Starting phenix.real_space_refine on Mon Jun 23 15:47:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b31_44120/06_2025/9b31_44120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b31_44120/06_2025/9b31_44120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b31_44120/06_2025/9b31_44120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b31_44120/06_2025/9b31_44120.map" model { file = "/net/cci-nas-00/data/ceres_data/9b31_44120/06_2025/9b31_44120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b31_44120/06_2025/9b31_44120.cif" } resolution = 3.2 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 Anisotropic ADP refinement not supported. Converting 334 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 8638 2.51 5 N 2204 2.21 5 O 2642 1.98 5 H 13549 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27078 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 15124 Classifications: {'peptide': 941} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 914} Chain breaks: 3 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} 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} Time building chain proxies: 13.25, per 1000 atoms: 0.49 Number of scatterers: 27078 At special positions: 0 Unit cell: (101.26, 146.08, 178.45, 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 45 16.00 O 2642 8.00 N 2204 7.00 C 8638 6.00 H 13549 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: 6.57 Conformation dependent library (CDL) restraints added in 2.2 seconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 8 sheets defined 74.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.654A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 32 Processing helix chain 'A' and resid 32 through 47 removed outlier: 4.243A pdb=" N VAL A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 69 removed outlier: 3.703A pdb=" N THR A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.690A pdb=" N ASN A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 123 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.902A pdb=" N ASP A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) 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 206 removed outlier: 4.187A pdb=" N SER A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 235 removed outlier: 3.761A pdb=" N THR A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.555A pdb=" N PHE A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 292 Processing helix chain 'A' and resid 303 through 321 Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.981A pdb=" N PHE A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 removed outlier: 3.510A pdb=" N LEU A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 402 Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.703A pdb=" N GLU A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) 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 493 Processing helix chain 'A' and resid 497 through 515 removed outlier: 3.770A pdb=" N PHE A 514 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 542 Proline residue: A 523 - end of helix removed outlier: 4.101A pdb=" N SER A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 removed outlier: 3.772A pdb=" N TYR A 562 " --> pdb=" O GLN A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.965A pdb=" N ASP A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 606 Processing helix chain 'A' and resid 610 through 635 removed outlier: 3.555A pdb=" N ASN A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A) Proline residue: A 623 - end of helix removed outlier: 3.616A pdb=" N ALA A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 656 Processing helix chain 'A' and resid 664 through 682 removed outlier: 3.575A pdb=" N ASN A 668 " --> pdb=" O PRO A 664 " (cutoff:3.500A) removed outlier: 4.877A 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 Processing helix chain 'A' and resid 733 through 745 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.719A pdb=" N GLN A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 767 removed outlier: 3.596A pdb=" N LYS A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 787 removed outlier: 3.778A pdb=" N VAL A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 798 Processing helix chain 'A' and resid 805 through 818 removed outlier: 4.052A pdb=" N GLU A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 840 removed outlier: 3.626A pdb=" N ASN A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'A' and resid 863 through 868 removed outlier: 4.389A pdb=" N LYS A 868 " --> pdb=" O ARG A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 895 Processing helix chain 'A' and resid 932 through 942 Processing helix chain 'A' and resid 964 through 980 Processing helix chain 'A' and resid 980 through 991 Processing helix chain 'A' and resid 992 through 1004 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 27 through 38 Processing helix chain 'B' and resid 46 through 74 removed outlier: 4.328A pdb=" N VAL B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'C' and resid 38 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 124 removed outlier: 3.675A pdb=" N LYS