (mm-40) REVERT: A 597 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7927 (tmmt) REVERT: A 599 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8226 (mp) REVERT: B 108 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7567 (mtp-110) REVERT: B 112 GLN cc_start: 0.8764 (tt0) cc_final: 0.8537 (tt0) REVERT: B 133 ILE cc_start: 0.8292 (mt) cc_final: 0.7974 (mp) REVERT: B 269 ARG cc_start: 0.8032 (ttt-90) cc_final: 0.7812 (ttt180) REVERT: C 96 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6611 (mtmt) REVERT: C 241 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.7015 (mpt-90) REVERT: D 11 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7813 (mtmm) REVERT: D 39 ARG cc_start: 0.6530 (ttm-80) cc_final: 0.6284 (ttm170) outliers start: 28 outliers final: 8 residues processed: 156 average time/residue: 0.5772 time to fit residues: 97.0770 Evaluate side-chains 139 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 96 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN B 81 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.085763 restraints weight = 13331.051| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.02 r_work: 0.2907 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11148 Z= 0.199 Angle : 0.692 9.828 15244 Z= 0.343 Chirality : 0.046 0.265 1810 Planarity : 0.004 0.038 1831 Dihedral : 10.839 113.240 2155 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.86 % Rotamer: Outliers : 3.73 % Allowed : 15.90 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.24), residues: 1303 helix: 1.85 (0.19), residues: 724 sheet: -0.84 (0.44), residues: 132 loop : -1.80 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 274 TYR 0.022 0.002 TYR A 173 PHE 0.029 0.002 PHE A 302 TRP 0.009 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (11123) covalent geometry : angle 0.67275 / 0.34 (15176) SS BOND : bond 0.00452 / 0.23 ( 4) SS BOND : angle 1.18946 / 0.59 ( 8) hydrogen bonds : bond 0.05832 / 3.77 ( 601) hydrogen bonds : angle 4.36104 / 3.12 ( 1728) Misc. bond : bond 0.00177 / 0.09 ( 1) link_BETA1-3 : bond 0.00783 / 0.41 ( 1) link_BETA1-3 : angle 1.30416 / 0.86 ( 3) link_BETA1-4 : bond 0.00256 / 0.13 ( 7) link_BETA1-4 : angle 1.95377 / 1.47 ( 21) link_BETA1-6 : bond 0.01568 / 0.83 ( 1) link_BETA1-6 : angle 1.97663 / 1.36 ( 3) link_NAG-ASN : bond 0.00521 / 0.24 ( 11) link_NAG-ASN : angle 3.09436 / 1.98 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8650 (tt0) REVERT: A 388 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: A 393 GLN cc_start: 0.8368 (mt0) cc_final: 0.8062 (mt0) REVERT: A 512 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8852 (tt0) REVERT: A 516 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8051 (mm-40) REVERT: A 597 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8041 (tmmt) REVERT: A 599 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8488 (mp) REVERT: B 112 GLN cc_start: 0.8809 (tt0) cc_final: 0.8591 (tt0) REVERT: B 133 ILE cc_start: 0.8459 (mt) cc_final: 0.8179 (mp) REVERT: B 228 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8323 (mtt) REVERT: B 269 ARG cc_start: 0.8352 (ttt-90) cc_final: 0.8086 (ttt180) REVERT: B 270 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7832 (mtp) REVERT: D 11 LYS cc_start: 0.8257 (mtmt) cc_final: 0.8048 (mtmm) REVERT: D 39 ARG cc_start: 0.6860 (ttm-80) cc_final: 0.6548 (ttm170) outliers start: 42 outliers final: 19 residues processed: 164 average time/residue: 0.5396 time to fit residues: 95.3596 Evaluate side-chains 151 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 52 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 0.0170 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 84 optimal weight: 0.0980 chunk 128 optimal weight: 3.