Starting phenix.real_space_refine on Sun Aug 24 00:53:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8brj_16217/08_2025/8brj_16217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8brj_16217/08_2025/8brj_16217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8brj_16217/08_2025/8brj_16217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8brj_16217/08_2025/8brj_16217.map" model { file = "/net/cci-nas-00/data/ceres_data/8brj_16217/08_2025/8brj_16217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8brj_16217/08_2025/8brj_16217.cif" } resolution = 4.08 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= 0.014 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 5092 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 7333 2.51 5 N 2081 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11627 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3209 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 19, 'TRANS': 416} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3214 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 416} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 5204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5204 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 38, 'TRANS': 671} Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'PHE:plan': 1, 'ARG:plan': 10, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 2.23, per 1000 atoms: 0.19 Number of scatterers: 11627 At special positions: 0 Unit cell: (82.8, 102.672, 131.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 2157 8.00 N 2081 7.00 C 7333 6.00 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: 0.63 Conformation dependent library (CDL) restraints added in 458.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 8 sheets defined 48.9% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.980A pdb=" N LEU A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 75 through 84 removed outlier: 4.093A pdb=" N GLU A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.722A pdb=" N ALA A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 removed outlier: 4.070A pdb=" N ARG A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 161 removed outlier: 3.542A pdb=" N ARG A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.745A pdb=" N GLU A 225 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 317 through 331 Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 349 through 359 Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.788A pdb=" N ALA A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.557A pdb=" N GLY A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 412 removed outlier: 4.516A pdb=" N GLY A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ALA A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.501A pdb=" N GLU B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 116 removed outlier: 3.540A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.792A pdb=" N LYS B 149 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 160 removed outlier: 3.543A pdb=" N ARG B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 198 through 220 removed outlier: 3.745A pdb=" N ALA B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 317 through 331 Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 346 through 358 removed outlier: 3.633A pdb=" N ALA B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.518A pdb=" N ALA B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.517A pdb=" N TYR B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 412 removed outlier: 4.512A pdb=" N ALA B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 48 removed outlier: 3.977A pdb=" N ARG C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 79 through 99 Processing helix chain 'C' and resid 114 through 123 removed outlier: 4.155A pdb=" N GLU C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 150 through 159 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 160 through 170 removed outlier: 4.437A pdb=" N GLU C 166 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 193 through 204 removed outlier: 3.565A pdb=" N ALA C 198 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 200 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 241 Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 261 through 278 removed outlier: 4.556A pdb=" N MET C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 298 removed outlier: 3.686A pdb=" N GLN C 283 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 removed outlier: 3.846A pdb=" N ILE C 323 " --> pdb=" O MET C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 362 removed outlier: 3.847A pdb=" N LYS C 359 " --> pdb=" O GLN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 375 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.880A pdb=" N HIS C 388 " --> pdb=" O GLY C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 413 Processing helix chain 'C' and resid 428 through 434 Processing helix chain 'C' and resid 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 466 through 480 Processing helix chain 'C' and resid 494 through 512 Proline residue: C 501 - end of helix removed outlier: 3.503A pdb=" N ALA C 506 " --> pdb=" O TYR C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 526 removed outlier: 3.569A pdb=" N LEU C 523 " --> pdb=" O ILE C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 540 Processing helix chain 'C' and resid 540 through 545 Processing helix chain 'C' and resid 547 through 556 removed outlier: 3.955A pdb=" N LEU C 551 " --> pdb=" O ILE C 547 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 552 " --> pdb=" O ILE C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 560 Processing helix chain 'C' and resid 565 through 571 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 