Starting phenix.real_space_refine on Mon Jun 23 06:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3f_44136/06_2025/9b3f_44136.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3f_44136/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3f_44136/06_2025/9b3f_44136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3f_44136/06_2025/9b3f_44136.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3f_44136/06_2025/9b3f_44136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3f_44136/06_2025/9b3f_44136.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.02, per 1000 atoms: 0.52 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: 7.28 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.38 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: 10.79 Time building geometry restraints manager: 8.86 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: 6.600 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: 0.470 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 60.260 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.240 ------------------------------------------------------------------------------- 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 : 7.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP A 28 HIS 0.003 0.001 HIS A 290 PHE 0.025 0.002 PHE A 893 TYR 0.040 0.002 TYR A 614 ARG 0.006 0.000 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.15099 ( 895) hydrogen bonds : angle 5.62011 ( 2640) covalent geometry : bond 0.00244 (13632) covalent geometry : angle 0.50531 (18438) *********************** 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 : 2.194 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: 0.8260 time to fit residues: 154.5537 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 : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 50.0000 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4570 r_free = 0.4570 target = 0.110546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.078636 restraints weight = 236319.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.080449 restraints weight = 117131.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.080006 restraints weight = 80325.647| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13632 Z= 0.170 Angle : 0.544 5.401 18438 Z= 0.308 Chirality : 0.037 0.147 2137 Planarity : 0.004 0.042 2370 Dihedral : 4.767 26.728 1771 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.20 % Allowed : 3.30 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.21), residues: 1648 helix: 1.54 (0.15), residues: 1136 sheet: 0.46 (0.47), residues: 103 loop : -0.23 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 28 HIS 0.005 0.001 HIS C 112 PHE 0.022 0.002 PHE A 249 TYR 0.020 0.001 TYR A 113 ARG 0.004 0.000 ARG D 337 Details of bonding type rmsd hydrogen bonds : bond 0.05478 ( 895) hydrogen bonds : angle 4.98198 ( 2640) covalent geometry : bond 0.00344 (13632) covalent geometry : angle 0.54441 (18438) *********************** 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 106 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 1.985 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: A 732 MET cc_start: 0.8104 (ptp) cc_final: 0.7863 (ptm) REVERT: C 51 THR cc_start: 0.8550 (m) cc_final: 0.8252 (p) REVERT: C 52 HIS cc_start: 0.8238 (m-70) cc_final: 0.7962 (m-70) REVERT: C 55 THR cc_start: 0.5358 (m) cc_final: 0.5131 (m) REVERT: C 62 MET cc_start: 0.5574 (mtp) cc_final: 0.5161 (mtp) REVERT: C 76 ILE cc_start: 0.8382 (mt) cc_final: 0.7962 (tp) outliers start: 3 outliers final: 2 residues processed: 105 average time/residue: 0.8012 time to fit residues: 113.5235 Evaluate side-chains 96 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4574 r_free = 0.4574 target = 0.110658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.079339 restraints weight = 237799.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.079555 restraints weight = 115946.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.080137 restraints weight = 67677.405| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13632 Z= 0.128 Angle : 0.499 7.328 18438 Z= 0.275 Chirality : 0.035 0.144 2137 Planarity : 0.004 0.043 2370 Dihedral : 4.675 24.311 1771 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.40 % Allowed : 4.22 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.21), residues: 1648 helix: 1.64 (0.15), residues: 1138 sheet: 0.44 (0.49), residues: 103 loop : -0.17 (0.34), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 132 HIS 0.005 0.001 HIS C 112 PHE 0.021 0.001 PHE A 249 TYR 0.021 0.001 TYR A 113 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 895) hydrogen bonds : angle 4.68785 ( 2640) covalent geometry : bond 0.00259 (13632) covalent geometry : angle 0.49926 (18438) *********************** 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 : 1.974 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 553 MET cc_start: 0.8799 (mmm) cc_final: 0.8591 (mmm) REVERT: A 732 MET cc_start: 0.8074 (ptp) cc_final: 0.7871 (ptm) REVERT: B 36 ARG cc_start: 0.8693 (tpp-160) cc_final: 0.8326 (tpm170) REVERT: C 55 THR cc_start: 0.5170 (m) cc_final: 0.4968 (m) REVERT: C 76 ILE cc_start: 0.8350 (mt) cc_final: 0.7897 (tp) outliers start: 6 outliers final: 5 residues processed: 101 average time/residue: 0.8360 time to fit residues: 115.0600 Evaluate side-chains 96 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 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 104 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 34 optimal weight: 50.0000 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 ASN A 274 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.107770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.077239 restraints weight = 244242.