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.093302 restraints weight = 13343.711| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.97 r_work: 0.3062 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11148 Z= 0.117 Angle : 0.586 9.653 15244 Z= 0.290 Chirality : 0.042 0.258 1810 Planarity : 0.004 0.033 1831 Dihedral : 9.964 109.316 2155 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 3.02 % Allowed : 17.23 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1303 helix: 2.20 (0.20), residues: 730 sheet: -0.58 (0.47), residues: 129 loop : -1.63 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.012 0.001 TYR A 173 PHE 0.029 0.001 PHE A 302 TRP 0.008 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (11123) covalent geometry : angle 0.57182 / 0.29 (15176) SS BOND : bond 0.00249 / 0.13 ( 4) SS BOND : angle 0.65549 / 0.38 ( 8) hydrogen bonds : bond 0.04573 / 2.94 ( 601) hydrogen bonds : angle 4.14718 / 3.00 ( 1728) Misc. bond : bond 0.00033 / 0.02 ( 1) link_BETA1-3 : bond 0.00855 / 0.45 ( 1) link_BETA1-3 : angle 1.59188 / 0.91 ( 3) link_BETA1-4 : bond 0.00389 / 0.19 ( 7) link_BETA1-4 : angle 1.48743 / 1.11 ( 21) link_BETA1-6 : bond 0.01576 / 0.83 ( 1) link_BETA1-6 : angle 2.21539 / 1.64 ( 3) link_NAG-ASN : bond 0.00454 / 0.26 ( 11) link_NAG-ASN : angle 2.51482 / 1.56 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7974 (tt0) cc_final: 0.7114 (tp30) REVERT: A 388 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: A 389 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7699 (p) REVERT: A 393 GLN cc_start: 0.8414 (mt0) cc_final: 0.8150 (mt0) REVERT: A 512 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8856 (tt0) REVERT: A 516 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8070 (mm-40) REVERT: A 597 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7984 (tmmt) REVERT: B 112 GLN cc_start: 0.8763 (tt0) cc_final: 0.8536 (tt0) REVERT: B 133 ILE cc_start: 0.8478 (mt) cc_final: 0.8175 (mp) REVERT: B 269 ARG cc_start: 0.8364 (ttt-90) cc_final: 0.8113 (ttt180) REVERT: C 241 ARG cc_start: 0.7525 (mtp-110) cc_final: 0.6871 (mpt-90) REVERT: D 11 LYS cc_start: 0.8257 (mtmt) cc_final: 0.8049 (mtmm) REVERT: D 39 ARG cc_start: 0.6873 (ttm-80) cc_final: 0.6582 (ttm170) outliers start: 34 outliers final: 11 residues processed: 157 average time/residue: 0.5028 time to fit residues: 85.3937 Evaluate side-chains 139 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 60 optimal weight: 0.0170 chunk 31 optimal weight: 0.0060 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.7436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.092892 restraints weight = 13343.807| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.97 r_work: 0.3058 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11148 Z= 0.127 Angle : 0.594 9.688 15244 Z= 0.294 Chirality : 0.043 0.256 1810 Planarity : 0.004 0.033 1831 Dihedral : 9.540 104.083 2155 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 3.29 % Allowed : 17.32 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1303 helix: 2.30 (0.20), residues: 731 sheet: -0.51 (0.47), residues: 129 loop : -1.48 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.016 0.001 TYR A 173 PHE 0.029 0.001 PHE A 302 TRP 0.008 0.001 TRP B 203 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (11123) covalent geometry : angle 0.57858 / 0.29 (15176) SS BOND : bond 0.00239 / 0.12 ( 4) SS BOND : angle 0.68502 / 0.37 ( 8) hydrogen bonds : bond 0.04654 / 2.99 ( 601) hydrogen bonds : angle 4.09918 / 2.96 ( 1728) Misc. bond : bond 0.00083 / 0.04 ( 1) link_BETA1-3 : bond 0.00870 / 0.46 ( 1) link_BETA1-3 : angle 1.97736 / 1.07 ( 3) link_BETA1-4 : bond 0.00268 / 0.14 ( 7) link_BETA1-4 : angle 1.56069 / 1.14 ( 21) link_BETA1-6 : bond 0.01391 / 0.73 ( 1) link_BETA1-6 : angle 2.20991 / 1.79 ( 3) link_NAG-ASN : bond 0.00383 / 0.18 ( 11) link_NAG-ASN : angle 2.54935 / 1.61 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7968 (tt0) cc_final: 0.6983 (tp30) REVERT: A 274 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8515 (mmp80) REVERT: A 364 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: A 388 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: A 393 GLN cc_start: 0.8418 (mt0) cc_final: 0.8133 (mt0) REVERT: A 512 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8845 (tt0) REVERT: A 516 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8092 (mm-40) REVERT: A 597 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8008 (tmmt) REVERT: A 599 