614 through 636 removed outlier: 3.555A pdb=" N MET C 626 " --> pdb=" O CYS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 652 Processing helix chain 'C' and resid 656 through 660 Processing helix chain 'C' and resid 661 through 670 Processing helix chain 'C' and resid 671 through 686 removed outlier: 3.907A pdb=" N VAL C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 681 " --> pdb=" O ILE C 677 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 682 " --> pdb=" O MET C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 690 removed outlier: 3.562A pdb=" N THR C 690 " --> pdb=" O SER C 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 687 through 690' Processing helix chain 'C' and resid 692 through 702 removed outlier: 3.670A pdb=" N ARG C 701 " --> pdb=" O GLU C 697 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 removed outlier: 4.444A pdb=" N ILE A 17 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET A 285 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SER A 19 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 283 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 61 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY A 65 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A 94 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 93 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 64 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 95 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN B 66 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 126 " --> pdb=" O GLY B 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.610A pdb=" N GLN A 61 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY A 65 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A 94 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 93 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 64 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 95 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN B 66 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 126 " --> pdb=" O GLY B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 308 removed outlier: 4.257A pdb=" N LEU A 301 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU A 434 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 421 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 420 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 301 through 308 removed outlier: 7.085A pdb=" N LEU B 339 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N THR B 420 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP B 341 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N CYS B 422 " --> pdb=" O ASP B 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 11 removed outlier: 6.477A pdb=" N ALA C 17 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL C 58 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 19 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 55 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA C 107 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N PHE C 57 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG C 126 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL C 189 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N CYS C 128 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 66 removed outlier: 5.386A pdb=" N ALA C 111 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 137 " --> pdb=" O CYS C 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 377 through 379 removed outlier: 5.767A pdb=" N ILE C 392 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE C 420 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU C 445 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 422 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 485 " --> pdb=" O VAL C 457 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3962 1.34 - 1.46: 1391 1.46 - 1.57: 6372 1.57 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 11824 Sorted by residual: bond pdb=" CA GLN A 313 " pdb=" C GLN A 313 " ideal model delta sigma weight residual 1.520 1.501 0.020 1.22e-02 6.72e+03 2.64e+00 bond pdb=" C SER C 449 " pdb=" N PRO C 450 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.54e+00 bond pdb=" N LEU C 138 " pdb=" CA LEU C 138 " ideal model delta sigma weight residual 1.460 1.445 0.016 1.04e-02 9.25e+03 2.33e+00 bond pdb=" CA LEU C 138 " pdb=" C LEU C 138 " ideal model delta sigma weight residual 1.523 1.507 0.017 1.22e-02 6.72e+03 1.84e+00 bond pdb=" N ASN C 564 " pdb=" CA ASN C 564 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.76e+00 ... (remaining 11819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 15547 1.58 - 3.16: 422 3.16 - 4.75: 62 4.75 - 6.33: 21 6.33 - 7.91: 5 Bond angle restraints: 16057 Sorted by residual: angle pdb=" N VAL B 67 " pdb=" CA VAL B 67 " pdb=" C VAL B 67 " ideal model delta sigma weight residual 110.05 104.90 5.15 1.09e+00 8.42e-01 2.23e+01 angle pdb=" C LEU A 165 " pdb=" CA LEU A 165 " pdb=" CB LEU A 165 " ideal model delta sigma weight residual 115.89 110.23 5.66 1.32e+00 5.74e-01 1.84e+01 angle pdb=" CA PRO C 139 " pdb=" C PRO C 139 " pdb=" O PRO C 139 " ideal model delta sigma weight residual 123.07 118.40 4.67 1.38e+00 5.25e-01 1.14e+01 angle pdb=" C VAL C 214 " pdb=" N ARG C 215 " pdb=" CA ARG C 215 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.30e+00 angle pdb=" C MET A 285 " pdb=" CA MET A 285 " pdb=" CB MET A 285 " ideal model delta sigma weight residual 109.72 114.13 -4.41 1.61e+00 3.86e-01 7.49e+00 ... (remaining 16052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6549 17.94 - 35.88: 495 35.88 - 53.81: 79 53.81 - 71.75: 10 71.75 - 89.69: 15 Dihedral angle restraints: 7148 sinusoidal: 2670 harmonic: 4478 Sorted by residual: dihedral pdb=" CA MET A 285 " pdb=" C MET A 285 " pdb=" N THR A 286 " pdb=" CA THR A 286 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLU A 200 " pdb=" C GLU A 200 " pdb=" N GLN A 201 " pdb=" CA GLN A 201 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY C 670 " pdb=" C GLY C 670 " pdb=" N ALA C 671 " pdb=" CA ALA C 671 " ideal model delta harmonic sigma weight residual -180.00 -160.30 -19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1584 0.055 - 0.109: 273 0.109 - 0.164: 29 0.164 - 0.219: 1 0.219 - 0.273: 1 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CB ILE B 17 " pdb=" CA ILE B 17 " pdb=" CG1 ILE B 17 " pdb=" CG2 ILE B 17 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASN C 564 " pdb=" N ASN C 564 " pdb=" C ASN C 564 " pdb=" CB ASN C 564 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" CA VAL B 67 " pdb=" N VAL B 67 " pdb=" C VAL B 67 " pdb=" CB VAL B 67 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 1885 not shown) Planarity restraints: 2103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 232 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO A 233 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 221 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.45e+00 pdb=" N PRO C 222 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 222 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 222 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 231 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 232 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 232 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 232 " -0.027 5.00e-02 4.00e+02 ... (remaining 2100 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 265 2.65 - 3.21: 12247 3.21 - 3.77: 19666 3.77 - 4.34: 26403 4.34 - 4.90: 40584 Nonbonded interactions: 99165 Sorted by model distance: nonbonded pdb=" O MET A 401 " pdb=" OG1 THR A 405 " model vdw 2.086 3.040 nonbonded pdb=" OD2 ASP A 377 " pdb=" OG SER A 379 " model vdw 2.137 3.040 nonbonded pdb=" O LEU B 384 " pdb=" OH TYR B 390 " model vdw 2.154 3.040 nonbonded pdb=" O GLU C 166 " pdb=" OG1 THR C 170 " model vdw 2.193 3.040 nonbonded pdb=" OG SER C 310 " pdb=" O HIS C 388 " model vdw 2.194 3.040 ... (remaining 99160 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 'A' and (resid 1 through 126 or (resid 127 and (name N or name CA or name \ C or name O or name CB )) or resid 128 through 201 or (resid 202 and (name N or \ name CA or name C or name O or name CB )) or resid 203 through 291 or (resid 29 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 293 through \ 324 or (resid 325 through 326 and (name N or name CA or name C or name O or name \ CB )) or resid 327 through 436)) selection = (chain 'B' and (resid 1 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB )) or resid 54 through 164 or (resid 165 through 167 and ( \ name N or name CA or name C or name O or name CB )) or resid 168 through 260 or \ (resid 261 and (name N or name CA or name C or name O or name CB )) or resid 262 \ through 436)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.510 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4658 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 : 0.003 0.042 11824 Z= 0.141 Angle : 0.645 7.910 16057 Z= 0.353 Chirality : 0.041 0.273 1888 Planarity : 0.005 0.056 2103 Dihedral : 13.328 89.691 4278 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.85 % Favored : 92.70 % Rotamer: Outliers : 0.17 % Allowed : 0.86 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.21), residues: 1576 helix: 0.28 (0.20), residues: 658 sheet: -0.23 (0.38), residues: 180 loop : -1.57 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 400 TYR 0.014 0.001 TYR A 93 PHE 0.012 0.001 PHE C 655 TRP 0.010 0.001 TRP B 217 HIS 0.003 0.001 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00274 (11824) covalent geometry : angle 0.64474 (16057) hydrogen bonds : bond 0.27694 ( 543) hydrogen bonds : angle 8.62592 ( 1665) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 327 time to evaluate : 0.364 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: A 22 ARG cc_start: 0.5756 (ttp80) cc_final: 0.4406 (ptm-80) REVERT: A 63 VAL cc_start: 0.5956 (t) cc_final: 0.4444 (m) REVERT: A 84 THR cc_start: 0.1214 (p) cc_final: 0.0682 (m) REVERT: A 108 ASN cc_start: 0.7744 (m-40) cc_final: 0.6711 (t0) REVERT: A 113 LEU cc_start: 0.8853 (tt) cc_final: 0.8628 (mp) REVERT: A 114 MET cc_start: 0.8458 (mmp) cc_final: 0.8033 (mmm) REVERT: A 118 ILE cc_start: 0.5504 (mm) cc_final: 0.5128 (mm) REVERT: A 276 THR cc_start: 0.6691 (p) cc_final: 0.6310 (p) REVERT: A 314 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7282 (t0) REVERT: A 315 MET cc_start: 0.5323 (pmm) cc_final: 0.3758 (ptm) REVERT: A 317 LEU cc_start: 0.7737 (mt) cc_final: 0.7164 (tp) REVERT: A 334 MET cc_start: 0.8727 (tpt) cc_final: 0.8380 (tmm) REVERT: A 357 LEU cc_start: 0.6491 (mp) cc_final: 0.5790 (mt) REVERT: A 382 ASN cc_start: 0.6499 (m-40) cc_final: 0.6219 (m110) REVERT: A 400 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7263 (tmm-80) REVERT: A 408 GLU cc_start: 0.7917 (tp30) cc_final: 0.7579 (tt0) REVERT: B 306 PHE cc_start: -0.0861 (m-80) cc_final: -0.1604 (m-80) REVERT: C 73 MET cc_start: 0.9342 (mmp) cc_final: 0.9081 (ppp) REVERT: C 98 HIS cc_start: 0.7213 (t70) cc_final: 0.6995 (t70) REVERT: C 126 ARG cc_start: 0.7575 (mtm-85) cc_final: 0.6859 (mmt180) REVERT: C 319 MET cc_start: 0.8139 (ptt) cc_final: 0.7780 (tpt) REVERT: C 347 HIS cc_start: 0.6892 (m90) cc_final: 0.6672 (m-70) REVERT: C 455 PRO cc_start: 0.5519 (Cg_exo) cc_final: 0.4631 (Cg_exo) REVERT: C 558 ARG cc_start: 0.7391 (ttp-110) cc_final: 0.5916 (mmm160) REVERT: C 643 ARG cc_start: 0.6054 (ppt170) cc_final: 0.4563 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 327 average time/residue: 0.0979 time to fit residues: 44.3765 Evaluate side-chains 195 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS B 349 GLN B 353 ASN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN C 98 HIS C 109 HIS C 124 HIS C 173 GLN C 191 HIS C 564 ASN ** C 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.112542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.085899 restraints weight = 43158.