C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 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 174 removed outlier: 3.787A pdb=" N GLN D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 187 through 196 Processing helix chain 'D' and resid 196 through 201 removed outlier: 4.180A pdb=" N ASP D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.930A 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 329 removed outlier: 3.975A pdb=" N GLU D 328 " --> pdb=" O GLU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 352 removed outlier: 3.683A pdb=" N ASP D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'E' and resid 89 through 141 removed outlier: 3.668A pdb=" N LYS E 93 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.551A 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 195 Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.986A pdb=" N THR E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 212 removed outlier: 3.523A pdb=" N GLU E 212 " --> pdb=" O ALA E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 4.058A 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: 4.341A pdb=" N ASP E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 799 through 800 Processing sheet with id=AA2, first strand: chain 'A' and resid 848 through 853 removed outlier: 4.767A pdb=" N VAL A 875 " --> pdb=" O GLY A 851 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.778A pdb=" N ARG B 43 " --> pdb=" O ILE C 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'D' and resid 216 through 221 removed outlier: 4.351A pdb=" N ASP D 216 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N CYS D 249 " --> pdb=" O GLY D 271 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY D 271 " --> pdb=" O CYS D 249 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR D 251 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA D 269 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE D 253 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE D 265 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 285 through 291 Processing sheet with id=AA7, first strand: chain 'E' and resid 214 through 222 removed outlier: 3.850A pdb=" N GLY E 228 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE E 229 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE E 253 " --> pdb=" O HIS E 268 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N HIS E 268 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 285 through 293 removed outlier: 3.694A pdb=" N THR E 307 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU E 288 " --> pdb=" O LYS E 305 " (cutoff:3.500A) 901 hydrogen bonds defined for protein. 2670 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: 10.74 Time building geometry restraints manager: 8.13 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: 13526 1.03 - 1.23: 29 1.23 - 1.42: 5627 1.42 - 1.62: 8061 1.62 - 1.81: 67 Bond restraints: 27310 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 6.34e+00 bond pdb=" C ASP E 317 " pdb=" O ASP E 317 " ideal model delta sigma weight residual 1.233 1.243 -0.010 4.80e-03 4.34e+04 4.13e+00 bond pdb=" CA ILE A 463 " pdb=" CB ILE A 463 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.30e+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 3.04e+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 2.99e+00 ... (remaining 27305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 48158 1.38 - 2.76: 1247 2.76 - 4.14: 79 4.14 - 5.51: 22 5.51 - 6.89: 3 Bond angle restraints: 49509 Sorted by residual: angle pdb=" CB ARG A 638 " pdb=" CG ARG A 638 " pdb=" CD ARG A 638 " ideal model delta sigma weight residual 111.30 118.19 -6.89 2.30e+00 1.89e-01 8.98e+00 angle pdb=" N ARG A 638 " pdb=" CA ARG A 638 " pdb=" CB ARG A 638 " ideal model delta sigma weight residual 110.26 114.39 -4.13 1.43e+00 4.89e-01 8.35e+00 angle pdb=" C TYR A 637 " pdb=" N ARG A 638 " pdb=" CA ARG A 638 " ideal model delta sigma weight residual 120.87 116.41 4.46 1.69e+00 3.50e-01 6.96e+00 angle pdb=" CB MET A 712 " pdb=" CG MET A 712 " pdb=" SD MET A 712 " ideal model delta sigma weight residual 112.70 119.58 -6.88 3.00e+00 1.11e-01 5.27e+00 angle pdb=" N TYR A 637 " pdb=" CA TYR A 637 " pdb=" CB TYR A 637 " ideal model delta sigma weight residual 112.30 108.91 3.39 1.52e+00 4.33e-01 4.99e+00 ... (remaining 49504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11729 17.98 - 35.96: 719 35.96 - 53.94: 223 53.94 - 71.91: 77 71.91 - 89.89: 27 Dihedral angle restraints: 12775 sinusoidal: 7018 harmonic: 5757 Sorted by residual: dihedral pdb=" CA LEU A 45 " pdb=" C LEU A 45 " pdb=" N GLN A 46 " pdb=" CA GLN A 46 " ideal model delta harmonic sigma weight residual 180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLN D 292 " pdb=" C GLN D 292 " pdb=" N ARG D 293 " pdb=" CA ARG D 293 " ideal model delta harmonic sigma weight residual 180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS D 351 " pdb=" C LYS D 351 " pdb=" N LEU D 352 " pdb=" CA LEU D 352 " ideal model delta harmonic sigma weight residual -180.00 -159.77 -20.23 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 12772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1340 