Starting phenix.real_space_refine on Mon Aug 25 09:22:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3f_44136/08_2025/9b3f_44136.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3f_44136/08_2025/9b3f_44136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b3f_44136/08_2025/9b3f_44136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3f_44136/08_2025/9b3f_44136.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b3f_44136/08_2025/9b3f_44136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3f_44136/08_2025/9b3f_44136.map" } resolution = 3.54 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 8559 2.51 5 N 2185 2.21 5 O 2620 1.98 5 H 13441 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26849 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4612 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "E" Number of atoms: 4589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4589 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain: "A" Number of atoms: 14895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 14895 Classifications: {'peptide': 927} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 901} Chain breaks: 5 Chain: "B" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1327 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "C" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1426 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Time building chain proxies: 4.09, per 1000 atoms: 0.15 Number of scatterers: 26849 At special positions: 0 Unit cell: (98.77, 141.93, 161.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 2620 8.00 N 2185 7.00 C 8559 6.00 H 13441 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 751.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3224 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 8 sheets defined 75.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'D' and resid 89 through 140 Proline residue: D 130 - end of helix Processing helix chain 'D' and resid 146 through 159 Processing helix chain 'D' and resid 162 through 166 Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 201 removed outlier: 4.157A pdb=" N ASP D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.813A pdb=" N VAL D 210 " --> pdb=" O ARG D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 316 Processing helix chain 'D' and resid 322 through 352 removed outlier: 3.934A pdb=" N GLU D 328 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 330 " --> pdb=" O GLN D 326 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 361 Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'E' and resid 89 through 140 removed outlier: 3.572A pdb=" N LYS E 93 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Proline residue: E 130 - end of helix Processing helix chain 'E' and resid 146 through 161 Processing helix chain 'E' and resid 162 through 166 removed outlier: 3.528A pdb=" N LEU E 165 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 198 through 203 removed outlier: 4.036A pdb=" N THR E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 203' Processing helix chain 'E' and resid 204 through 212 Processing helix chain 'E' and resid 259 through 263 removed outlier: 4.129A pdb=" N ASP E 263 " --> pdb=" O TYR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 316 Processing helix chain 'E' and resid 324 through 326 No H-bonds generated for 'chain 'E' and resid 324 through 326' Processing helix chain 'E' and resid 327 through 351 removed outlier: 4.374A pdb=" N ASP E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 362 Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 17 through 29 removed outlier: 4.023A pdb=" N CYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 50 through 66 removed outlier: 3.689A pdb=" N THR A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 100 removed outlier: 4.050A pdb=" N PHE A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 122 Processing helix chain 'A' and resid 127 through 141 Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 186 through 207 removed outlier: 4.066A pdb=" N HIS A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 236 removed outlier: 3.608A pdb=" N THR A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 264 Processing helix chain 'A' and resid 270 through 291 Processing helix chain 'A' and resid 303 through 321 Processing helix chain 'A' and resid 327 through 343 Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.996A pdb=" N PHE A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.598A pdb=" N SER A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 403 Processing helix chain 'A' and resid 404 through 407 removed outlier: 5.740A pdb=" N SER A 407 " --> pdb=" O CYS A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 407' Processing helix chain 'A' and resid 408 through 421 Processing helix chain 'A' and resid 430 through 448 Processing helix chain 'A' and resid 452 through 470 