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8425 (mp) REVERT: B 112 GLN cc_start: 0.8748 (tt0) cc_final: 0.8458 (tt0) REVERT: B 133 ILE cc_start: 0.8495 (mt) cc_final: 0.8193 (mp) REVERT: B 228 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8364 (mtt) REVERT: B 269 ARG cc_start: 0.8345 (ttt-90) cc_final: 0.8112 (ttt180) REVERT: C 241 ARG cc_start: 0.7766 (mtp-110) cc_final: 0.7115 (mpt-90) REVERT: D 11 LYS cc_start: 0.8254 (mtmt) cc_final: 0.8039 (mtmm) REVERT: D 39 ARG cc_start: 0.6915 (ttm-80) cc_final: 0.6619 (ttm170) outliers start: 37 outliers final: 18 residues processed: 155 average time/residue: 0.5615 time to fit residues: 93.9716 Evaluate side-chains 152 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 242 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 37 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093739 restraints weight = 13290.931| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.91 r_work: 0.3080 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11148 Z= 0.136 Angle : 0.604 9.851 15244 Z= 0.298 Chirality : 0.043 0.254 1810 Planarity : 0.004 0.033 1831 Dihedral : 9.352 98.985 2155 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.09 % Rotamer: Outliers : 3.11 % Allowed : 17.58 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1303 helix: 2.30 (0.20), residues: 732 sheet: -0.54 (0.47), residues: 129 loop : -1.44 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 160 TYR 0.016 0.001 TYR A 173 PHE 0.030 0.001 PHE A 302 TRP 0.008 0.001 TRP B 203 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (11123) covalent geometry : angle 0.58870 / 0.30 (15176) SS BOND : bond 0.00279 / 0.14 ( 4) SS BOND : angle 0.67711 / 0.38 ( 8) hydrogen bonds : bond 0.04739 / 3.04 ( 601) hydrogen bonds : angle 4.09619 / 2.96 ( 1728) Misc. bond : bond 0.00101 / 0.05 ( 1) link_BETA1-3 : bond 0.00865 / 0.46 ( 1) link_BETA1-3 : angle 2.09813 / 1.13 ( 3) link_BETA1-4 : bond 0.00312 / 0.15 ( 7) link_BETA1-4 : angle 1.58651 / 1.15 ( 21) link_BETA1-6 : bond 0.01344 / 0.71 ( 1) link_BETA1-6 : angle 2.46198 / 1.99 ( 3) link_NAG-ASN : bond 0.00385 / 0.18 ( 11) link_NAG-ASN : angle 2.56769 / 1.63 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8010 (tt0) cc_final: 0.7189 (tp30) REVERT: A 274 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8468 (mmp80) REVERT: A 364 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8629 (tt0) REVERT: A 388 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: A 393 GLN cc_start: 0.8451 (mt0) cc_final: 0.8206 (mt0) REVERT: A 512 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8883 (tt0) REVERT: A 516 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8149 (mm-40) REVERT: A 531 ASN cc_start: 0.7653 (m110) cc_final: 0.7448 (m-40) REVERT: A 587 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: A 597 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8020 (tmmt) REVERT: A 599 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8499 (mp) REVERT: A 601 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: B 133 ILE cc_start: 0.8575 (mt) cc_final: 0.8287 (mp) REVERT: B 228 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8415 (mtt) REVERT: B 269 ARG cc_start: 0.8417 (ttt-90) cc_final: 0.8174 (ttt180) REVERT: C 241 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.7153 (mpt-90) REVERT: D 11 LYS cc_start: 0.8311 (mtmt) cc_final: 0.8096 (mtmm) REVERT: D 39 ARG cc_start: 0.7011 (ttm-80) cc_final: 0.6715 (ttm170) outliers start: 35 outliers final: 20 residues processed: 150 average time/residue: 0.5424 time to fit residues: 87.9878 Evaluate side-chains 152 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 242 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 118 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 17 optimal weight: 0.0570 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092349 restraints weight = 13167.730| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.93 r_work: 0.3058 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11148 Z= 0.161 Angle : 0.633 9.837 15244 Z= 0.313 Chirality : 0.044 0.253 1810 Planarity : 0.004 0.034 1831 Dihedral : 9.302 93.690 2155 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 3.37 % Allowed : 17.14 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.24), residues: 1303 helix: 2.27 (0.20), residues: 730 sheet: -0.63 (0.46), residues: 132 loop : -1.43 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 184 TYR 0.019 0.002 TYR A 173 PHE 0.031 0.002 PHE A 302 TRP 0.009 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (11123) covalent geometry : angle 0.61571 / 0.31 (15176) SS BOND : bond 0.00299 / 0.15 ( 4) SS BOND : angle 0.75510 / 0.38 ( 8) hydrogen bonds : bond 0.05095 / 3.28 ( 601) hydrogen bonds : angle 4.14007 / 2.98 ( 1728) Misc. bond : bond 0.00153 / 0.08 ( 1) link_BETA1-3 : bond 0.00835 / 0.44 ( 1) link_BETA1-3 : angle 2.31384 / 1.24 ( 3) link_BETA1-4 : bond 0.00241 / 0.12 ( 7) link_BETA1-4 : angle 1.70962 / 1.24 ( 21) link_BETA1-6 : bond 0.01494 / 0.79 ( 1) link_BETA1-6 : angle 2.70882 / 2.18 ( 3) link_NAG-ASN : bond 0.00405 / 0.19 ( 11) link_NAG-ASN : angle 2.73180 / 1.74 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8069 (tt0) cc_final: 0.7230 (tp30) REVERT: A 274 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8372 (mmp80) REVERT: A 364 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: A 388 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: A 393 GLN cc_start: 0.8469 (mt0) cc_final: 0.8222 (mt0) REVERT: A 512 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8879 (tt0) REVERT: A 516 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8154 (mm-40) REVERT: A 587 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7438 (mp10) REVERT: A 597 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8038 (tmmt) REVERT: A 599 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8533 (mp) REVERT: A 601 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: B 133 ILE cc_start: 0.8583 (mt) cc_final: 0.8316 (mp) REVERT: B 228 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8411 (mtt) REVERT: B 269 ARG cc_start: 0.8450 (ttt-90) cc_final: 0.8210 (ttt180) REVERT: C 184 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7647 (mtm-85) REVERT: C 241 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7176 (mpt-90) REVERT: D 11 LYS cc_start: 0.8318 (mtmt) cc_final: 0.8106 (mtmm) REVERT: D 39 ARG cc_start: 0.7036 (ttm-80) cc_final: 0.6740 (ttm170) outliers start: 38 outliers final: 20 residues processed: 155 average time/residue: 0.4895 time to fit residues: 82.0547 Evaluate side-chains 154 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 242 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 70 optimal weight: 0.0370 chunk 123 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN A 367 GLN A 531 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.091867 restraints weight = 13211.083| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.91 r_work: 0.3053 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11148 Z= 0.173 Angle : 0.654 10.395 15244 Z= 0.322 Chirality : 0.045 0.255 1810 Planarity : 0.004 0.035 1831 Dihedral : 9.250 87.344 2155 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 3.37 % Allowed : 17.05 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1303 helix: 2.23 (0.19), residues: 730 sheet: -0.84 (0.43), residues: 142 loop : -1.55 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 184 TYR 0.019 0.002 TYR A 173 PHE 0.031 0.002 PHE A 302 TRP 0.009 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (11123) covalent geometry : angle 0.63595 / 0.32 (15176) SS BOND : bond 0.00303 / 0.15 ( 4) SS BOND : angle 0.77050 / 0.38 ( 8) hydrogen bonds : bond 0.05282 / 3.40 ( 601) hydrogen bonds : angle 4.16969 / 3.00 ( 1728) Misc. bond : bond 0.00178 / 0.09 ( 1) link_BETA1-3 : bond 0.00772 / 0.41 ( 1) link_BETA1-3 : angle 2.55343 / 1.36 ( 3) link_BETA1-4 : bond 0.00233 / 0.12 ( 7) link_BETA1-4 : angle 1.77524 / 1.29 ( 21) link_BETA1-6 : bond 0.01522 / 0.80 ( 1) link_BETA1-6 : angle 2.93319 / 2.35 ( 3) link_NAG-ASN : bond 0.00451 / 0.20 ( 11) link_NAG-ASN : angle 2.83456 / 1.81 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: A 388 