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.076977 restraints weight = 117858.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.077963 restraints weight = 69444.769| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13632 Z= 0.208 Angle : 0.557 7.167 18438 Z= 0.311 Chirality : 0.037 0.227 2137 Planarity : 0.004 0.044 2370 Dihedral : 4.726 24.774 1771 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.79 % Allowed : 6.00 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.21), residues: 1648 helix: 1.42 (0.15), residues: 1128 sheet: 0.52 (0.50), residues: 103 loop : -0.21 (0.34), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 189 HIS 0.006 0.001 HIS A 142 PHE 0.022 0.002 PHE A 249 TYR 0.018 0.002 TYR A 113 ARG 0.005 0.000 ARG A 710 Details of bonding type rmsd hydrogen bonds : bond 0.04947 ( 895) hydrogen bonds : angle 4.81555 ( 2640) covalent geometry : bond 0.00428 (13632) covalent geometry : angle 0.55651 (18438) *********************** 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 105 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 2.196 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: A 553 MET cc_start: 0.8864 (mmm) cc_final: 0.8512 (mmm) REVERT: C 76 ILE cc_start: 0.8404 (mt) cc_final: 0.7927 (tp) REVERT: C 102 ARG cc_start: 0.8785 (tpt-90) cc_final: 0.8527 (tpp80) outliers start: 12 outliers final: 11 residues processed: 101 average time/residue: 0.8164 time to fit residues: 112.1306 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 : 2.549 ------------------------------------------------------------------------------- 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 476 ASP Chi-restraints excluded: chain A residue 614 TYR 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 B residue 66 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 52 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 128 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4540 r_free = 0.4540 target = 0.108003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.077174 restraints weight = 245083.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.078217 restraints weight = 115748.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.078767 restraints weight = 72248.564| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2447 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= 0.158 Angle : 0.513 7.122 18438 Z= 0.285 Chirality : 0.036 0.214 2137 Planarity : 0.004 0.076 2370 Dihedral : 4.679 24.142 1771 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.86 % Allowed : 7.25 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.21), residues: 1648 helix: 1.50 (0.15), residues: 1131 sheet: 0.79 (0.53), residues: 93 loop : -0.17 (0.34), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 359 HIS 0.003 0.001 HIS A 985 PHE 0.020 0.002 PHE A 249 TYR 0.019 0.001 TYR A 113 ARG 0.005 0.000 ARG A 821 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 895) hydrogen bonds : angle 4.67000 ( 2640) covalent geometry : bond 0.00328 (13632) covalent geometry : angle 0.51335 (18438) *********************** 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 103 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 2.013 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: A 553 MET cc_start: 0.8873 (mmm) cc_final: 0.8549 (mmm) REVERT: B 92 ASP cc_start: 0.7612 (t0) cc_final: 0.7233 (p0) REVERT: C 62 MET cc_start: 0.5404 (mpp) cc_final: 0.5057 (mpp) REVERT: C 76 ILE cc_start: 0.8418 (mt) cc_final: 0.7926 (tp) outliers start: 13 outliers final: 11 residues processed: 98 average time/residue: 0.8132 time to fit residues: 107.0856 Evaluate side-chains 100 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 614 TYR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 837 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 126 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 96 optimal weight: 0.2980 chunk 57 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.107046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.076047 restraints weight = 247309.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.076041 restraints weight = 118954.