0.028 - 0.056: 543 0.056 - 0.085: 181 0.085 - 0.113: 66 0.113 - 0.141: 20 Chirality restraints: 2150 Sorted by residual: chirality pdb=" CA ILE A 854 " pdb=" N ILE A 854 " pdb=" C ILE A 854 " pdb=" CB ILE A 854 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 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 -0.14 2.00e-01 2.50e+01 4.69e-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 4.44e-01 ... (remaining 2147 not shown) Planarity restraints: 4013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 638 " -0.151 9.50e-02 1.11e+02 5.17e-02 5.54e+00 pdb=" NE ARG A 638 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 638 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG A 638 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 638 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 638 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG A 638 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG A 638 " 0.009 2.00e-02 2.50e+03 pdb="HH22 ARG A 638 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 735 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.99e+00 pdb=" N PRO A 736 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 736 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 736 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 249 " 0.020 2.00e-02 2.50e+03 1.18e-02 4.18e+00 pdb=" CG PHE A 249 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 249 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 249 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 249 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 249 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 249 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 249 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 249 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 249 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 249 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 249 " 0.001 2.00e-02 2.50e+03 ... (remaining 4010 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 647 2.13 - 2.75: 51295 2.75 - 3.36: 80658 3.36 - 3.98: 97549 3.98 - 4.60: 158643 Nonbonded interactions: 388792 Sorted by model distance: nonbonded pdb=" H TYR A 639 " pdb=" OE2 GLU A 684 " model vdw 1.511 2.450 nonbonded pdb=" O LEU A 679 " pdb="HH11 ARG A 720 " model vdw 1.533 2.450 nonbonded pdb=" H PHE D 235 " pdb=" O ASP D 246 " model vdw 1.554 2.450 nonbonded pdb="HH21 ARG A 91 " pdb=" OD2 ASP A 122 " model vdw 1.595 2.450 nonbonded pdb=" HG SER D 237 " pdb=" OD1 ASP D 246 " model vdw 1.598 2.450 ... (remaining 388787 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.420 Extract box with map and model: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 58.520 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13761 Z= 0.184 Angle : 0.543 6.893 18615 Z= 0.303 Chirality : 0.037 0.141 2150 Planarity : 0.005 0.066 2393 Dihedral : 13.351 87.808 5181 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.78 (0.20), residues: 1666 helix: 1.71 (0.15), residues: 1130 sheet: 1.16 (0.50), residues: 90 loop : -0.07 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 127 HIS 0.005 0.001 HIS C 112 PHE 0.035 0.002 PHE A 249 TYR 0.016 0.001 TYR A 511 ARG 0.026 0.001 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.14653 ( 901) hydrogen bonds : angle 5.80266 ( 2670) covalent geometry : bond 0.00400 (13761) covalent geometry : angle 0.54343 (18615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 2.606 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 229 PHE cc_start: 0.7217 (p90) cc_final: 0.6924 (p90) REVERT: D 350 ASP cc_start: 0.8773 (m-30) cc_final: 0.8545 (m-30) REVERT: E 231 LEU cc_start: 0.9261 (mt) cc_final: 0.8887 (mt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.7491 time to fit residues: 153.5928 Evaluate side-chains 109 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 0.0470 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 ASN A 876 GLN ** D 122 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 = 0.4390 r_free = 0.4390 target = 0.132289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.095959 restraints weight = 135820.041| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 4.20 r_work: 0.3434 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13761 Z= 0.137 Angle : 0.521 5.587 18615 Z= 0.292 Chirality : 0.036 0.147 2150 Planarity : 0.005 0.050 2393 Dihedral : 4.642 24.613 1790 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.39 % Allowed : 2.88 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.00 (0.20), residues: 1666 helix: 1.95 (0.15), residues: 1153 sheet: 0.82 (0.50), residues: 93 loop : -0.25 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 359 HIS 0.005 0.001 HIS D 281 PHE 0.025 0.001 PHE A 249 TYR 0.013 0.001 TYR A 511 ARG 0.004 0.000 ARG A 705 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 901) hydrogen bonds : angle 4.79981 ( 2670) covalent geometry : bond 0.00273 (13761) covalent geometry : angle 0.52053 (18615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 1.953 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: D 350 ASP cc_start: 0.9017 (m-30) cc_final: 