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: A 393 GLN cc_start: 0.8447 (mt0) cc_final: 0.8146 (mt0) REVERT: A 512 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8877 (tt0) REVERT: A 516 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8144 (mm-40) REVERT: A 587 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: A 597 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8021 (tmmt) REVERT: A 599 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 601 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: B 127 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7436 (mm-40) REVERT: B 133 ILE cc_start: 0.8565 (mt) cc_final: 0.8297 (mp) REVERT: B 228 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8406 (mtt) REVERT: B 269 ARG cc_start: 0.8441 (ttt-90) cc_final: 0.8193 (ttt180) REVERT: C 241 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.7157 (mpt-90) REVERT: D 39 ARG cc_start: 0.7031 (ttm-80) cc_final: 0.6737 (ttm170) outliers start: 38 outliers final: 23 residues processed: 155 average time/residue: 0.5274 time to fit residues: 88.1824 Evaluate side-chains 154 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 242 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN A 531 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.092142 restraints weight = 13286.477| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.88 r_work: 0.3057 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11148 Z= 0.161 Angle : 0.641 10.081 15244 Z= 0.316 Chirality : 0.044 0.256 1810 Planarity : 0.004 0.034 1831 Dihedral : 9.116 83.782 2155 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 3.37 % Allowed : 17.32 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.24), residues: 1303 helix: 2.25 (0.19), residues: 730 sheet: -0.82 (0.43), residues: 142 loop : -1.52 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.018 0.002 TYR A 173 PHE 0.031 0.002 PHE A 302 TRP 0.008 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (11123) covalent geometry : angle 0.62279 / 0.31 (15176) SS BOND : bond 0.00262 / 0.13 ( 4) SS BOND : angle 0.70885 / 0.36 ( 8) hydrogen bonds : bond 0.05149 / 3.31 ( 601) hydrogen bonds : angle 4.16492 / 3.00 ( 1728) Misc. bond : bond 0.00148 / 0.08 ( 1) link_BETA1-3 : bond 0.00811 / 0.43 ( 1) link_BETA1-3 : angle 2.49573 / 1.33 ( 3) link_BETA1-4 : bond 0.00319 / 0.15 ( 7) link_BETA1-4 : angle 1.75531 / 1.27 ( 21) link_BETA1-6 : bond 0.01380 / 0.73 ( 1) link_BETA1-6 : angle 3.06430 / 2.49 ( 3) link_NAG-ASN : bond 0.00404 / 0.18 ( 11) link_NAG-ASN : angle 2.77783 / 1.76 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8577 (tt0) REVERT: A 388 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: A 393 GLN cc_start: 0.8445 (mt0) cc_final: 0.8141 (mt0) REVERT: A 512 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8870 (tt0) REVERT: A 516 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8145 (mm-40) REVERT: A 587 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7431 (mp10) REVERT: A 597 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8017 (tmmt) REVERT: A 599 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8518 (mp) REVERT: A 601 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7904 (mm-30) REVERT: A 619 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7019 (ptt180) REVERT: B 127 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7424 (mm-40) REVERT: B 133 ILE cc_start: 0.8553 (mt) cc_final: 0.8285 (mp) REVERT: B 157 ARG cc_start: 0.4448 (OUTLIER) cc_final: 0.3022 (ppt170) REVERT: B 228 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8409 (mtt) REVERT: B 269 ARG cc_start: 0.8381 (ttt-90) cc_final: 0.8133 (ttt180) REVERT: C 241 ARG cc_start: 0.7769 (mtp-110) cc_final: 0.7146 (mpt-90) REVERT: D 39 ARG cc_start: 0.7027 (ttm-80) cc_final: 0.6733 (ttm170) outliers start: 38 outliers final: 26 residues processed: 150 average time/residue: 0.5046 time to fit residues: 81.6697 Evaluate side-chains 157 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 242 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 37 optimal weight: 0.0370 chunk 104 