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.087603 restraints weight = 31080.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.088917 restraints weight = 24773.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.089682 restraints weight = 21118.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.090257 restraints weight = 19040.712| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 11824 Z= 0.220 Angle : 0.813 14.185 16057 Z= 0.422 Chirality : 0.047 0.209 1888 Planarity : 0.006 0.060 2103 Dihedral : 5.339 66.319 1701 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.41 % Favored : 93.08 % Rotamer: Outliers : 0.77 % Allowed : 6.95 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.21), residues: 1576 helix: 0.15 (0.19), residues: 685 sheet: -0.38 (0.40), residues: 161 loop : -1.57 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 14 TYR 0.021 0.002 TYR A 93 PHE 0.029 0.003 PHE C 65 TRP 0.018 0.002 TRP C 353 HIS 0.018 0.002 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00488 (11824) covalent geometry : angle 0.81288 (16057) hydrogen bonds : bond 0.04710 ( 543) hydrogen bonds : angle 5.90506 ( 1665) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 240 time to evaluate : 0.471 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: A 23 THR cc_start: 0.7523 (m) cc_final: 0.6948 (p) REVERT: A 111 GLU cc_start: 0.8483 (tt0) cc_final: 0.8202 (tp30) REVERT: A 291 LYS cc_start: 0.8830 (tmtt) cc_final: 0.8480 (pttm) REVERT: A 315 MET cc_start: 0.7391 (pmm) cc_final: 0.7061 (ppp) REVERT: A 392 HIS cc_start: 0.8102 (t70) cc_final: 0.7517 (t70) REVERT: A 400 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7973 (tmm-80) REVERT: A 401 MET cc_start: 0.8400 (ptp) cc_final: 0.8169 (ptp) REVERT: B 401 MET cc_start: 0.6897 (ptp) cc_final: 0.6199 (ptp) REVERT: B 436 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7450 (mt-10) REVERT: C 264 SER cc_start: 0.8068 (m) cc_final: 0.7684 (p) REVERT: C 643 ARG cc_start: 0.6222 (ppt170) cc_final: 0.4651 (mmt-90) outliers start: 9 outliers final: 3 residues processed: 244 average time/residue: 0.1135 time to fit residues: 39.3992 Evaluate side-chains 188 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 69 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 131 optimal weight: 0.0020 chunk 150 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 108 ASN A 190 GLN A 202 GLN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS A 382 ASN B 343 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS ** C 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.110531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.080649 restraints weight = 43762.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.082516 restraints weight = 31671.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.083753 restraints weight = 25411.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.084842 restraints weight = 21779.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.085312 restraints weight = 19606.792| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 11824 Z= 0.246 Angle : 0.822 17.896 16057 Z= 0.421 Chirality : 0.048 0.240 1888 Planarity : 0.006 0.049 2103 Dihedral : 5.309 62.399 1701 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.92 % Favored : 92.64 % Rotamer: Outliers : 0.34 % Allowed : 6.61 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.20), residues: 1576 helix: -0.02 (0.19), residues: 690 sheet: -0.32 (0.45), residues: 135 loop : -1.83 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 183 TYR 0.021 0.002 TYR A 93 PHE 0.025 0.003 PHE C 65 TRP 0.048 0.004 TRP C 706 HIS 0.009 0.002 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00553 (11824) covalent geometry : angle 0.82233 (16057) hydrogen bonds : bond 0.05309 ( 543) hydrogen bonds : angle 5.63264 ( 1665) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 234 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8961 (mmp) cc_final: 0.8498 (mmm) REVERT: A 315 MET cc_start: 0.7824 (pmm) cc_final: 0.7323 (ppp) REVERT: A 381 PHE cc_start: 0.8461 (t80) cc_final: 0.7607 (t80) REVERT: A 382 ASN cc_start: 0.8067 (m-40) cc_final: 0.7315 (m-40) REVERT: A 392 HIS cc_start: 0.8434 (t70) cc_final: 0.7646 (t70) REVERT: A 401 MET cc_start: 0.8771 (ptp) cc_final: 0.8430 (ptp) REVERT: B 21 LEU cc_start: 0.8244 (tt) cc_final: 0.7996 (tp) REVERT: B 33 HIS cc_start: 0.8869 (t70) cc_final: 0.8641 (t70) REVERT: B 43 MET cc_start: 0.8229 (ptm) cc_final: 0.7977 (ptp) REVERT: B 75 ASN cc_start: 0.6751 (t0) cc_final: 0.5135 (t0) REVERT: B 86 MET cc_start: 0.7983 (tpt) cc_final: 0.7461 (tpt) REVERT: B 102 SER cc_start: 0.8341 (m) cc_final: 0.7674 (t) REVERT: B 234 TYR cc_start: 0.6835 (m-80) cc_final: 0.6588 (m-10) REVERT: B 277 ASP cc_start: 0.4495 (m-30) cc_final: 0.3894 (p0) REVERT: B 388 ILE cc_start: 0.5557 (mm) cc_final: 0.5160 (mm) REVERT: C 43 ILE cc_start: 0.7617 (tp) cc_final: 0.7296 (tt) REVERT: C 108 ILE cc_start: 0.7427 (pt) cc_final: 0.6986 (pt) REVERT: C 248 GLU cc_start: 0.7128 (pm20) cc_final: 0.5964 (pm20) REVERT: C 249 ARG cc_start: 0.7613 (mmm160) cc_final: 0.7311 (tpp-160) REVERT: C 252 GLU cc_start: 0.8404 (mp0) cc_final: 0.7730 (mp0) REVERT: C 288 ILE cc_start: 0.7244 (mt) cc_final: 0.7040 (mt) REVERT: C 341 ASN cc_start: 0.8365 (m-40) cc_final: 0.7929 (m-40) REVERT: C 454 MET cc_start: 0.6012 (tpt) cc_final: 0.5569 (tpt) REVERT: C 470 ILE cc_start: 0.8221 (mt) cc_final: 0.7961 (mm) outliers start: 4 outliers final: 0 residues processed: 237 average time/residue: 0.1060 time to fit residues: 36.6285 Evaluate side-chains 167 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 50 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 50.0000 chunk 154 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN A 190 GLN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 343 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN C 462 HIS ** C 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.105615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.076654 restraints weight = 44203.