Starting phenix.real_space_refine on Tue Dec 31 13:48:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8brj_16217/12_2024/8brj_16217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8brj_16217/12_2024/8brj_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_16217/12_2024/8brj_16217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8brj_16217/12_2024/8brj_16217.map" model { file = "/net/cci-nas-00/data/ceres_data/8brj_16217/12_2024/8brj_16217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8brj_16217/12_2024/8brj_16217.cif" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} 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, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 9.66, per 1000 atoms: 0.83 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: 2.79 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.48 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: 4.12 Time building geometry restraints manager: 3.25 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: 10.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 31.670 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.410 ------------------------------------------------------------------------------- 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= 0.184 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP B 217 HIS 0.003 0.001 HIS B 407 PHE 0.012 0.001 PHE C 655 TYR 0.014 0.001 TYR A 93 ARG 0.009 0.001 ARG B 400 *********************** 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 : 1.323 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: 0.2721 time to fit residues: 122.7110 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 : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 98 HIS ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS C 173 GLN ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 ASN ** C 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4910 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 11824 Z= 0.292 Angle : 0.776 14.321 16057 Z= 0.402 Chirality : 0.046 0.204 1888 Planarity : 0.006 0.063 2103 Dihedral : 5.281 65.956 1701 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.15 % Favored : 93.34 % Rotamer: Outliers : 0.69 % Allowed : 6.78 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1576 helix: 0.19 (0.19), residues: 685 sheet: -0.21 (0.41), residues: 149 loop : -1.57 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 353 HIS 0.014 0.002 HIS C 109 PHE 0.027 0.002 PHE C 655 TYR 0.018 0.002 TYR A 93 ARG 0.005 0.001 ARG B 410 *********************** 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 247 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 239 time to evaluate : 1.353 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: A 22 ARG cc_start: 0.4251 (ttp80) cc_final: 0.3924 (ptm-80) REVERT: A 23 THR cc_start: 0.4816 (m) cc_final: 0.4575 (p) REVERT: A 40 LEU cc_start: 0.5983 (mt) cc_final: 0.5119 (mt) REVERT: A 108 ASN cc_start: 0.7547 (m-40) cc_final: 0.7012 (t0) REVERT: A 113 LEU cc_start: 0.8873 (tt) cc_final: 0.8656 (mp) REVERT: A 114 MET cc_start: 0.8259 (mmp) cc_final: 0.7836 (mmm) REVERT: A 118 ILE cc_start: 0.5656 (mm) cc_final: 0.5184 (mm) REVERT: A 291 LYS cc_start: 0.8806 (tmtt) cc_final: 0.8377 (pttm) REVERT: A 314 ASP cc_start: 0.7294 (p0) cc_final: 0.6986 (t0) REVERT: A 315 MET cc_start: 0.5249 (pmm) cc_final: 0.4600 (ppp) REVERT: A 321 TRP cc_start: 0.7702 (m100) cc_final: 0.7420 (m100) REVERT: A 362 PHE cc_start: 0.8151 (t80) cc_final: 0.7948 (t80) REVERT: B 9 THR cc_start: 0.6127 (t) cc_final: 0.5905 (t) REVERT: B 35 ILE cc_start: 0.6375 (pt) cc_final: 0.5788 (pt) REVERT: B 314 ASP cc_start: 0.6700 (m-30) cc_final: 0.5937 (m-30) REVERT: B 341 ASP cc_start: 0.7247 (t70) cc_final: 0.6888 (t70) REVERT: B 349 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6526 (pp30) REVERT: B 401 MET cc_start: 0.7294 (ptp) cc_final: 0.6744 (ptp) REVERT: B 419 VAL cc_start: 0.7231 (t) cc_final: 0.6916 (t) REVERT: C 73 MET cc_start: 0.9311 (mmp) cc_final: 0.8971 (ptt) REVERT: C 98 HIS cc_start: 0.6929 (t-90) cc_final: 0.6310 (t-90) REVERT: C 135 VAL cc_start: 0.6127 (p) cc_final: 0.5883 (p) REVERT: C 140 GLU cc_start: 0.7870 (tp30) cc_final: 0.7663 (tp30) REVERT: C 285 LEU cc_start: 0.7610 (mt) cc_final: 0.7401 (mt) REVERT: C 319 MET cc_start: 0.8237 (ptt) cc_final: 0.7819 (tpt) REVERT: C 643 ARG cc_start: 0.6170 (ppt170) cc_final: 0.4602 (mmt-90) outliers start: 8 outliers final: 1 residues processed: 243 average time/residue: 0.2542 time to fit residues: 86.7183 Evaluate side-chains 184 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 142 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 114 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN B 108 ASN B 343 HIS B 349 GLN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS C 373 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4991 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11824 Z= 0.214 Angle : 0.679 10.661 16057 Z= 0.346 Chirality : 0.044 0.178 1888 Planarity : 0.005 0.053 2103 Dihedral : 5.020 61.342 1701 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.71 % Favored : 93.78 % Rotamer: Outliers : 0.17 % Allowed : 5.32 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1576 helix: 0.20 (0.19), residues: 688 sheet: -0.36 (0.39), residues: 165 loop : -1.57 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 706 HIS 0.006 0.001 HIS B 392 PHE 0.016 0.002 PHE C 655 TYR 0.020 0.002 TYR C 325 ARG 0.011 0.001 ARG A 400 *********************** 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 233 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 231 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 THR cc_start: 0.5298 (m) cc_final: 0.4992 (p) REVERT: A 113 LEU cc_start: 0.8812 (tt) cc_final: 0.8584 (mp) REVERT: A 114 MET cc_start: 0.8228 (mmp) cc_final: 0.7957 (mmm) REVERT: A 118 ILE cc_start: 0.5721 (mm) cc_final: 0.5260 (mm) REVERT: A 243 ASN cc_start: 0.3482 (t0) cc_final: 0.2408 (t0) REVERT: A 264 HIS cc_start: 0.7289 (m90) cc_final: 0.7089 (m90) REVERT: A 291 LYS cc_start: 0.8900 (tmtt) cc_final: 0.8473 (ptpp) REVERT: A 314 ASP cc_start: 0.7565 (p0) cc_final: 0.6904 (t0) REVERT: A 315 MET cc_start: 0.5214 (pmm) cc_final: 0.4526 (ppp) REVERT: A 341 ASP cc_start: 0.7144 (p0) cc_final: 0.6488 (p0) REVERT: A 362 PHE cc_start: 0.8114 (t80) cc_final: 0.7897 (t80) REVERT: A 382 ASN cc_start: 0.7166 (m-40) cc_final: 0.6901 (m-40) REVERT: A 392 HIS cc_start: 0.7811 (t70) cc_final: 0.7547 (t70) REVERT: B 9 THR cc_start: 0.6275 (t) cc_final: 0.5932 (t) REVERT: B 30 THR cc_start: 0.5783 (p) cc_final: 0.5450 (p) REVERT: B 59 ILE cc_start: 0.8597 (mm) cc_final: 0.8371 (mm) REVERT: B 70 MET cc_start: 0.7512 (tmm) cc_final: 0.7287 (tmm) REVERT: B 80 ILE cc_start: 0.6394 (pt) cc_final: 0.6086 (pt) REVERT: B 86 MET cc_start: 0.2001 (tpt) cc_final: 0.1574 (tpt) REVERT: B 128 SER cc_start: -0.3122 (t) cc_final: -0.4734 (p) REVERT: B 277 ASP cc_start: 0.3272 (m-30) cc_final: 0.2591 (p0) REVERT: B 306 PHE cc_start: -0.0067 (m-80) cc_final: -0.0535 (m-80) REVERT: B 349 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6505 (pp30) REVERT: B 433 LEU cc_start: 0.7909 (mt) cc_final: 0.7686 (mp) REVERT: C 73 MET cc_start: 0.9280 (mmp) cc_final: 0.8939 (ptt) REVERT: C 285 LEU cc_start: 0.7476 (mt) cc_final: 0.7264 (mt) REVERT: C 319 MET cc_start: 0.8202 (ptt) cc_final: 0.7763 (tpt) REVERT: C 325 TYR cc_start: 0.6663 (t80) cc_final: 0.6427 (t80) REVERT: C 355 GLN cc_start: 0.7165 (mm110) cc_final: 0.6837 (mp10) REVERT: C 411 GLU cc_start: 0.7679 (tp30) cc_final: 0.6906 (mt-10) REVERT: C 643 ARG cc_start: 0.6627 (ppt170) cc_final: 0.4776 (tpp80) outliers start: 2 outliers final: 0 residues processed: 233 average time/residue: 0.2491 time to fit residues: 82.9935 Evaluate side-chains 190 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN C 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5208 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11824 Z= 0.266 Angle : 0.771 16.883 16057 Z= 0.385 Chirality : 0.046 0.195 1888 Planarity : 0.006 0.075 2103 Dihedral : 5.151 75.382 1701 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.96 % Favored : 93.53 % Rotamer: Outliers : 0.17 % Allowed : 5.32 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1576 helix: 0.24 (0.19), residues: 693 sheet: -0.59 (0.37), residues: 188 loop : -1.64 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 321 HIS 0.007 0.001 HIS C 109 PHE 0.019 0.002 PHE C 65 TYR 0.016 0.002 TYR A 93 ARG 0.014 0.001 ARG C 286 *********************** 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 229 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 THR cc_start: 0.6337 (m) cc_final: 0.6031 (p) REVERT: A 63 VAL cc_start: 0.6448 (t) cc_final: 0.6167 (m) REVERT: A 113 LEU cc_start: 0.8930 (tt) cc_final: 0.8657 (mp) REVERT: A 114 MET cc_start: 0.8303 (mmp) cc_final: 0.7977 (mmm) REVERT: A 118 ILE cc_start: 0.6161 (mm) cc_final: 0.5772 (mm) REVERT: A 264 HIS cc_start: 0.7373 (m90) cc_final: 0.7140 (m90) REVERT: A 291 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8695 (ptpt) REVERT: A 315 MET cc_start: 0.5453 (pmm) cc_final: 0.4848 (ppp) REVERT: A 341 ASP cc_start: 0.6923 (p0) cc_final: 0.6194 (p0) REVERT: A 362 PHE cc_start: 0.8179 (t80) cc_final: 0.7826 (t80) REVERT: A 382 ASN cc_start: 0.7726 (m-40) cc_final: 0.7488 (m-40) REVERT: A 422 CYS cc_start: 0.7246 (p) cc_final: 0.7023 (p) REVERT: A 431 MET cc_start: 0.8016 (tmm) cc_final: 0.7812 (tmm) REVERT: B 35 ILE cc_start: 0.5974 (pt) cc_final: 0.5504 (pt) REVERT: B 40 LEU cc_start: 0.6973 (mt) cc_final: 0.6436 (mt) REVERT: B 59 ILE cc_start: 0.8647 (mm) cc_final: 0.8388 (tp) REVERT: B 70 MET cc_start: 0.7638 (tmm) cc_final: 0.7416 (tmm) REVERT: B 128 SER cc_start: -0.2632 (t) cc_final: -0.3398 (p) REVERT: B 191 MET cc_start: 0.7251 (mmt) cc_final: 0.7036 (mmt) REVERT: B 223 LYS cc_start: 0.7792 (ttpp) cc_final: 0.7518 (tptp) REVERT: B 306 PHE cc_start: 0.1386 (m-80) cc_final: 0.1027 (m-80) REVERT: B 341 ASP cc_start: 0.6826 (t70) cc_final: 0.6595 (m-30) REVERT: B 350 THR cc_start: 0.9294 (m) cc_final: 0.9079 (p) REVERT: C 73 MET cc_start: 0.9279 (mmp) cc_final: 0.8947 (ptt) REVERT: C 248 GLU cc_start: 0.7849 (pm20) cc_final: 0.7250 (tp30) REVERT: C 319 MET cc_start: 0.8221 (ptt) cc_final: 0.7727 (tpt) REVERT: C 323 ILE cc_start: 0.7364 (mp) cc_final: 0.7136 (mm) REVERT: C 355 GLN cc_start: 0.7402 (mm110) cc_final: 0.7138 (mp10) REVERT: C 411 GLU cc_start: 0.8147 (tp30) cc_final: 0.7332 (mt-10) outliers start: 2 outliers final: 0 residues processed: 229 average time/residue: 0.2241 time to fit residues: 74.6301 Evaluate side-chains 174 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 343 HIS ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 0.7511 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= 0.233 Angle : 0.729 13.254 16057 Z= 0.365 Chirality : 0.045 0.179 1888 Planarity : 0.005 0.050 2103 Dihedral : 5.062 81.577 1701 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.03 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1576 helix: 0.36 (0.20), residues: 689 sheet: -0.52 (0.39), residues: 180 loop : -1.60 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 321 HIS 0.003 0.001 HIS A 210 PHE 0.026 0.002 PHE B 32 TYR 0.022 0.002 TYR B 300 ARG 0.007 0.001 ARG B 27 *********************** 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 227 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 THR cc_start: 0.6701 (m) cc_final: 0.6415 (p) REVERT: A 113 LEU cc_start: 0.8998 (tt) cc_final: 0.8743 (mp) REVERT: A 114 MET cc_start: 0.8325 (mmp) cc_final: 0.7860 (mmm) REVERT: A 264 HIS cc_start: 0.8260 (m90) cc_final: 0.7827 (m90) REVERT: A 291 LYS cc_start: 0.9156 (tmtt) cc_final: 0.8861 (ptpt) REVERT: A 315 MET cc_start: 0.6019 (pmm) cc_final: 0.5173 (ppp) REVERT: A 341 ASP cc_start: 0.6764 (p0) cc_final: 0.6415 (p0) REVERT: B 35 ILE cc_start: 0.6568 (pt) cc_final: 0.6036 (pt) REVERT: B 59 ILE cc_start: 0.8600 (mm) cc_final: 0.8266 (tp) REVERT: B 70 MET cc_start: 0.7677 (tmm) cc_final: 0.7458 (tmm) REVERT: B 223 LYS cc_start: 0.7940 (pttp) cc_final: 0.7630 (tptp) REVERT: B 277 ASP cc_start: 0.2538 (m-30) cc_final: 0.1811 (p0) REVERT: B 306 PHE cc_start: 0.2337 (m-80) cc_final: 0.1288 (m-80) REVERT: B 315 MET cc_start: 0.5006 (ttt) cc_final: 0.4498 (tpp) REVERT: B 339 LEU cc_start: 0.8460 (tt) cc_final: 0.7772 (tt) REVERT: B 344 GLU cc_start: 0.6009 (mt-10) cc_final: 0.5506 (mp0) REVERT: B 388 ILE cc_start: 0.6517 (mm) cc_final: 0.5497 (mm) REVERT: C 43 ILE cc_start: 0.8251 (tp) cc_final: 0.7974 (tt) REVERT: C 73 MET cc_start: 0.9257 (mmp) cc_final: 0.8949 (ptt) REVERT: C 135 VAL cc_start: 0.6330 (p) cc_final: 0.6009 (p) REVERT: C 188 VAL cc_start: 0.2995 (m) cc_final: 0.2650 (m) REVERT: C 248 GLU cc_start: 0.7836 (pm20) cc_final: 0.7161 (tp30) REVERT: C 252 GLU cc_start: 0.8101 (mp0) cc_final: 0.7875 (mp0) REVERT: C 319 MET cc_start: 0.8247 (ptt) cc_final: 0.7654 (tpt) REVERT: C 406 MET cc_start: 0.8572 (mmp) cc_final: 0.8355 (mmm) REVERT: C 411 GLU cc_start: 0.8401 (tp30) cc_final: 0.7540 (mt-10) REVERT: C 460 ILE cc_start: 0.5034 (pt) cc_final: 0.4752 (pt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2422 time to fit residues: 79.3397 Evaluate side-chains 165 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 