Starting phenix.real_space_refine on Mon Aug 25 10:31:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b31_44120/08_2025/9b31_44120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b31_44120/08_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_44120/08_2025/9b31_44120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b31_44120/08_2025/9b31_44120.map" model { file = "/net/cci-nas-00/data/ceres_data/9b31_44120/08_2025/9b31_44120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b31_44120/08_2025/9b31_44120.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.36, per 1000 atoms: 0.20 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: 2.75 Conformation dependent library (CDL) restraints added in 823.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.67 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: 6.42 Time building geometry restraints manager: 3.68 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: 7.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.180 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 27.100 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.350 ------------------------------------------------------------------------------- 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 : 5.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (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 ARG 0.026 0.001 ARG A 638 TYR 0.016 0.001 TYR A 511 PHE 0.035 0.002 PHE A 249 TRP 0.017 0.001 TRP A 127 HIS 0.005 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00400 (13761) covalent geometry : angle 0.54343 (18615) hydrogen bonds : bond 0.14653 ( 901) hydrogen bonds : angle 5.80266 ( 2670) *********************** 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 : 0.790 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: D 229 PHE cc_start: 0.7217 (p90) cc_final: 0.6949 (p90) REVERT: D 350 ASP cc_start: 0.8773 (m-30) cc_final: 0.8429 (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: 0.3807 time to fit residues: 77.6197 Evaluate side-chains 111 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- 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 876 GLN ** D 122 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 = 0.4377 r_free = 0.4377 target = 0.132052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.095429 restraints weight = 135719.156| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 4.39 r_work: 0.3405 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13761 Z= 0.176 Angle : 0.545 5.797 18615 Z= 0.307 Chirality : 0.037 0.145 2150 Planarity : 0.005 0.051 2393 Dihedral : 4.694 24.861 1790 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.39 % Allowed : 3.07 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.20), residues: 1666 helix: 1.88 (0.15), residues: 1154 sheet: 1.14 (0.51), residues: 87 loop : -0.30 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 705 TYR 0.013 0.001 TYR A 511 PHE 0.025 0.002 PHE A 249 TRP 0.009 0.001 TRP E 359 HIS 0.005 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00381 (13761) covalent geometry : angle 0.54509 (18615) hydrogen bonds : bond 0.05087 ( 901) hydrogen bonds : angle 4.80340 ( 2670) *********************** 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 117 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.772 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: E 133 GLU cc_start: 0.9274 (tt0) cc_final: 0.8769 (tp30) REVERT: E 213 TYR cc_start: 0.7906 (m-80) cc_final: 0.7657 (m-80) REVERT: E 231 LEU cc_start: 0.9432 (mt) cc_final: 0.9134 (mt) outliers start: 6 outliers final: 5 residues processed: 111 average time/residue: 0.3498 time to fit residues: 53.8761 Evaluate side-chains 109 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 122 ASN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.131651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.095263 restraints weight = 136164.592| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 4.24 r_work: 0.3431 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1696 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= 0.139 Angle : 0.486 5.891 18615 Z= 0.269 Chirality : 0.036 0.149 2150 Planarity : 0.004 0.047 2393 Dihedral : 4.525 23.237 1790 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.39 % Allowed : 4.38 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.21), residues: 1666 helix: 2.07 (0.15), residues: 1161 sheet: 0.70 (0.54), residues: 91 loop : -0.31 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.011 0.001 TYR A 511 PHE 0.023 0.001 PHE A 249 TRP 0.007 0.001 TRP E 359 HIS 0.008 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00292 (13761) covalent geometry : angle 0.48579 (18615) hydrogen bonds : bond 0.04566 ( 901) hydrogen bonds : angle 4.50808 ( 2670) *********************** 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 114 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.621 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: E 133 GLU cc_start: 0.9249 (tt0) cc_final: 0.8649 (tp30) REVERT: E 213 TYR cc_start: 0.8023 (m-80) cc_final: 0.7780 (m-80) REVERT: E 231 LEU cc_start: 0.9448 (mt) cc_final: 0.9157 (mt) outliers start: 6 outliers final: 5 residues processed: 108 average time/residue: 0.3032 time to fit residues: 46.8523 Evaluate side-chains 102 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 E residue 113 PHE Chi-restraints excluded: chain E residue 117 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 43 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.129767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.093660 restraints weight = 136910.765| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 4.16 r_work: 0.3408 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13761 Z= 0.154 Angle : 0.484 5.976 18615 Z= 0.268 Chirality : 0.036 0.143 2150 Planarity : 0.004 0.047 2393 Dihedral : 4.448 22.773 1790 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.46 % Allowed : 4.77 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.21), residues: 1666 helix: 2.15 (0.15), residues: 1158 sheet: 0.83 (0.56), residues: 94 loop : -0.25 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 18 TYR 0.029 0.001 TYR A 113 PHE 0.021 0.001 PHE A 249 TRP 0.012 0.001 TRP D 189 HIS 0.005 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00339 (13761) covalent geometry : angle 0.48394 (18615) hydrogen bonds : bond 0.04330 ( 901) hydrogen bonds : angle 4.41114 ( 2670) *********************** 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 109 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.566 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: D 122 ASN cc_start: 0.9102 (m-40) cc_final: 0.8864 (m110) REVERT: E 133 GLU cc_start: 0.9248 (tt0) cc_final: 0.8633 (tp30) REVERT: E 231 LEU cc_start: 0.9426 (mt) cc_final: 0.9157 (mt) outliers start: 7 outliers final: 5 residues processed: 102 average time/residue: 0.2954 time to fit residues: 43.2273 Evaluate side-chains 103 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 653 PHE 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 150 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 138 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 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 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** 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 = 0.4356 r_free = 0.4356 target = 0.128157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092332 restraints weight = 137945.633| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.12 r_work: 0.3423 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13761 Z= 0.138 Angle : 0.465 5.932 18615 Z= 0.258 Chirality : 0.035 0.140 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.376 22.614 1790 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.65 % Allowed : 5.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.21), residues: 1666 helix: 2.26 (0.15), residues: 1153 sheet: 0.87 (0.55), residues: 89 loop : -0.27 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.010 0.001 TYR A 511 PHE 0.020 0.001 PHE A 249 TRP 0.012 0.001 TRP D 189 HIS 0.009 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00300 (13761) covalent geometry : angle 0.46503 (18615) hydrogen bonds : bond 0.04187 ( 901) hydrogen bonds : angle 4.28504 ( 2670) *********************** 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 110 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.840 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: A 724 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7562 (tt) REVERT: E 133 GLU cc_start: 0.9255 (tt0) cc_final: 0.8635 (tp30) REVERT: E 231 LEU cc_start: 0.9429 (mt) cc_final: 0.9155 (mt) outliers start: 10 outliers final: 7 residues processed: 102 average time/residue: 0.3254 time to fit residues: 47.6056 Evaluate side-chains 106 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 312 PHE Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 117 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 0.1980 chunk 99 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.128463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.092697 restraints weight = 140635.515| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 4.15 r_work: 0.3435 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2317 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= 0.139 Angle : 0.464 5.895 18615 Z= 0.257 Chirality : 0.035 0.142 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.325 22.339 1790 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.21), residues: 1666 helix: 2.30 (0.15), residues: 1153 sheet: 1.01 (0.55), residues: 87 loop : -0.28 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.021 0.001 TYR B 51 PHE 0.019 0.001 PHE A 249 TRP 0.007 0.001 TRP D 359 HIS 0.008 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00304 (13761) covalent geometry : angle 0.46426 (18615) hydrogen bonds : bond 0.04102 ( 901) hydrogen bonds : angle 4.22957 ( 2670) *********************** 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 