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.077085 restraints weight = 70973.624| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13632 Z= 0.191 Angle : 0.532 6.788 18438 Z= 0.298 Chirality : 0.037 0.212 2137 Planarity : 0.004 0.043 2370 Dihedral : 4.653 23.811 1771 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.92 % Allowed : 7.71 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1648 helix: 1.46 (0.15), residues: 1131 sheet: 0.68 (0.51), residues: 94 loop : -0.25 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 189 HIS 0.004 0.001 HIS A 142 PHE 0.019 0.002 PHE A 249 TYR 0.018 0.002 TYR A 113 ARG 0.003 0.000 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 895) hydrogen bonds : angle 4.68186 ( 2640) covalent geometry : bond 0.00396 (13632) covalent geometry : angle 0.53221 (18438) *********************** 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 104 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 2.267 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: 0.8895 (mmm) cc_final: 0.8547 (mmm) REVERT: A 755 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7771 (mmm-85) REVERT: A 870 MET cc_start: 0.7565 (ptm) cc_final: 0.7216 (ptp) REVERT: B 92 ASP cc_start: 0.7797 (t0) cc_final: 0.7371 (p0) REVERT: C 62 MET cc_start: 0.5590 (mpp) cc_final: 0.5337 (mpp) REVERT: C 76 ILE cc_start: 0.8532 (mt) cc_final: 0.8045 (tp) REVERT: C 102 ARG cc_start: 0.8833 (tpt-90) cc_final: 0.8585 (tpp80) outliers start: 14 outliers final: 12 residues processed: 100 average time/residue: 0.8150 time to fit residues: 110.1664 Evaluate side-chains 97 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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 614 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 0.0270 chunk 5 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 23 optimal weight: 0.0470 chunk 37 optimal weight: 50.0000 chunk 84 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.1940 ------------------------------------------------------------------------------- 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 = 0.4528 r_free = 0.4528 target = 0.107338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.075183 restraints weight = 248562.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.076416 restraints weight = 124367.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.077380 restraints weight = 72611.848| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13632 Z= 0.142 Angle : 0.505 6.388 18438 Z= 0.278 Chirality : 0.036 0.146 2137 Planarity : 0.004 0.042 2370 Dihedral : 4.579 23.202 1771 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.86 % Allowed : 8.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.21), residues: 1648 helix: 1.63 (0.15), residues: 1128 sheet: 0.71 (0.53), residues: 94 loop : -0.16 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 359 HIS 0.003 0.001 HIS C 112 PHE 0.019 0.002 PHE A 973 TYR 0.023 0.002 TYR D 254 ARG 0.017 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 895) hydrogen bonds : angle 4.52602 ( 2640) covalent geometry : bond 0.00290 (13632) covalent geometry : angle 0.50477 (18438) *********************** 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 100 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.979 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: A 553 MET cc_start: 0.8909 (mmm) cc_final: 0.8566 (mmm) REVERT: B 92 ASP cc_start: 0.7736 (t0) cc_final: 0.7335 (p0) REVERT: C 62 MET cc_start: 0.5489 (mpp) cc_final: 0.5213 (mpp) REVERT: C 76 ILE cc_start: 0.8518 (mt) cc_final: 0.8019 (tp) REVERT: C 102 ARG cc_start: 0.8841 (tpt-90) cc_final: 0.8584 (tpp80) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.7687 time to fit residues: 101.0125 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 : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 614 TYR 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 61 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.107518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.074403 restraints weight = 245534.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.076620 restraints weight = 123024.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.078332 restraints weight = 74580.782| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13632 Z= 0.123 Angle : 0.492 6.855 18438 Z= 0.268 Chirality : 0.036 0.179 2137 Planarity : 0.004 0.058 2370 Dihedral : 4.510 22.769 1771 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.79 % Allowed : 8.57 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.21), residues: 1648 helix: 1.75 (0.15), residues: 1130 sheet: 0.75 (0.54), residues: 94 loop : -0.09 (0.34), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 359 HIS 0.004 0.001 HIS C 112 PHE 0.017 0.001 PHE A 249 TYR 0.020 0.001 TYR A 113 ARG 0.008 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 895) hydrogen bonds : angle 4.42429 ( 2640) covalent geometry : bond 0.00253 (13632) covalent geometry : angle 0.49216 (18438) *********************** 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: 12 poor density : 85 time to evaluate : 2.189 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: 0.8913 (mmm) cc_final: 0.8579 (mmm) REVERT: A 870 MET cc_start: 0.7473 (ptm) cc_final: 0.7204 (ptp) REVERT: B 92 ASP cc_start: 0.7741 (t0) cc_final: 0.7366 (p0) REVERT: C 76 ILE cc_start: 0.8518 (mt) cc_final: 0.8020 (tp) REVERT: C 102 ARG cc_start: 0.8839 (tpt-90) cc_final: 0.8581 (tpp80) outliers start: 12 outliers final: 11 residues processed: 92 average time/residue: 1.2552 time to fit residues: 166.4800 Evaluate side-chains 95 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 4.056 ------------------------------------------------------------------------------- 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 614 TYR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 794 PHE 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 61 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.107094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.075380 restraints weight = 248369.