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 497 through 515 removed outlier: 3.530A pdb=" N TYR A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 522 Processing helix chain 'A' and resid 522 through 541 Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 545 through 563 removed outlier: 3.847A pdb=" N TYR A 562 " --> pdb=" O GLN A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 4.364A pdb=" N ASP A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 607 Processing helix chain 'A' and resid 611 through 614 Processing helix chain 'A' and resid 615 through 621 removed outlier: 4.247A pdb=" N GLU A 619 " --> pdb=" O LYS A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.581A pdb=" N PHE A 625 " --> pdb=" O CYS A 621 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 657 Processing helix chain 'A' and resid 664 through 682 removed outlier: 4.127A pdb=" N ASN A 668 " --> pdb=" O PRO A 664 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 710 through 723 removed outlier: 3.700A pdb=" N ILE A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 733 removed outlier: 4.166A pdb=" N ASN A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 745 removed outlier: 3.678A pdb=" N LEU A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 767 removed outlier: 4.413A pdb=" N GLY A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ARG A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 787 Processing helix chain 'A' and resid 787 through 798 Processing helix chain 'A' and resid 805 through 818 Processing helix chain 'A' and resid 822 through 840 removed outlier: 3.599A pdb=" N ASN A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 847 Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 879 through 895 Processing helix chain 'A' and resid 932 through 942 removed outlier: 3.552A pdb=" N LEU A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 938 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 980 Processing helix chain 'A' and resid 980 through 991 removed outlier: 4.047A pdb=" N CYS A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1004 removed outlier: 3.536A pdb=" N LEU A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 46 through 74 removed outlier: 4.051A pdb=" N VAL B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'C' and resid 40 through 52 Processing helix chain 'C' and resid 58 through 87 Processing helix chain 'C' and resid 93 through 105 Processing helix chain 'C' and resid 106 through 126 Processing sheet with id=AA1, first strand: chain 'D' and resid 216 through 221 removed outlier: 4.310A pdb=" N ASP D 216 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N CYS D 249 " --> pdb=" O GLY D 271 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY D 271 " --> pdb=" O CYS D 249 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR D 251 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA D 269 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE D 253 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 285 through 294 Processing sheet with id=AA3, first strand: chain 'E' and resid 214 through 222 removed outlier: 6.378A pdb=" N ARG E 234 " --> pdb=" O GLN E 215 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE E 217 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU E 232 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU E 219 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS E 230 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR E 221 " --> pdb=" O GLY E 228 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY E 228 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 229 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N CYS E 249 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY E 271 " --> pdb=" O CYS E 249 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR E 251 " --> pdb=" O ALA E 269 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA E 269 " --> pdb=" O THR E 251 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE E 253 " --> pdb=" O ASP E 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 285 through 293 removed outlier: 3.597A pdb=" N THR E 307 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU E 288 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 799 through 800 Processing sheet with id=AA6, first strand: chain 'A' and resid 848 through 849 Processing sheet with id=AA7, first strand: chain 'A' and resid 853 through 854 Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 79 895 hydrogen bonds defined for protein. 