108 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.797 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: A 162 MET cc_start: 0.8731 (mtm) cc_final: 0.8452 (mtm) REVERT: A 724 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7534 (tt) REVERT: A 988 TYR cc_start: 0.7813 (t80) cc_final: 0.7609 (t80) REVERT: D 252 TYR cc_start: 0.8499 (m-80) cc_final: 0.8257 (m-80) REVERT: E 133 GLU cc_start: 0.9212 (tt0) cc_final: 0.8565 (tp30) REVERT: E 231 LEU cc_start: 0.9448 (mt) cc_final: 0.9162 (mt) outliers start: 7 outliers final: 6 residues processed: 102 average time/residue: 0.3292 time to fit residues: 48.3937 Evaluate side-chains 103 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 254 TYR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain D residue 346 GLU 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 7 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4358 r_free = 0.4358 target = 0.127079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.092145 restraints weight = 142185.876| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.94 r_work: 0.3402 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13761 Z= 0.175 Angle : 0.482 5.908 18615 Z= 0.269 Chirality : 0.036 0.142 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.320 21.559 1790 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.59 % Allowed : 6.21 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.21), residues: 1666 helix: 2.27 (0.15), residues: 1154 sheet: 0.72 (0.55), residues: 91 loop : -0.28 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 373 TYR 0.010 0.001 TYR A 113 PHE 0.020 0.001 PHE A 249 TRP 0.009 0.001 TRP E 359 HIS 0.010 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00389 (13761) covalent geometry : angle 0.48154 (18615) hydrogen bonds : bond 0.04229 ( 901) hydrogen bonds : angle 4.23817 ( 2670) *********************** 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 107 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.792 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: A 724 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7543 (tt) REVERT: A 988 TYR cc_start: 0.7792 (t80) cc_final: 0.7569 (t80) REVERT: D 252 TYR cc_start: 0.8698 (m-80) cc_final: 0.8355 (m-80) REVERT: E 133 GLU cc_start: 0.9196 (tt0) cc_final: 0.8546 (tp30) REVERT: E 231 LEU cc_start: 0.9468 (mt) cc_final: 0.9194 (mt) outliers start: 9 outliers final: 8 residues processed: 100 average time/residue: 0.3368 time to fit residues: 47.9225 Evaluate side-chains 104 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 249 CYS Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain D residue 346 GLU 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 68 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 151 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 55 optimal weight: 0.0970 chunk 7 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4368 r_free = 0.4368 target = 0.127317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.092463 restraints weight = 142123.515| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.95 r_work: 0.3419 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13761 Z= 0.124 Angle : 0.455 5.745 18615 Z= 0.252 Chirality : 0.035 0.140 2150 Planarity : 0.004 0.045 2393 Dihedral : 4.259 21.826 1790 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.52 % Allowed : 6.54 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.21), residues: 1666 helix: 2.32 (0.15), residues: 1163 sheet: 0.84 (0.56), residues: 91 loop : -0.26 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.014 0.001 TYR B 51 PHE 0.029 0.001 PHE D 124 TRP 0.006 0.001 TRP D 359 HIS 0.009 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00268 (13761) covalent geometry : angle 0.45542 (18615) hydrogen bonds : bond 0.03986 ( 901) hydrogen bonds : angle 4.12110 ( 2670) *********************** 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 110 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.838 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: A 162 MET cc_start: 0.8719 (mtm) cc_final: 0.8431 (mtm) REVERT: A 724 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7542 (tt) REVERT: A 988 TYR cc_start: 0.7800 (t80) cc_final: 0.7563 (t80) REVERT: B 51 TYR cc_start: 0.8828 (t80) cc_final: 0.8621 (t80) REVERT: D 215 GLN cc_start: 0.7880 (mt0) cc_final: 0.7505 (tp40) REVERT: D 252 TYR cc_start: 0.8681 (m-80) cc_final: 0.8309 (m-80) REVERT: E 133 GLU cc_start: 0.9191 (tt0) cc_final: 0.8530 (tp30) REVERT: E 231 LEU cc_start: 0.9470 (mt) cc_final: 0.9195 (mt) outliers start: 8 outliers final: 7 residues processed: 104 average time/residue: 0.3095 time to fit residues: 46.1290 Evaluate side-chains 106 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 D residue 346 GLU 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 23 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 143 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.126417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.091539 restraints weight = 142586.434| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.95 r_work: 0.3382 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13761 Z= 0.191 Angle : 0.498 6.107 18615 Z= 0.277 Chirality : 0.036 0.141 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.291 21.402 1790 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.52 % Allowed : 6.74 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.21), residues: 1666 helix: 2.23 (0.15), residues: 1161 sheet: 0.85 (0.57), residues: 91 loop : -0.33 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 710 TYR 0.012 0.001 TYR A 933 PHE 0.031 0.001 PHE D 124 TRP 0.010 0.001 TRP D 132 HIS 0.010 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00427 (13761) covalent geometry : angle 0.49752 (18615) hydrogen bonds : bond 0.04293 ( 901) hydrogen bonds : angle 4.22648 ( 2670) *********************** 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 107 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.653 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: 0.7797 (OUTLIER) cc_final: 0.7521 (tt) REVERT: A 988 TYR cc_start: 0.7819 (t80) cc_final: 0.7560 (t80) REVERT: D 215 GLN cc_start: 0.7999 (mt0) cc_final: 0.7527 (tp40) REVERT: D 252 TYR cc_start: 0.8682 (m-80) cc_final: 0.8332 (m-80) REVERT: E 231 LEU cc_start: 0.9501 (mt) cc_final: 0.9235 (mt) outliers start: 8 outliers final: 7 residues processed: 101 average time/residue: 0.2734 time to fit residues: 39.7412 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 : 0.509 ------------------------------------------------------------------------------- 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 D residue 346 GLU 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 68 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 151 optimal weight: 0.0670 chunk 119 optimal weight: 4.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.127239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.092419 restraints weight = 142249.122| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.96 r_work: 0.3403 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2864 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= 0.131 Angle : 0.460 5.959 18615 Z= 0.254 Chirality : 0.035 0.138 2150 Planarity : 0.004 0.045 2393 Dihedral : 4.244 20.810 1790 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.65 % Allowed : 7.13 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.21), residues: 1666 helix: 2.33 (0.15), residues: 1163 sheet: 0.91 (0.57), residues: 91 loop : -0.24 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 137 TYR 0.015 0.001 TYR A 933 PHE 0.033 0.001 PHE D 124 TRP 0.007 0.001 TRP D 132 HIS 0.011 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00285 (13761) covalent geometry : angle 0.45999 (18615) hydrogen bonds : bond 0.04026 ( 901) hydrogen bonds : angle 4.10389 ( 2670) ********************** 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 108 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.780 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: 0.8761 (mtm) cc_final: 0.8494 (mtm) REVERT: A 724 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7507 (tt) REVERT: A 802 ASN cc_start: 0.8899 (t0) cc_final: 0.8413 (t0) REVERT: D 215 GLN cc_start: 0.7966 (mt0) cc_final: 0.7357 (tp40) REVERT: D 252 TYR cc_start: 0.8650 (m-80) cc_final: 0.8278 (m-80) REVERT: E 133 GLU cc_start: 0.9213 (tt0) cc_final: 0.8558 (tp30) REVERT: E 231 LEU cc_start: 0.9486 (mt) cc_final: 0.9221 (mt) outliers start: 10 outliers final: 8 residues processed: 102 average time/residue: 0.3167 time to fit residues: 46.3607 Evaluate side-chains 106 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 GLU 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 D residue 346 GLU 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 68 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 90 optimal weight: 0.0770 chunk 39 optimal weight: 0.3980 chunk 143 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.127300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.092408 restraints weight = 141478.342| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 4.10 r_work: 0.3427 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13761 Z= 0.115 Angle : 0.446 5.961 18615 Z= 0.245 Chirality : 0.035 0.138 2150 Planarity : 0.004 0.046 2393 Dihedral : 4.148 20.602 1790 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.46 % Allowed : 7.26 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.21), residues: 1666 helix: 2.44 (0.15), residues: 1162 sheet: 1.00 (0.58), residues: 91 loop : -0.19 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.014 0.001 TYR A 933 PHE 0.033 0.001 PHE D 124 TRP 0.006 0.001 TRP A 127 HIS 0.011 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00247 (13761) covalent geometry : angle 0.44562 (18615) hydrogen bonds : bond 0.03799 ( 901) hydrogen bonds : angle 4.00229 ( 2670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8392.16 seconds wall clock time: 142 minutes 53.74 seconds (8573.74 seconds total)