0.8806 (m-30) REVERT: E 133 GLU cc_start: 0.9269 (tt0) cc_final: 0.8759 (tp30) REVERT: E 134 GLN cc_start: 0.9108 (tt0) cc_final: 0.8848 (tt0) REVERT: E 213 TYR cc_start: 0.7849 (m-80) cc_final: 0.7564 (m-80) REVERT: E 231 LEU cc_start: 0.9411 (mt) cc_final: 0.9100 (mt) outliers start: 6 outliers final: 5 residues processed: 114 average time/residue: 0.7235 time to fit residues: 117.7016 Evaluate side-chains 106 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 289 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 71 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 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 = 0.4373 r_free = 0.4373 target = 0.130260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.094188 restraints weight = 137034.636| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 4.13 r_work: 0.3440 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13761 Z= 0.154 Angle : 0.495 5.318 18615 Z= 0.276 Chirality : 0.036 0.154 2150 Planarity : 0.004 0.049 2393 Dihedral : 4.535 23.485 1790 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.26 % Allowed : 4.12 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.10 (0.20), residues: 1666 helix: 2.05 (0.15), residues: 1161 sheet: 0.94 (0.55), residues: 86 loop : -0.33 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 359 HIS 0.007 0.001 HIS D 281 PHE 0.024 0.001 PHE A 249 TYR 0.010 0.001 TYR A 511 ARG 0.005 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 901) hydrogen bonds : angle 4.56251 ( 2670) covalent geometry : bond 0.00334 (13761) covalent geometry : angle 0.49469 (18615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 2.272 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: E 133 GLU cc_start: 0.9266 (tt0) cc_final: 0.8756 (tp30) REVERT: E 213 TYR cc_start: 0.7956 (m-80) cc_final: 0.7705 (m-80) REVERT: E 231 LEU cc_start: 0.9441 (mt) cc_final: 0.9145 (mt) outliers start: 4 outliers final: 3 residues processed: 103 average time/residue: 0.6652 time to fit residues: 97.3234 Evaluate side-chains 95 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain E residue 113 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 104 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 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 = 0.4334 r_free = 0.4334 target = 0.127080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.091097 restraints weight = 138673.347| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 4.13 r_work: 0.3361 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13761 Z= 0.222 Angle : 0.532 5.868 18615 Z= 0.298 Chirality : 0.037 0.146 2150 Planarity : 0.004 0.047 2393 Dihedral : 4.520 22.500 1790 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.46 % Allowed : 4.84 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.99 (0.21), residues: 1666 helix: 2.00 (0.15), residues: 1150 sheet: 0.55 (0.55), residues: 95 loop : -0.34 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 189 HIS 0.007 0.001 HIS C 112 PHE 0.024 0.002 PHE A 249 TYR 0.012 0.001 TYR B 58 ARG 0.004 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 901) hydrogen bonds : angle 4.56049 ( 2670) covalent geometry : bond 0.00498 (13761) covalent geometry : angle 0.53196 (18615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 3.184 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: E 134 GLN cc_start: 0.9184 (tt0) cc_final: 0.8889 (tt0) REVERT: E 213 TYR cc_start: 0.8082 (m-80) cc_final: 0.7863 (m-80) REVERT: E 231 LEU cc_start: 0.9497 (mt) cc_final: 0.9231 (mt) outliers start: 7 outliers final: 6 residues processed: 97 average time/residue: 0.7586 time to fit residues: 108.5334 Evaluate side-chains 100 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 117 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 154 optimal weight: 0.0370 chunk 111 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.128293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092449 restraints weight = 137012.711| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 4.11 r_work: 0.3392 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13761 Z= 0.119 Angle : 0.469 6.136 18615 Z= 0.259 Chirality : 0.035 0.141 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.417 22.076 1790 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.52 % Allowed : 5.30 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.24 (0.21), residues: 1666 helix: 2.18 (0.15), residues: 1153 sheet: 0.66 (0.57), residues: 93 loop : -0.27 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 189 HIS 0.008 0.001 HIS D 281 PHE 0.018 0.001 PHE A 249 TYR 0.009 0.001 TYR A 511 ARG 0.005 0.000 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 901) hydrogen bonds : angle 4.33521 ( 2670) covalent geometry : bond 0.00253 (13761) covalent geometry : angle 0.46915 (18615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 1.951 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: A 653 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8625 (t80) REVERT: A 724 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7653 (tt) REVERT: E 133 GLU cc_start: 0.9238 (tt0) cc_final: 0.8786 (tm-30) REVERT: E 231 LEU