2640 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: 5.97 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13418 1.03 - 1.23: 25 1.23 - 1.42: 5564 1.42 - 1.62: 8001 1.62 - 1.81: 65 Bond restraints: 27073 Sorted by residual: bond pdb=" N GLY E 83 " pdb=" CA GLY E 83 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.36e+00 bond pdb=" N ASN A 4 " pdb=" CA ASN A 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N ASP D 81 " pdb=" CA ASP D 81 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N SER B 17 " pdb=" CA SER B 17 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N LYS C 37 " pdb=" CA LYS C 37 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 27068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 46783 1.14 - 2.28: 2157 2.28 - 3.42: 89 3.42 - 4.56: 46 4.56 - 5.70: 11 Bond angle restraints: 49086 Sorted by residual: angle pdb=" N ASN A 850 " pdb=" CA ASN A 850 " pdb=" C ASN A 850 " ideal model delta sigma weight residual 111.36 114.33 -2.97 1.09e+00 8.42e-01 7.40e+00 angle pdb=" CA TYR A 113 " pdb=" CB TYR A 113 " pdb=" CG TYR A 113 " ideal model delta sigma weight residual 113.90 118.34 -4.44 1.80e+00 3.09e-01 6.08e+00 angle pdb=" CA VAL A 157 " pdb=" C VAL A 157 " pdb=" N VAL A 158 " ideal model delta sigma weight residual 118.90 121.20 -2.30 9.40e-01 1.13e+00 6.01e+00 angle pdb=" CB LYS A 615 " pdb=" CG LYS A 615 " pdb=" CD LYS A 615 " ideal model delta sigma weight residual 111.30 116.87 -5.57 2.30e+00 1.89e-01 5.88e+00 angle pdb=" N GLY A 851 " pdb=" CA GLY A 851 " pdb=" C GLY A 851 " ideal model delta sigma weight residual 113.18 118.65 -5.47 2.37e+00 1.78e-01 5.33e+00 ... (remaining 49081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11489 17.76 - 35.53: 840 35.53 - 53.29: 223 53.29 - 71.06: 73 71.06 - 88.82: 31 Dihedral angle restraints: 12656 sinusoidal: 6962 harmonic: 5694 Sorted by residual: dihedral pdb=" CA ASN A 850 " pdb=" C ASN A 850 " pdb=" N GLY A 851 " pdb=" CA GLY A 851 " ideal model delta harmonic sigma weight residual -180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASN A 852 " pdb=" C ASN A 852 " pdb=" N LEU A 853 " pdb=" CA LEU A 853 " ideal model delta harmonic sigma weight residual -180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TRP A 127 " pdb=" C TRP A 127 " pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta harmonic sigma weight residual -180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 12653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1420 0.027 - 0.053: 427 0.053 - 0.080: 195 0.080 - 0.106: 64 0.106 - 0.133: 31 Chirality restraints: 2137 Sorted by residual: chirality pdb=" CA ILE D 185 " pdb=" N ILE D 185 " pdb=" C ILE D 185 " pdb=" CB ILE D 185 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE A 451 " pdb=" N ILE A 451 " pdb=" C ILE A 451 " pdb=" CB ILE A 451 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA PHE A 649 " pdb=" N PHE A 649 " pdb=" C PHE A 649 " pdb=" CB PHE A 649 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 2134 not shown) Planarity restraints: 3975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 614 " 0.029 2.00e-02 2.50e+03 1.47e-02 6.44e+00 pdb=" CG TYR A 614 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 614 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 614 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 614 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 614 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 614 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 614 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 TYR A 614 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR A 614 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR A 614 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 614 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 478 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 479 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 129 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO E 130 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 130 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 130 " -0.023 5.00e-02 4.00e+02 ... (remaining 3972 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 986 2.16 - 2.77: 54270 2.77 - 3.38: 80866 3.38 - 3.99: 97570 3.99 - 4.60: 156386 Nonbonded interactions: 390078 Sorted by model distance: nonbonded pdb=" HH TYR A 254 " pdb=" OD2 ASP A 284 " model vdw 1.546 2.450 nonbonded pdb=" H PHE D 235 " pdb=" O ASP D 246 " model vdw 1.557 2.450 nonbonded pdb="HH11 ARG A 864 " pdb=" OE2 GLU B 93 " model vdw 1.576 2.450 nonbonded pdb=" OD1 ASN B 69 " pdb="HH21 ARG B 72 " model vdw 1.586 2.450 nonbonded pdb=" O TYR B 40 " pdb=" HG SER C 81 " model vdw 1.595 2.450 ... (remaining 390073 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 'D' and resid 83 through 365) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.780 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: 0.130 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.410 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 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 : 0.002 0.040 13632 Z= 0.126 Angle : 0.505 5.575 18438 Z= 0.288 Chirality : 0.035 0.133 2137 Planarity : 0.003 0.041 2370 Dihedral : 14.013 88.820 5133 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.21), residues: 1648 