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.078440 restraints weight = 32057.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.079748 restraints weight = 25575.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.080361 restraints weight = 21920.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.080656 restraints weight = 20097.971| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.9333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 11824 Z= 0.220 Angle : 0.829 13.014 16057 Z= 0.429 Chirality : 0.050 0.316 1888 Planarity : 0.007 0.096 2103 Dihedral : 5.455 67.603 1701 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.98 % Favored : 92.58 % Rotamer: Outliers : 0.34 % Allowed : 7.04 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.20), residues: 1576 helix: 0.04 (0.19), residues: 698 sheet: -0.73 (0.38), residues: 182 loop : -1.92 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 400 TYR 0.023 0.003 TYR A 93 PHE 0.037 0.003 PHE C 65 TRP 0.024 0.003 TRP A 321 HIS 0.022 0.002 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00488 (11824) covalent geometry : angle 0.82918 (16057) hydrogen bonds : bond 0.04313 ( 543) hydrogen bonds : angle 5.41209 ( 1665) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 216 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8174 (pm20) cc_final: 0.7943 (pm20) REVERT: A 70 MET cc_start: -0.3772 (ttp) cc_final: -0.4195 (ttp) REVERT: A 75 ASN cc_start: 0.7265 (t0) cc_final: 0.6388 (p0) REVERT: A 114 MET cc_start: 0.9018 (mmp) cc_final: 0.8575 (mmm) REVERT: A 275 LEU cc_start: 0.8628 (pp) cc_final: 0.8354 (pp) REVERT: A 315 MET cc_start: 0.7918 (pmm) cc_final: 0.7302 (ppp) REVERT: A 367 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5672 (mp) REVERT: A 382 ASN cc_start: 0.8213 (m-40) cc_final: 0.7777 (m110) REVERT: A 392 HIS cc_start: 0.8509 (t70) cc_final: 0.7714 (t70) REVERT: A 436 GLU cc_start: 0.7003 (mp0) cc_final: 0.6658 (mp0) REVERT: B 21 LEU cc_start: 0.8818 (tt) cc_final: 0.8398 (tt) REVERT: B 75 ASN cc_start: 0.7655 (t0) cc_final: 0.6865 (p0) REVERT: B 315 MET cc_start: 0.6921 (mmm) cc_final: 0.6484 (tpp) REVERT: B 344 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6953 (tt0) REVERT: C 43 ILE cc_start: 0.7978 (tp) cc_final: 0.7613 (tt) REVERT: C 281 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8026 (pp30) REVERT: C 323 ILE cc_start: 0.8357 (mt) cc_final: 0.8157 (mm) REVERT: C 374 LEU cc_start: 0.8213 (mt) cc_final: 0.7987 (mt) REVERT: C 473 THR cc_start: 0.8809 (m) cc_final: 0.8395 (p) REVERT: C 616 PRO cc_start: 0.8344 (Cg_exo) cc_final: 0.8064 (Cg_endo) REVERT: C 624 MET cc_start: 0.5633 (mtt) cc_final: 0.5222 (mmp) REVERT: C 683 THR cc_start: 0.8659 (p) cc_final: 0.8457 (t) outliers start: 4 outliers final: 0 residues processed: 219 average time/residue: 0.1036 time to fit residues: 33.5497 Evaluate side-chains 169 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 156 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 0.0060 chunk 143 optimal weight: 9.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 108 ASN A 190 GLN A 210 HIS ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.106100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.077100 restraints weight = 43648.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.078843 restraints weight = 30937.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.079994 restraints weight = 24428.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.080610 restraints weight = 20876.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.081357 restraints weight = 19199.398| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 1.0083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 11824 Z= 0.161 Angle : 0.724 19.963 16057 Z= 0.362 Chirality : 0.045 0.165 1888 Planarity : 0.005 0.058 2103 Dihedral : 5.087 61.715 1701 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.54 % Favored : 92.96 % Rotamer: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.21), residues: 1576 helix: 0.24 (0.20), residues: 700 sheet: -0.56 (0.39), residues: 182 loop : -1.88 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 508 TYR 0.025 0.002 TYR A 93 PHE 0.026 0.002 PHE C 526 TRP 0.008 0.001 TRP A 217 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00362 (11824) covalent geometry : angle 0.72369 (16057) hydrogen bonds : bond 0.04070 ( 543) hydrogen bonds : angle 5.14990 ( 1665) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7290 (t0) cc_final: 0.6515 (p0) REVERT: A 114 MET cc_start: 0.8925 (mmp) cc_final: 0.8449 (mmm) REVERT: A 315 MET cc_start: 0.7956 (pmm) cc_final: 0.7277 (ppp) REVERT: A 334 MET cc_start: 0.8412 (tmm) cc_final: 0.8141 (tmm) REVERT: A 382 ASN cc_start: 0.8281 (m-40) cc_final: 0.7802 (m110) REVERT: A 392 HIS cc_start: 0.8269 (t70) cc_final: 0.7562 (t70) REVERT: B 21 LEU cc_start: 0.8843 (tt) cc_final: 0.8350 (tt) REVERT: B 66 GLN cc_start: 0.7849 (pm20) cc_final: 0.7591 (pp30) REVERT: B 75 ASN cc_start: 0.7693 (t0) cc_final: 0.6995 (p0) REVERT: B 223 LYS cc_start: 0.8449 (pttm) cc_final: 0.8235 (ttpp) REVERT: B 342 MET cc_start: 0.8643 (ttt) cc_final: 0.7517 (ttp) REVERT: B 344 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6204 (mp0) REVERT: B 393 PRO cc_start: 0.8953 (Cg_exo) cc_final: 0.8721 (Cg_exo) REVERT: C 43 ILE cc_start: 0.8011 (tp) cc_final: 0.7748 (tt) REVERT: C 616 PRO cc_start: 0.8392 (Cg_exo) cc_final: 0.8069 (Cg_endo) REVERT: C 659 LEU cc_start: 0.8551 (mp) cc_final: 0.8281 (mp) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.1001 time to fit residues: 31.5995 Evaluate side-chains 159 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 152 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 123 optimal weight: 0.0370 chunk 67 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 46 optimal weight: 0.0370 chunk 153 optimal weight: 0.