0.0370 chunk 79 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 210 HIS ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 343 HIS ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5398 moved from start: 0.8149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11824 Z= 0.200 Angle : 0.669 10.886 16057 Z= 0.336 Chirality : 0.044 0.163 1888 Planarity : 0.005 0.053 2103 Dihedral : 4.987 84.599 1701 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.65 % Favored : 93.85 % Rotamer: Outliers : 0.09 % Allowed : 2.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1576 helix: 0.40 (0.20), residues: 693 sheet: -0.61 (0.38), residues: 190 loop : -1.49 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 321 HIS 0.005 0.001 HIS A 210 PHE 0.026 0.002 PHE C 65 TYR 0.018 0.002 TYR A 93 ARG 0.008 0.000 ARG C 249 *********************** 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 221 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: A 23 THR cc_start: 0.6798 (m) cc_final: 0.6523 (p) REVERT: A 113 LEU cc_start: 0.9022 (tt) cc_final: 0.8779 (mp) REVERT: A 114 MET cc_start: 0.8398 (mmp) cc_final: 0.8031 (mmm) REVERT: A 291 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8901 (ptpt) REVERT: A 315 MET cc_start: 0.5912 (pmm) cc_final: 0.4948 (ppp) REVERT: A 341 ASP cc_start: 0.6701 (p0) cc_final: 0.6264 (p0) REVERT: A 420 THR cc_start: 0.7393 (p) cc_final: 0.6983 (p) REVERT: B 35 ILE cc_start: 0.6236 (pt) cc_final: 0.5531 (pt) REVERT: B 40 LEU cc_start: 0.7801 (mt) cc_final: 0.7335 (mt) REVERT: B 70 MET cc_start: 0.7743 (tmm) cc_final: 0.7530 (tmm) REVERT: B 79 GLU cc_start: 0.7552 (mp0) cc_final: 0.7317 (mp0) REVERT: B 114 MET cc_start: 0.8049 (ptm) cc_final: 0.7831 (ptm) REVERT: B 223 LYS cc_start: 0.8058 (pttp) cc_final: 0.7727 (tptp) REVERT: B 306 PHE cc_start: 0.1298 (m-80) cc_final: 0.1024 (m-80) REVERT: B 315 MET cc_start: 0.4952 (ttt) cc_final: 0.4630 (tpp) REVERT: B 339 LEU cc_start: 0.8022 (tt) cc_final: 0.7604 (tt) REVERT: B 344 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5697 (mp0) REVERT: C 43 ILE cc_start: 0.8293 (tp) cc_final: 0.8014 (tt) REVERT: C 73 MET cc_start: 0.9263 (mmp) cc_final: 0.8937 (ptt) REVERT: C 188 VAL cc_start: 0.3817 (m) cc_final: 0.3571 (m) REVERT: C 248 GLU cc_start: 0.7827 (pm20) cc_final: 0.7536 (pm20) REVERT: C 252 GLU cc_start: 0.8026 (mp0) cc_final: 0.7783 (mp0) REVERT: C 319 MET cc_start: 0.8437 (ptt) cc_final: 0.7807 (tpp) REVERT: C 411 GLU cc_start: 0.8475 (tp30) cc_final: 0.7598 (mt-10) REVERT: C 473 THR cc_start: 0.7900 (m) cc_final: 0.7630 (p) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.2349 time to fit residues: 75.6009 Evaluate side-chains 161 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN C 49 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN C 347 HIS ** C 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 moved from start: 1.