helix: 1.73 (0.15), residues: 1110 sheet: 0.61 (0.46), residues: 108 loop : 0.05 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 843 TYR 0.040 0.002 TYR A 614 PHE 0.025 0.002 PHE A 893 TRP 0.008 0.001 TRP A 28 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00244 (13632) covalent geometry : angle 0.50531 (18438) hydrogen bonds : bond 0.15099 ( 895) hydrogen bonds : angle 5.62011 ( 2640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.6720 (tpp) cc_final: 0.6515 (tpp) REVERT: C 51 THR cc_start: 0.8639 (m) cc_final: 0.8265 (p) REVERT: C 52 HIS cc_start: 0.8489 (m-70) cc_final: 0.8062 (m-70) REVERT: C 55 THR cc_start: 0.5079 (m) cc_final: 0.4826 (m) REVERT: C 62 MET cc_start: 0.5583 (mtp) cc_final: 0.4933 (mtp) REVERT: C 76 ILE cc_start: 0.8317 (mt) cc_final: 0.7942 (tp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3741 time to fit residues: 69.3397 Evaluate side-chains 98 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.111628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.079657 restraints weight = 236113.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.079996 restraints weight = 113278.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.080681 restraints weight = 66422.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.081535 restraints weight = 48995.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.082175 restraints weight = 43941.710| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13632 Z= 0.133 Angle : 0.518 5.172 18438 Z= 0.291 Chirality : 0.036 0.146 2137 Planarity : 0.004 0.042 2370 Dihedral : 4.720 25.355 1771 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.33 % Allowed : 2.97 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.21), residues: 1648 helix: 1.66 (0.15), residues: 1136 sheet: 0.50 (0.48), residues: 103 loop : -0.22 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 337 TYR 0.021 0.001 TYR A 113 PHE 0.021 0.002 PHE A 249 TRP 0.005 0.001 TRP A 28 HIS 0.005 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00264 (13632) covalent geometry : angle 0.51827 (18438) hydrogen bonds : bond 0.05292 ( 895) hydrogen bonds : angle 4.85588 ( 2640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 MET cc_start: 0.8118 (ptp) cc_final: 0.7851 (ptm) REVERT: C 51 THR cc_start: 0.8423 (m) cc_final: 0.8186 (p) REVERT: C 52 HIS cc_start: 0.7978 (m-70) cc_final: 0.7774 (m-70) REVERT: C 55 THR cc_start: 0.5139 (m) cc_final: 0.4924 (m) REVERT: C 62 MET cc_start: 0.5392 (mtp) cc_final: 0.5019 (mtp) REVERT: C 76 ILE cc_start: 0.8363 (mt) cc_final: 0.7921 (tp) outliers start: 5 outliers final: 3 residues processed: 103 average time/residue: 0.4230 time to fit residues: 58.0094 Evaluate side-chains 96 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 856 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 50.0000 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 ASN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.109055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.077348 restraints weight = 236427.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.077554 restraints weight = 115322.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.078573 restraints weight = 68310.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.078913 restraints weight = 51761.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.079648 restraints weight = 45413.317| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13632 Z= 0.196 Angle : 0.555 6.723 18438 Z= 0.307 Chirality : 0.036 0.152 2137 Planarity : 0.004 0.050 2370 Dihedral : 4.737 24.959 1771 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.40 % Allowed : 4.61 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.21), residues: 1648 helix: 1.51 (0.15), residues: 1130 sheet: 0.33 (0.48), residues: 103 loop : -0.22 (0.33), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 755 TYR 0.019 0.002 TYR A 113 PHE 0.021 0.002 PHE A 249 TRP 0.015 0.002 TRP D 132 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00403 (13632) covalent geometry : angle 0.55458 (18438) hydrogen bonds : bond 0.04985 ( 895) hydrogen bonds : angle 4.83906 ( 2640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 MET cc_start: 0.8777 (mmm) cc_final: 0.8567 (mmm) REVERT: A 732 MET cc_start: 0.8157 (ptp) cc_final: 0.7943 (ptm) REVERT: B 36 ARG cc_start: 0.8719 (tpp-160) cc_final: 0.8255 (tpm170) REVERT: C 51 THR cc_start: 0.8472 (m) cc_final: 0.8269 (p) REVERT: C 76 ILE cc_start: 0.8343 (mt) cc_final: 0.7899 (tp) outliers start: 6 outliers final: 6 residues processed: 101 average time/residue: 0.4161 time to fit residues: 56.2880 Evaluate side-chains 91 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 139 optimal weight: 0.2980 chunk 128 optimal weight: 0.8980 chunk 36 optimal weight: 50.0000 chunk 23 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.109821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.079286 restraints weight = 238158.