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 108 ASN A 190 GLN A 210 HIS A 243 ASN ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS ** C 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.107097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.077936 restraints weight = 44152.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.079583 restraints weight = 31682.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.080852 restraints weight = 25311.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.081930 restraints weight = 21677.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.082451 restraints weight = 19415.694| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 1.0420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11824 Z= 0.128 Angle : 0.669 11.672 16057 Z= 0.341 Chirality : 0.045 0.181 1888 Planarity : 0.005 0.054 2103 Dihedral : 4.873 55.488 1701 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.65 % Favored : 93.85 % Rotamer: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.21), residues: 1576 helix: 0.39 (0.20), residues: 698 sheet: -0.72 (0.38), residues: 183 loop : -1.80 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 370 TYR 0.021 0.002 TYR A 93 PHE 0.053 0.002 PHE C 655 TRP 0.023 0.002 TRP A 321 HIS 0.007 0.001 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00273 (11824) covalent geometry : angle 0.66923 (16057) hydrogen bonds : bond 0.03636 ( 543) hydrogen bonds : angle 4.89238 ( 1665) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: -0.3739 (ttp) cc_final: -0.4157 (ttp) REVERT: A 75 ASN cc_start: 0.7247 (t0) cc_final: 0.6480 (p0) REVERT: A 84 THR cc_start: 0.9097 (t) cc_final: 0.8797 (p) REVERT: A 114 MET cc_start: 0.8881 (mmp) cc_final: 0.8445 (mmm) REVERT: A 315 MET cc_start: 0.7603 (pmm) cc_final: 0.7375 (ppp) REVERT: A 321 TRP cc_start: 0.7255 (m100) cc_final: 0.7024 (m100) REVERT: A 382 ASN cc_start: 0.8214 (m-40) cc_final: 0.7761 (m110) REVERT: A 392 HIS cc_start: 0.8205 (t70) cc_final: 0.7552 (t70) REVERT: B 21 LEU cc_start: 0.8760 (tt) cc_final: 0.8358 (tt) REVERT: B 66 GLN cc_start: 0.7844 (pm20) cc_final: 0.7616 (pp30) REVERT: B 75 ASN cc_start: 0.7702 (t0) cc_final: 0.6938 (p0) REVERT: B 78 ARG cc_start: 0.8442 (tpp-160) cc_final: 0.7786 (tpp-160) REVERT: B 223 LYS cc_start: 0.8409 (pttm) cc_final: 0.8164 (ttpp) REVERT: B 342 MET cc_start: 0.8560 (ttt) cc_final: 0.7525 (ttp) REVERT: B 344 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6335 (mp0) REVERT: C 43 ILE cc_start: 0.8010 (tp) cc_final: 0.7761 (tt) REVERT: C 470 ILE cc_start: 0.9145 (mt) cc_final: 0.8935 (mt) REVERT: C 473 THR cc_start: 0.9011 (m) cc_final: 0.8757 (p) REVERT: C 552 GLU cc_start: 0.6543 (mp0) cc_final: 0.4395 (mm-30) REVERT: C 616 PRO cc_start: 0.8495 (Cg_exo) cc_final: 0.7761 (Cg_endo) REVERT: C 617 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8391 (mp10) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.1046 time to fit residues: 33.0217 Evaluate side-chains 163 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 91 optimal weight: 0.8980 chunk 128 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 99 optimal weight: 0.0040 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 108 ASN A 190 GLN A 210 HIS A 243 ASN ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.105769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.077261 restraints weight = 42993.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.078930 restraints weight = 31126.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.079649 restraints weight = 24970.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.080346 restraints weight = 21981.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.081430 restraints weight = 20027.432| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 1.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11824 Z= 0.126 Angle : 0.665 11.714 16057 Z= 0.337 Chirality : 0.044 0.181 1888 Planarity : 0.005 0.070 2103 Dihedral : 4.734 49.867 1701 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.84 % Favored : 93.65 % Rotamer: Outliers : 0.17 % Allowed : 2.49 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.21), residues: 1576 helix: 0.46 (0.20), residues: 700 sheet: -0.71 (0.38), residues: 183 loop : -1.79 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 411 TYR 0.018 0.002 TYR A 93 PHE 0.031 0.002 PHE C 655 TRP 0.021 0.002 TRP A 217 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00276 (11824) covalent geometry : angle 0.66494 (16057) hydrogen bonds : bond 0.03549 ( 543) hydrogen bonds : angle 4.81940 ( 1665) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7434 (t0) cc_final: 0.6682 (p0) REVERT: A 84 THR cc_start: 0.9109 (t) cc_final: 0.8790 (p) REVERT: A 114 MET cc_start: 0.8946 (mmp) cc_final: 0.8580 (mmm) REVERT: A 315 MET cc_start: 0.7634 (pmm) cc_final: 0.7329 (ppp) REVERT: A 341 ASP cc_start: 0.8520 (p0) cc_final: 0.7834 (p0) REVERT: A 382 ASN cc_start: 0.8247 (m-40) cc_final: 0.7740 (m110) REVERT: A 392 HIS cc_start: 0.8168 (t70) cc_final: 0.7620 (t70) REVERT: A 401 MET cc_start: 0.8688 (ptm) cc_final: 0.8225 (ptp) REVERT: B 66 GLN cc_start: 0.7782 (pm20) cc_final: 0.7509 (pp30) REVERT: B 75 ASN cc_start: 0.7447 (t0) cc_final: 0.6976 (t0) REVERT: B 113 LEU cc_start: 0.8848 (tp) cc_final: 0.8434 (mm) REVERT: B 223 LYS cc_start: 0.8491 (pttm) cc_final: 0.8226 (ttpp) REVERT: B 227 MET cc_start: 0.7845 (ptm) cc_final: 0.7506 (ppp) REVERT: B 285 MET cc_start: 0.8584 (tmm) cc_final: 0.8235 (tmm) REVERT: B 351 LEU cc_start: 0.8818 (mm) cc_final: 0.8399 (mm) REVERT: C 473 THR cc_start: 0.9115 (m) cc_final: 0.8851 (p) REVERT: C 685 TYR cc_start: 0.7331 (m-80) cc_final: 0.7063 (m-80) outliers start: 2 outliers final: 0 residues processed: 194 average time/residue: 0.0960 time to fit residues: 28.2714 Evaluate side-chains 156 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 43 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 91 optimal weight: 0.0980 chunk 135 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 108 ASN A 190 GLN A 210 HIS A 243 ASN ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.105196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.076763 restraints weight = 44005.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.078370 restraints weight = 31813.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.079199 restraints weight = 25438.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.080036 restraints weight = 22395.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.080317 restraints weight = 20283.503| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 1.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11824 Z= 0.131 Angle : 0.672 11.018 16057 Z= 0.339 Chirality : 0.044 0.182 1888 Planarity : 0.005 0.071 2103 Dihedral : 4.679 44.029 1701 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.84 % Favored : 93.65 % Rotamer: Outliers : 0.09 % Allowed : 2.23 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.21), residues: 1576 helix: 0.49 (0.21), residues: 697 sheet: -0.84 (0.37), residues: 185 loop : -1.75 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 410 TYR 0.023 0.002 TYR C 494 PHE 0.033 0.002 PHE C 655 TRP 0.018 0.001 TRP A 217 HIS 0.004 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00293 (11824) covalent geometry : angle 0.67222 (16057) hydrogen bonds : bond 0.03450 ( 543) hydrogen bonds : angle 4.85026 ( 1665) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7516 (t0) cc_final: 0.6612 (p0) REVERT: A 84 THR cc_start: 0.9096 (t) cc_final: 0.8820 (p) REVERT: A 114 MET cc_start: 0.8924 (mmp) cc_final: 0.8576 (mmm) REVERT: A 315 MET cc_start: 0.7746 (pmm) cc_final: 0.7311 (ppp) REVERT: A 341 ASP cc_start: 0.8434 (p0) cc_final: 0.7788 (p0) REVERT: A 382 ASN cc_start: 0.8264 (m-40) cc_final: 0.7741 (m110) REVERT: A 392 HIS cc_start: 0.8037 (t70) cc_final: 0.7502 (t70) REVERT: A 401 MET cc_start: 0.8695 (ptm) cc_final: 0.8275 (ptp) REVERT: B 66 GLN cc_start: 0.7931 (pm20) cc_final: 0.7539 (pp30) REVERT: B 75 ASN cc_start: 0.7207 (t0) cc_final: 0.6464 (t0) REVERT: B 78 ARG cc_start: 0.8442 (tpp-160) cc_final: 0.7766 (tpp-160) REVERT: B 79 GLU cc_start: 0.8095 (mp0) cc_final: 0.7776 (mp0) REVERT: B 113 LEU cc_start: 0.8830 (tp) cc_final: 0.8484 (mm) REVERT: B 223 LYS cc_start: 0.8496 (pttm) cc_final: 0.8238 (ttpp) REVERT: B 227 MET cc_start: 0.7842 (ptm) cc_final: 0.7536 (ppp) REVERT: B 351 LEU cc_start: 0.8828 (mm) cc_final: 0.8394 (mm) REVERT: C 28 MET cc_start: 0.7531 (mmp) cc_final: 0.7117 (mmp) REVERT: C 406 MET cc_start: 0.8789 (mmt) cc_final: 0.8471 (tpp) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.0964 time to fit residues: 28.5788 Evaluate side-chains 156 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 0.0970 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 119 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 108 ASN A 210 HIS A 243 ASN A 349 GLN ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.104558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.075417 restraints weight = 42943.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.076968 restraints weight = 30600.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.078132 restraints weight = 24523.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.078810 restraints weight = 21143.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.079339 restraints weight = 19276.718| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 1.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11824 Z= 0.141 Angle : 0.695 11.046 16057 Z= 0.350 Chirality : 0.044 0.161 1888 Planarity : 0.005 0.072 2103 Dihedral : 4.703 41.188 1701 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.96 % Favored : 93.53 % Rotamer: Outliers : 0.17 % Allowed : 0.69 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.21), residues: 1576 helix: 0.49 (0.21), residues: 697 sheet: -0.78 (0.38), residues: 185 loop : -1.74 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 497 TYR 0.038 0.002 TYR C 351 PHE 0.045 0.002 PHE C 655 TRP 0.033 0.002 TRP A 321 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00317 (11824) covalent geometry : angle 0.69472 (16057) hydrogen bonds : bond 0.03585 ( 543) hydrogen bonds : angle 4.87730 ( 1665) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7524 (t0) cc_final: 0.7221 (t0) REVERT: A 84 THR cc_start: 0.9009 (t) cc_final: 0.8782 (p) REVERT: A 114 MET cc_start: 0.8930 (mmp) cc_final: 0.8555 (mmm) REVERT: A 315 MET cc_start: 0.7880 (pmm) cc_final: 0.7475 (ppp) REVERT: A 341 ASP cc_start: 0.8404 (p0) cc_final: 0.7734 (p0) REVERT: A 382 ASN cc_start: 0.8360 (m-40) cc_final: 0.7860 (m110) REVERT: A 392 HIS cc_start: 0.8048 (t70) cc_final: 0.7472 (t70) REVERT: A 401 MET cc_start: 0.8771 (ptm) cc_final: 0.8247 (ptp) REVERT: B 66 GLN cc_start: 0.7836 (pm20) cc_final: 0.7504 (pp30) REVERT: B 75 ASN cc_start: 0.7328 (t0) cc_final: 0.6367 (p0) REVERT: B 78 ARG cc_start: 0.8347 (tpp-160) cc_final: 0.7474 (tpp-160) REVERT: B 79 GLU cc_start: 0.8001 (mp0) cc_final: 0.7557 (mp0) REVERT: B 113 LEU cc_start: 0.8866 (tp) cc_final: 0.8529 (mm) REVERT: B 223 LYS cc_start: 0.8528 (pttm) cc_final: 0.8287 (ttpp) REVERT: B 333 THR cc_start: 0.7732 (m) cc_final: 0.7301 (p) REVERT: C 28 MET cc_start: 0.7625 (mmp) cc_final: 0.7235 (mmp) REVERT: C 406 MET cc_start: 0.8772 (mmt) cc_final: 0.8456 (tpp) REVERT: C 552 GLU cc_start: 0.6560 (mp0) cc_final: 0.5842 (mp0) REVERT: C 646 ASP cc_start: 0.6548 (t0) cc_final: 0.6269 (t70) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.0960 time to fit residues: 27.9841 Evaluate side-chains 152 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 93 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 131 optimal weight: 0.0870 chunk 110 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 190 GLN A 210 HIS A 243 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.104786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.075533 restraints weight = 44565.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.077188 restraints weight = 31733.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.078229 restraints weight = 25266.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.079404 restraints weight = 21921.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.079873 restraints weight = 19696.949| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 1.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11824 Z= 0.128 Angle : 0.683 11.293 16057 Z= 0.342 Chirality : 0.044 0.167 1888 Planarity : 0.005 0.075 2103 Dihedral : 4.646 39.723 1701 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.71 % Favored : 93.78 % Rotamer: Outliers : 0.09 % Allowed : 0.60 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.22), residues: 1576 helix: 0.42 (0.20), residues: 713 sheet: -0.77 (0.38), residues: 191 loop : -1.72 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 410 TYR 0.019 0.002 TYR A 93 PHE 0.027 0.002 PHE A 362 TRP 0.022 0.002 TRP A 321 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00285 (11824) covalent geometry : angle 0.68286 (16057) hydrogen bonds : bond 0.03475 ( 543) hydrogen bonds : angle 4.76202 ( 1665) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7554 (t0) cc_final: 0.6609 (p0) REVERT: A 84 THR cc_start: 0.8909 (t) cc_final: 0.8709 (p) REVERT: A 114 MET cc_start: 0.8931 (mmp) cc_final: 0.8569 (mmm) REVERT: A 285 MET cc_start: 0.7611 (tmm) cc_final: 0.7395 (tmm) REVERT: A 315 MET cc_start: 0.7919 (pmm) cc_final: 0.7429 (ppp) REVERT: A 321 TRP cc_start: 0.7365 (m100) cc_final: 0.7103 (m100) REVERT: A 341 ASP cc_start: 0.8332 (p0) cc_final: 0.7588 (p0) REVERT: A 382 ASN cc_start: 0.8481 (m-40) cc_final: 0.8012 (m110) REVERT: A 392 HIS cc_start: 0.7954 (t70) cc_final: 0.7447 (t70) REVERT: A 401 MET cc_start: 0.8776 (ptm) cc_final: 0.8145 (ptp) REVERT: B 66 GLN cc_start: 0.7739 (pm20) cc_final: 0.7509 (pp30) REVERT: B 75 ASN cc_start: 0.7301 (t0) cc_final: 0.6428 (p0) REVERT: B 78 ARG cc_start: 0.8436 (tpp-160) cc_final: 0.7846 (tpp-160) REVERT: B 79 GLU cc_start: 0.7919 (mp0) cc_final: 0.7537 (mp0) REVERT: B 113 LEU cc_start: 0.8878 (tp) cc_final: 0.8581 (mm) REVERT: B 191 MET cc_start: 0.8744 (mtt) cc_final: 0.8039 (mtt) REVERT: B 223 LYS cc_start: 0.8514 (pttm) cc_final: 0.8251 (tptp) REVERT: B 333 THR cc_start: 0.7842 (m) cc_final: 0.7403 (p) REVERT: B 351 LEU cc_start: 0.9032 (mm) cc_final: 0.8628 (mm) REVERT: B 354 ILE cc_start: 0.9191 (pt) cc_final: 0.8817 (tt) REVERT: C 28 MET cc_start: 0.7627 (mmp) cc_final: 0.7247 (mmp) REVERT: C 65 PHE cc_start: 0.6570 (p90) cc_final: 0.6330 (p90) REVERT: C 512 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8398 (tm-30) REVERT: C 552 GLU cc_start: 0.6765 (mp0) cc_final: 0.6054 (mp0) REVERT: C 646 ASP cc_start: 0.6672 (t0) cc_final: 0.6288 (t70) REVERT: C 655 PHE cc_start: 0.7314 (t80) cc_final: 0.7085 (t80) REVERT: C 656 PRO cc_start: 0.9219 (Cg_exo) cc_final: 0.8551 (Cg_endo) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.0936 time to fit residues: 27.1825 Evaluate side-chains 156 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 27 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 190 GLN A 202 GLN A 243 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN C 446 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.099587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.070459 restraints weight = 45136.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.072014 restraints weight = 32026.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.073088 restraints weight = 25499.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073949 restraints weight = 21992.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.074306 restraints weight = 19908.739| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 1.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11824 Z= 0.208 Angle : 0.780 12.333 16057 Z= 0.401 Chirality : 0.048 0.256 1888 Planarity : 0.006 0.074 2103 Dihedral : 5.170 37.752 1701 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.80 % Favored : 91.75 % Rotamer: Outliers : 0.17 % Allowed : 0.86 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.21), residues: 1576 helix: 0.05 (0.20), residues: 711 sheet: -0.98 (0.38), residues: 193 loop : -1.70 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 262 TYR 0.026 0.002 TYR A 93 PHE 0.035 0.003 PHE B 64 TRP 0.023 0.002 TRP A 217 HIS 0.004 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00470 (11824) covalent geometry : angle 0.78015 (16057) hydrogen bonds : bond 0.04293 ( 543) hydrogen bonds : angle 5.22020 ( 1665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2212.13 seconds wall clock time: 39 minutes 9.16 seconds (2349.16 seconds total)