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.0470 chunk 29 optimal weight: 0.6980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.095319 restraints weight = 13187.308| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.91 r_work: 0.3105 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11148 Z= 0.110 Angle : 0.581 10.205 15244 Z= 0.285 Chirality : 0.042 0.263 1810 Planarity : 0.004 0.032 1831 Dihedral : 8.657 79.139 2155 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 2.31 % Allowed : 18.38 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.25), residues: 1303 helix: 2.44 (0.20), residues: 733 sheet: -0.69 (0.46), residues: 137 loop : -1.37 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 184 TYR 0.012 0.001 TYR B 256 PHE 0.028 0.001 PHE A 302 TRP 0.008 0.001 TRP B 203 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (11123) covalent geometry : angle 0.56491 / 0.28 (15176) SS BOND : bond 0.00189 / 0.10 ( 4) SS BOND : angle 0.51626 / 0.36 ( 8) hydrogen bonds : bond 0.04306 / 2.77 ( 601) hydrogen bonds : angle 4.04773 / 2.93 ( 1728) Misc. bond : bond 0.00029 / 0.02 ( 1) link_BETA1-3 : bond 0.00947 / 0.50 ( 1) link_BETA1-3 : angle 2.08394 / 1.12 ( 3) link_BETA1-4 : bond 0.00378 / 0.20 ( 7) link_BETA1-4 : angle 1.50167 / 1.09 ( 21) link_BETA1-6 : bond 0.01282 / 0.67 ( 1) link_BETA1-6 : angle 3.57659 / 2.98 ( 3) link_NAG-ASN : bond 0.00353 / 0.17 ( 11) link_NAG-ASN : angle 2.48750 / 1.54 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8005 (tt0) cc_final: 0.7472 (mm-30) REVERT: A 364 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8617 (tt0) REVERT: A 388 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: A 389 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.7748 (p) REVERT: A 393 GLN cc_start: 0.8441 (mt0) cc_final: 0.8151 (mt0) REVERT: A 516 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8140 (mm-40) REVERT: A 587 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: A 601 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: A 666 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8215 (mmtp) REVERT: B 133 ILE cc_start: 0.8576 (mt) cc_final: 0.8285 (mp) REVERT: B 269 ARG cc_start: 0.8426 (ttt-90) cc_final: 0.8200 (ttt180) REVERT: C 224 MET cc_start: 0.9000 (mmm) cc_final: 0.8706 (mmm) REVERT: C 241 ARG cc_start: 0.7570 (mtp-110) cc_final: 0.6937 (mpt-90) REVERT: D 39 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6755 (ttm170) outliers start: 26 outliers final: 17 residues processed: 145 average time/residue: 0.5153 time to fit residues: 80.6956 Evaluate side-chains 143 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 242 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092718 restraints weight = 13243.870| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.93 r_work: 0.3065 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11148 Z= 0.157 Angle : 0.628 10.069 15244 Z= 0.309 Chirality : 0.044 0.253 1810 Planarity : 0.004 0.036 1831 Dihedral : 8.687 79.523 2155 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.09 % Rotamer: Outliers : 2.31 % Allowed : 18.29 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.24), residues: 1303 helix: 2.36 (0.19), residues: 730 sheet: -0.81 (0.44), residues: 141 loop : -1.42 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 184 TYR 0.018 0.002 TYR A 173 PHE 0.030 0.002 PHE A 302 TRP 0.008 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (11123) covalent geometry : angle 0.60951 / 0.31 (15176) SS BOND : bond 0.00271 / 0.14 ( 4) SS BOND : angle 0.69253 / 0.35 ( 8) hydrogen bonds : bond 0.04947 / 3.18 ( 601) hydrogen bonds : angle 4.11851 / 2.97 ( 1728) Misc. bond : bond 0.00161 / 0.08 ( 1) link_BETA1-3 : bond 0.00785 / 0.41 ( 1) link_BETA1-3 : angle 2.46832 / 1.32 ( 3) link_BETA1-4 : bond 0.00248 / 0.13 ( 7) link_BETA1-4 : angle 1.70473 / 1.22 ( 21) link_BETA1-6 : bond 0.01184 / 0.62 ( 1) link_BETA1-6 : angle 3.48235 / 2.86 ( 3) link_NAG-ASN : bond 0.00424 / 0.19 ( 11) link_NAG-ASN : angle 2.73489 / 1.73 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3931.91 seconds wall clock time: 67 minutes 36.63 seconds (4056.63 seconds total)