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.079421 restraints weight = 113929.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.080497 restraints weight = 67359.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.081312 restraints weight = 49366.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.081388 restraints weight = 40804.783| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13632 Z= 0.120 Angle : 0.491 7.433 18438 Z= 0.269 Chirality : 0.036 0.227 2137 Planarity : 0.004 0.073 2370 Dihedral : 4.608 24.171 1771 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.59 % Allowed : 5.93 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.21), residues: 1648 helix: 1.70 (0.15), residues: 1135 sheet: 0.75 (0.51), residues: 93 loop : -0.15 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 135 TYR 0.020 0.001 TYR A 113 PHE 0.021 0.001 PHE A 249 TRP 0.006 0.001 TRP E 359 HIS 0.004 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00246 (13632) covalent geometry : angle 0.49112 (18438) hydrogen bonds : bond 0.04466 ( 895) hydrogen bonds : angle 4.54015 ( 2640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 MET cc_start: 0.8844 (mmm) cc_final: 0.8572 (mmm) REVERT: A 837 PHE cc_start: 0.7581 (t80) cc_final: 0.7320 (t80) REVERT: B 36 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8213 (tpm170) REVERT: B 92 ASP cc_start: 0.7631 (t0) cc_final: 0.7187 (p0) REVERT: C 62 MET cc_start: 0.5538 (mtp) cc_final: 0.5247 (mpp) REVERT: C 76 ILE cc_start: 0.8316 (mt) cc_final: 0.7836 (tp) outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 0.4315 time to fit residues: 52.7800 Evaluate side-chains 92 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 74 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 86 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 9 optimal weight: 30.0000 chunk 147 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.109600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.078699 restraints weight = 241184.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.078470 restraints weight = 114456.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.079744 restraints weight = 69159.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.080199 restraints weight = 50531.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.080669 restraints weight = 42772.044| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13632 Z= 0.121 Angle : 0.481 7.059 18438 Z= 0.264 Chirality : 0.035 0.212 2137 Planarity : 0.004 0.048 2370 Dihedral : 4.532 23.282 1771 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.59 % Allowed : 6.33 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.21), residues: 1648 helix: 1.77 (0.15), residues: 1136 sheet: 0.73 (0.51), residues: 95 loop : -0.12 (0.34), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.020 0.001 TYR A 113 PHE 0.018 0.001 PHE A 249 TRP 0.005 0.001 TRP E 359 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00248 (13632) covalent geometry : angle 0.48141 (18438) hydrogen bonds : bond 0.04334 ( 895) hydrogen bonds : angle 4.48809 ( 2640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 MET cc_start: 0.8813 (mmm) cc_final: 0.8537 (mmm) REVERT: B 36 ARG cc_start: 0.8665 (tpp-160) cc_final: 0.8353 (tpm170) REVERT: C 62 MET cc_start: 0.5754 (mtp) cc_final: 0.5339 (mpp) REVERT: C 76 ILE cc_start: 0.8314 (mt) cc_final: 0.7836 (tp) outliers start: 9 outliers final: 9 residues processed: 92 average time/residue: 0.3367 time to fit residues: 41.4770 Evaluate side-chains 94 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 984 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 157 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 160 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 0.0060 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.109247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.077066 restraints weight = 241101.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.077849 restraints weight = 118514.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.079255 restraints weight = 70265.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.079655 restraints weight = 50251.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.079962 restraints weight = 42303.168| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13632 Z= 0.121 Angle : 0.474 5.268 18438 Z= 0.259 Chirality : 0.035 0.178 2137 Planarity : 0.004 0.043 2370 Dihedral : 4.446 23.046 1771 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.92 % Allowed : 6.72 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.21), residues: 1648 helix: 1.86 (0.15), residues: 1135 sheet: 0.69 (0.52), residues: 95 loop : -0.06 (0.34), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.020 0.001 TYR A 113 PHE 0.018 0.001 PHE A 249 TRP 0.005 0.001 TRP E 359 HIS 0.005 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00248 (13632) covalent geometry : angle 