cc_start: 0.9432 (mt) cc_final: 0.9167 (mt) outliers start: 8 outliers final: 5 residues processed: 97 average time/residue: 0.6645 time to fit residues: 91.9953 Evaluate side-chains 100 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 113 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 18 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.127065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.091715 restraints weight = 142173.369| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 4.01 r_work: 0.3410 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13761 Z= 0.173 Angle : 0.486 5.852 18615 Z= 0.272 Chirality : 0.036 0.141 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.387 21.741 1790 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.46 % Allowed : 5.76 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.25 (0.21), residues: 1666 helix: 2.18 (0.15), residues: 1152 sheet: 0.95 (0.57), residues: 89 loop : -0.28 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.008 0.001 HIS D 281 PHE 0.021 0.001 PHE A 249 TYR 0.016 0.001 TYR B 51 ARG 0.005 0.000 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 901) hydrogen bonds : angle 4.34783 ( 2670) covalent geometry : bond 0.00381 (13761) covalent geometry : angle 0.48613 (18615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 2.295 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: A 724 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7490 (tt) REVERT: D 252 TYR cc_start: 0.8665 (m-80) cc_final: 0.8284 (m-80) REVERT: E 133 GLU cc_start: 0.9218 (tt0) cc_final: 0.8701 (tm-30) REVERT: E 231 LEU cc_start: 0.9463 (mt) cc_final: 0.9177 (mt) outliers start: 7 outliers final: 6 residues processed: 98 average time/residue: 0.6587 time to fit residues: 93.2797 Evaluate side-chains 99 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 113 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 157 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 154 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 160 optimal weight: 40.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.127206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.091934 restraints weight = 141446.907| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.99 r_work: 0.3407 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13761 Z= 0.145 Angle : 0.471 5.520 18615 Z= 0.262 Chirality : 0.035 0.142 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.350 21.147 1790 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.46 % Allowed : 6.02 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.34 (0.21), residues: 1666 helix: 2.25 (0.15), residues: 1152 sheet: 0.97 (0.58), residues: 89 loop : -0.26 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 359 HIS 0.010 0.001 HIS D 281 PHE 0.019 0.001 PHE A 249 TYR 0.019 0.001 TYR A 988 ARG 0.005 0.000 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 901) hydrogen bonds : angle 4.25928 ( 2670) covalent geometry : bond 0.00319 (13761) covalent geometry : angle 0.47055 (18615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 2.011 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: A 724 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7571 (tt) REVERT: A 988 TYR cc_start: 0.7564 (t80) cc_final: 0.7061 (t80) REVERT: D 252 TYR cc_start: 0.8607 (m-80) cc_final: 0.8205 (m-80) REVERT: E 133 GLU cc_start: 0.9229 (tt0) cc_final: 0.8908 (tm-30) REVERT: E 231 LEU cc_start: 0.9450 (mt) cc_final: 0.9182 (mt) outliers start: 7 outliers final: 6 residues processed: 97 average time/residue: 0.6935 time to fit residues: 96.8526 Evaluate side-chains 96 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 113 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 148 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 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 = 0.4358 r_free = 0.4358 target = 0.126677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.091562 restraints weight = 142044.372| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 4.03 r_work: 0.3404 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13761 Z= 0.146 Angle : 0.466 5.785 18615 Z= 0.259 Chirality : 0.035 0.139 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.287 21.468 1790 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.46 % Allowed : 6.28 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.39 (0.21), residues: 1666 helix: 2.27 (0.15), residues: 1157 sheet: 0.93 (0.58), residues: 91 loop : -0.22 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 359 HIS 0.010 0.001 HIS D 281 PHE 0.019 0.001 PHE A 249 TYR 0.013 0.001 TYR B 51 ARG 0.004 0.000 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 901) hydrogen bonds : angle 4.18978 ( 2670) covalent geometry : bond 0.00320 (13761) covalent geometry : angle 0.46605 (18615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 2.577 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: A 162 MET cc_start: 0.8776 (mtm) cc_final: 0.8519 (mtm) REVERT: A 724 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7534 (tt) REVERT: D 215 GLN cc_start: 0.7905 (mt0) cc_final: 0.7522 (tp40) REVERT: D 252 TYR cc_start: 0.8583 (m-80) cc_final: 0.8185 (m-80) REVERT: E 133 GLU cc_start: 0.9220 (tt0) cc_final: 0.8851 (tm-30) REVERT: E 231 LEU cc_start: 0.9479 (mt) cc_final: 0.9211 (mt) outliers start: 7 outliers final: 6 residues processed: 94 average time/residue: 0.7602 time to fit residues: 102.8420 Evaluate side-chains 98 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 113 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 153 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.126368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.091574 restraints weight = 143176.240| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.94 r_work: 0.3386 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13761 Z= 0.160 Angle : 0.477 5.778 18615 Z= 0.264 Chirality : 0.035 0.138 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.266 20.894 1790 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.52 % Allowed : 6.41 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.38 (0.21), residues: 1666 helix: 2.25 (0.15), residues: 1162 sheet: 0.99 (0.58), residues: 91 loop : -0.21 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 132 HIS 0.010 0.001 HIS D 281 PHE 0.020 0.001 PHE A 249 TYR 0.012 0.001 TYR B 51 ARG 0.004 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 901) hydrogen bonds : angle 4.16672 ( 2670) covalent geometry : bond 0.00354 (13761) covalent geometry : angle 0.47691 (18615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 1.992 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: A 724 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7525 (tt) REVERT: A 802 ASN cc_start: 0.8920 (t0) cc_final: 0.8439 (t0) REVERT: A 988 TYR cc_start: 0.7724 (t80) cc_final: 0.7298 (t80) REVERT: D 215 GLN cc_start: 0.7990 (mt0) cc_final: 0.7260 (tp40) REVERT: D 252 TYR cc_start: 0.8616 (m-80) cc_final: 0.8249 (m-80) REVERT: E 133 GLU cc_start: 0.9265 (tt0) cc_final: 0.8877 (tm-30) REVERT: E 231 LEU cc_start: 0.9480 (mt) cc_final: 0.9215 (mt) outliers start: 8 outliers final: 7 residues processed: 98 average time/residue: 0.6781 time to fit residues: 96.3278 Evaluate side-chains 99 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 113 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 153 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.126331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.091543 restraints weight = 142536.452| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.96 r_work: 0.3403 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13761 Z= 0.140 Angle : 0.466 5.976 18615 Z= 0.258 Chirality : 0.035 0.147 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.241 21.365 1790 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.52 % Allowed : 6.80 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.42 (0.21), residues: 1666 helix: 2.29 (0.15), residues: 1163 sheet: 0.91 (0.57), residues: 91 loop : -0.22 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 189 HIS 0.010 0.001 HIS D 281 PHE 0.040 0.001 PHE D 124 TYR 0.015 0.001 TYR A 933 ARG 0.004 0.000 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 901) hydrogen bonds : angle 4.10484 ( 2670) covalent geometry : bond 0.00307 (13761) covalent geometry : angle 0.46584 (18615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 2.308 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: A 162 MET cc_start: 0.8794 (mtm) cc_final: 0.8530 (mtm) REVERT: A 724 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7505 (tt) REVERT: A 802 ASN cc_start: 0.8890 (t0) cc_final: 0.8403 (t0) REVERT: A 988 TYR cc_start: 0.7679 (t80) cc_final: 0.7261 (t80) REVERT: D 215 GLN cc_start: 0.8024 (mt0) cc_final: 0.7249 (tp40) REVERT: E 133 GLU cc_start: 0.9249 (tt0) cc_final: 0.8856 (tm-30) REVERT: E 231 LEU cc_start: 0.9483 (mt) cc_final: 0.9212 (mt) outliers start: 8 outliers final: 7 residues processed: 97 average time/residue: 0.6759 time to fit residues: 95.1014 Evaluate side-chains 102 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 113 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 161 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.126402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.091544 restraints weight = 142683.420| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.98 r_work: 0.3419 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13761 Z= 0.124 Angle : 0.453 6.035 18615 Z= 0.250 Chirality : 0.035 0.137 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.184 21.048 1790 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.46 % Allowed : 6.87 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.51 (0.21), residues: 1666 helix: 2.37 (0.15), residues: 1162 sheet: 0.88 (0.58), residues: 91 loop : -0.19 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 189 HIS 0.010 0.001 HIS D 281 PHE 0.033 0.001 PHE D 124 TYR 0.014 0.001 TYR A 933 ARG 0.004 0.000 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 901) hydrogen bonds : angle 4.03293 ( 2670) covalent geometry : bond 0.00268 (13761) covalent geometry : angle 0.45263 (18615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16390.57 seconds wall clock time: 281 minutes 53.51 seconds (16913.51 seconds total)