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.075824 restraints weight = 120703.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.076841 restraints weight = 71145.763| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3186 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= 0.136 Angle : 0.499 7.827 18438 Z= 0.273 Chirality : 0.036 0.169 2137 Planarity : 0.004 0.042 2370 Dihedral : 4.467 22.327 1771 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.79 % Allowed : 8.64 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1648 helix: 1.81 (0.15), residues: 1130 sheet: 0.73 (0.55), residues: 94 loop : -0.08 (0.34), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 359 HIS 0.004 0.001 HIS C 112 PHE 0.017 0.002 PHE A 249 TYR 0.020 0.001 TYR A 113 ARG 0.007 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 895) hydrogen bonds : angle 4.43317 ( 2640) covalent geometry : bond 0.00280 (13632) covalent geometry : angle 0.49944 (18438) *********************** 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 96 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 2.266 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: D 249 CYS cc_start: 0.7170 (p) cc_final: 0.6482 (m) REVERT: A 870 MET cc_start: 0.7600 (ptm) cc_final: 0.7375 (ptp) REVERT: B 92 ASP cc_start: 0.7768 (t0) cc_final: 0.7414 (p0) REVERT: C 76 ILE cc_start: 0.8561 (mt) cc_final: 0.8053 (tp) REVERT: C 102 ARG cc_start: 0.8836 (tpt-90) cc_final: 0.8565 (tpp80) outliers start: 12 outliers final: 12 residues processed: 92 average time/residue: 0.7968 time to fit residues: 100.4510 Evaluate side-chains 96 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 614 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 794 PHE 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 61 SER 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 77 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.106854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.075859 restraints weight = 243381.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.076398 restraints weight = 115110.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.077605 restraints weight = 70340.833| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13632 Z= 0.134 Angle : 0.503 7.677 18438 Z= 0.278 Chirality : 0.036 0.160 2137 Planarity : 0.004 0.043 2370 Dihedral : 4.434 22.073 1771 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.86 % Allowed : 8.57 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1648 helix: 1.82 (0.15), residues: 1139 sheet: 0.64 (0.54), residues: 94 loop : -0.13 (0.34), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 359 HIS 0.018 0.001 HIS D 268 PHE 0.017 0.001 PHE A 249 TYR 0.020 0.001 TYR A 113 ARG 0.005 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 895) hydrogen bonds : angle 4.40006 ( 2640) covalent geometry : bond 0.00276 (13632) covalent geometry : angle 0.50304 (18438) ********************** 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 98 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 2.207 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: D 249 CYS cc_start: 0.7121 (p) cc_final: 0.6394 (m) REVERT: B 92 ASP cc_start: 0.7821 (t0) cc_final: 0.7455 (p0) REVERT: C 62 MET cc_start: 0.4563 (mpt) cc_final: 0.4247 (mpt) REVERT: C 76 ILE cc_start: 0.8589 (mt) cc_final: 0.8078 (tp) REVERT: C 102 ARG cc_start: 0.8830 (tpt-90) cc_final: 0.8611 (tpp80) outliers start: 13 outliers final: 12 residues processed: 94 average time/residue: 0.7748 time to fit residues: 100.4968 Evaluate side-chains 96 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 651 THR 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 984 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 61 SER 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 49 optimal weight: 50.0000 chunk 145 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** A 985 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.106006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.075628 restraints weight = 246282.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.077816 restraints weight = 116141.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.077514 restraints weight = 70454.146| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13632 Z= 0.164 Angle : 0.516 6.322 18438 Z= 0.284 Chirality : 0.036 0.158 2137 Planarity : 0.004 0.042 2370 Dihedral : 4.462 21.954 1771 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.73 % Allowed : 8.83 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.21), residues: 1648 helix: 1.76 (0.15), residues: 1136 sheet: 0.55 (0.54), residues: 94 loop : -0.14 (0.34), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 189 HIS 0.013 0.001 HIS D 268 PHE 0.017 0.002 PHE A 249 TYR 0.020 0.002 TYR A 113 ARG 0.005 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 895) hydrogen bonds : angle 4.48741 ( 2640) covalent geometry : bond 0.00337 (13632) covalent geometry : angle 0.51575 (18438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12467.53 seconds wall clock time: 216 minutes 7.13 seconds (12967.13 seconds total)