0.47350 (18438) hydrogen bonds : bond 0.04199 ( 895) hydrogen bonds : angle 4.39279 ( 2640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 MET cc_start: 0.8853 (mmm) cc_final: 0.8562 (mmm) REVERT: A 755 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7711 (mmm-85) REVERT: A 870 MET cc_start: 0.7327 (ptm) cc_final: 0.7067 (ptp) REVERT: B 92 ASP cc_start: 0.7768 (t0) cc_final: 0.7358 (p0) REVERT: C 62 MET cc_start: 0.5716 (mtp) cc_final: 0.5234 (mpp) REVERT: C 76 ILE cc_start: 0.8385 (mt) cc_final: 0.7888 (tp) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.3336 time to fit residues: 44.5013 Evaluate side-chains 96 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 984 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 668 ASN A 669 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.107176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.076285 restraints weight = 242935.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.076756 restraints weight = 116294.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.077833 restraints weight = 71682.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.078706 restraints weight = 52676.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.079408 restraints weight = 43372.054| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13632 Z= 0.182 Angle : 0.531 6.229 18438 Z= 0.296 Chirality : 0.036 0.180 2137 Planarity : 0.004 0.043 2370 Dihedral : 4.486 23.088 1771 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.73 % Allowed : 7.58 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.21), residues: 1648 helix: 1.63 (0.15), residues: 1131 sheet: 0.64 (0.52), residues: 94 loop : -0.17 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 290 TYR 0.019 0.001 TYR A 113 PHE 0.018 0.002 PHE A 249 TRP 0.008 0.001 TRP E 189 HIS 0.006 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00376 (13632) covalent geometry : angle 0.53122 (18438) hydrogen bonds : bond 0.04499 ( 895) hydrogen bonds : angle 4.56194 ( 2640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 MET cc_start: 0.8887 (mmm) cc_final: 0.8553 (mmm) REVERT: A 870 MET cc_start: 0.7505 (ptm) cc_final: 0.7245 (ptp) REVERT: B 92 ASP cc_start: 0.7811 (t0) cc_final: 0.7406 (p0) REVERT: C 62 MET cc_start: 0.5997 (mtp) cc_final: 0.5444 (mpp) REVERT: C 76 ILE cc_start: 0.8462 (mt) cc_final: 0.7966 (tp) REVERT: C 102 ARG cc_start: 0.8781 (tpt-90) cc_final: 0.8523 (tpp80) outliers start: 11 outliers final: 11 residues processed: 95 average time/residue: 0.3243 time to fit residues: 41.2301 Evaluate side-chains 96 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 984 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 79 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN A 669 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.108218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.077370 restraints weight = 249828.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.077270 restraints weight = 115181.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.078459 restraints weight = 68538.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.078878 restraints weight = 48989.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.079364 restraints weight = 42419.909| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13632 Z= 0.111 Angle : 0.478 6.322 18438 Z= 0.260 Chirality : 0.035 0.164 2137 Planarity : 0.004 0.042 2370 Dihedral : 4.395 22.595 1771 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.73 % Allowed : 7.58 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.21), residues: 1648 helix: 1.86 (0.15), residues: 1131 sheet: 0.66 (0.53), residues: 94 loop : -0.05 (0.34), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 864 TYR 0.020 0.001 TYR A 113 PHE 0.017 0.001 PHE A 973 TRP 0.008 0.001 TRP E 359 HIS 0.005 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00229 (13632) covalent geometry : angle 0.47751 (18438) hydrogen bonds : bond 0.04128 ( 895) hydrogen bonds : angle 4.32343 ( 2640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 MET cc_start: 0.8879 (mmm) cc_final: 0.8563 (mmm) REVERT: B 92 ASP cc_start: 0.7822 (t0) cc_final: 0.7443 (p0) REVERT: C 62 MET cc_start: 0.5896 (mtp) cc_final: 0.5378 (mpp) REVERT: C 76 ILE cc_start: 0.8411 (mt) cc_final: 0.7905 (tp) REVERT: C 102 ARG cc_start: 0.8768 (tpt-90) cc_final: 0.8520 (tpp80) outliers start: 11 outliers final: 11 residues processed: 93 average time/residue: 0.3318 time to fit residues: 41.5986 Evaluate side-chains 97 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 984 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 49 optimal weight: 50.0000 chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN A 668 ASN A 669 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.105548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.074856 restraints weight = 247624.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.075410 restraints weight = 118955.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.076467 restraints weight = 71106.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.077331 restraints weight = 52983.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.077967 restraints weight = 43283.016| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13632 Z= 0.227 Angle : 0.577 5.882 18438 Z= 0.324 Chirality : 0.038 0.180 2137 Planarity : 0.004 0.041 2370 Dihedral : 4.517 23.374 1771 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.73 % Allowed : 7.84 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.21), residues: 1648 helix: 1.54 (0.15), residues: 1121 sheet: 0.51 (0.53), residues: 94 loop : -0.33 (0.33), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 290 TYR 0.018 0.002 TYR A 113 PHE 0.040 0.002 PHE A 973 TRP 0.011 0.001 TRP E 189 HIS 0.008 0.002 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00473 (13632) covalent geometry : angle 0.57743 (18438) hydrogen bonds : bond 0.04709 ( 895) hydrogen bonds : angle 4.66922 ( 2640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 870 MET cc_start: 0.7693 (ptm) cc_final: 0.7482 (ptp) REVERT: B 92 ASP cc_start: 0.7887 (t0) cc_final: 0.7507 (p0) REVERT: C 62 MET cc_start: 0.6208 (mtp) cc_final: 0.5612 (mpp) REVERT: C 76 ILE cc_start: 0.8519 (mt) cc_final: 0.8022 (tp) REVERT: C 102 ARG cc_start: 0.8782 (tpt-90) cc_final: 0.8518 (tpp80) outliers start: 11 outliers final: 10 residues processed: 94 average time/residue: 0.3263 time to fit residues: 41.6349 Evaluate side-chains 93 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 128 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 125 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN A 669 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.106377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.075318 restraints weight = 251892.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.076393 restraints weight = 120682.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.076956 restraints weight = 73294.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.077863 restraints weight = 56129.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.078047 restraints weight = 44596.615| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13632 Z= 0.145 Angle : 0.510 8.063 18438 Z= 0.280 Chirality : 0.036 0.182 2137 Planarity : 0.004 0.041 2370 Dihedral : 4.473 22.999 1771 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.73 % Allowed : 8.17 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.21), residues: 1648 helix: 1.63 (0.15), residues: 1137 sheet: 0.55 (0.53), residues: 94 loop : -0.22 (0.34), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 864 TYR 0.025 0.001 TYR A 154 PHE 0.018 0.002 PHE A 249 TRP 0.009 0.001 TRP E 359 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00300 (13632) covalent geometry : angle 0.50980 (18438) hydrogen bonds : bond 0.04309 ( 895) hydrogen bonds : angle 4.44221 ( 2640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 249 CYS cc_start: 0.7205 (p) cc_final: 0.6471 (m) REVERT: A 880 TYR cc_start: 0.7991 (m-10) cc_final: 0.7648 (m-10) REVERT: B 92 ASP cc_start: 0.7861 (t0) cc_final: 0.7531 (p0) REVERT: C 62 MET cc_start: 0.6060 (mtp) cc_final: 0.5510 (mpp) REVERT: C 76 ILE cc_start: 0.8521 (mt) cc_final: 0.7995 (tp) REVERT: C 102 ARG cc_start: 0.8778 (tpt-90) cc_final: 0.8560 (tpp80) outliers start: 11 outliers final: 10 residues processed: 93 average time/residue: 0.3140 time to fit residues: 39.9790 Evaluate side-chains 95 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.107037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.073861 restraints weight = 245967.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.076450 restraints weight = 114118.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.077355 restraints weight = 71506.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.078561 restraints weight = 55292.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.078511 restraints weight = 47178.157| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13632 Z= 0.115 Angle : 0.490 7.092 18438 Z= 0.265 Chirality : 0.036 0.185 2137 Planarity : 0.004 0.042 2370 Dihedral : 4.385 22.251 1771 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.66 % Allowed : 8.44 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.21), residues: 1648 helix: 1.85 (0.15), residues: 1136 sheet: 0.56 (0.54), residues: 94 loop : -0.14 (0.34), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 864 TYR 0.020 0.001 TYR A 113 PHE 0.016 0.001 PHE A 249 TRP 0.011 0.001 TRP E 359 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00239 (13632) covalent geometry : angle 0.49026 (18438) hydrogen bonds : bond 0.04069 ( 895) hydrogen bonds : angle 4.30605 ( 2640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6907.06 seconds wall clock time: 117 minutes 58.39 seconds (7078.39 seconds total)