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 11824 Z= 0.445 Angle : 0.971 13.102 16057 Z= 0.505 Chirality : 0.054 0.356 1888 Planarity : 0.007 0.058 2103 Dihedral : 6.166 79.194 1701 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.57 % Favored : 90.93 % Rotamer: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.20), residues: 1576 helix: -0.79 (0.18), residues: 705 sheet: -1.20 (0.37), residues: 199 loop : -1.81 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 321 HIS 0.011 0.002 HIS C 347 PHE 0.039 0.003 PHE C 65 TYR 0.035 0.004 TYR A 93 ARG 0.019 0.001 ARG C 508 *********************** 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 205 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8964 (ttt) cc_final: 0.8753 (mmt) REVERT: A 291 LYS cc_start: 0.9325 (tmtt) cc_final: 0.9109 (ptpt) REVERT: A 315 MET cc_start: 0.5625 (pmm) cc_final: 0.4524 (ptm) REVERT: A 341 ASP cc_start: 0.6988 (p0) cc_final: 0.5879 (p0) REVERT: A 362 PHE cc_start: 0.7948 (t80) cc_final: 0.7679 (t80) REVERT: A 401 MET cc_start: 0.8568 (ptp) cc_final: 0.8136 (ptp) REVERT: A 420 THR cc_start: 0.7276 (p) cc_final: 0.6877 (p) REVERT: B 315 MET cc_start: 0.4086 (ttt) cc_final: 0.3725 (tpp) REVERT: B 344 GLU cc_start: 0.6618 (mt-10) cc_final: 0.6050 (tt0) REVERT: B 393 PRO cc_start: 0.7690 (Cg_exo) cc_final: 0.7395 (Cg_exo) REVERT: C 73 MET cc_start: 0.9181 (mmp) cc_final: 0.8950 (ptt) REVERT: C 128 CYS cc_start: 0.7629 (p) cc_final: 0.7348 (p) REVERT: C 167 MET cc_start: 0.8406 (mmp) cc_final: 0.8203 (mmm) REVERT: C 319 MET cc_start: 0.8489 (ptt) cc_final: 0.7705 (tpp) REVERT: C 374 LEU cc_start: 0.7554 (pp) cc_final: 0.7233 (mt) REVERT: C 398 GLU cc_start: 0.8338 (pm20) cc_final: 0.7542 (mt-10) REVERT: C 406 MET cc_start: 0.8485 (mmp) cc_final: 0.7983 (mmt) REVERT: C 454 MET cc_start: 0.7433 (tpt) cc_final: 0.6735 (pmm) REVERT: C 456 LEU cc_start: 0.8711 (tp) cc_final: 0.8211 (tp) REVERT: C 655 PHE cc_start: 0.7268 (t80) cc_final: 0.6750 (t80) REVERT: C 656 PRO cc_start: 0.5129 (Cg_exo) cc_final: 0.4435 (Cg_endo) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.2313 time to fit residues: 69.8062 Evaluate side-chains 145 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 0.0040 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN A 243 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 1.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11824 Z= 0.258 Angle : 0.746 11.957 16057 Z= 0.383 Chirality : 0.047 0.212 1888 Planarity : 0.006 0.065 2103 Dihedral : 5.510 76.392 1701 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.15 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.21), residues: 1576 helix: -0.11 (0.19), residues: 708 sheet: -1.11 (0.38), residues: 201 loop : -1.73 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 321 HIS 0.004 0.001 HIS B 33 PHE 0.021 0.002 PHE C 65 TYR 0.028 0.002 TYR A 93 ARG 0.013 0.001 ARG A 142 *********************** 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 196 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8970 (ttt) cc_final: 0.8728 (mmt) REVERT: A 226 VAL cc_start: 0.7765 (t) cc_final: 0.6303 (m) REVERT: A 315 MET cc_start: 0.6332 (pmm) cc_final: 0.5502 (ppp) REVERT: A 341 ASP cc_start: 0.7237 (p0) cc_final: 0.6558 (p0) REVERT: A 342 MET cc_start: 0.7963 (tpp) cc_final: 0.7668 (mmm) REVERT: A 420 THR cc_start: 0.7451 (p) cc_final: 0.7054 (t) REVERT: B 32 PHE cc_start: 0.3165 (m-80) cc_final: 0.2952 (m-80) REVERT: B 70 MET cc_start: 0.7737 (tmm) cc_final: 0.7517 (tmm) REVERT: B 113 LEU cc_start: 0.9166 (tp) cc_final: 0.8925 (mm) REVERT: B 118 ILE cc_start: 0.5049 (pt) cc_final: 0.3886 (pt) REVERT: B 315 MET cc_start: 0.4160 (ttt) cc_final: 0.3705 (tpp) REVERT: B 393 PRO cc_start: 0.7248 (Cg_exo) cc_final: 0.6927 (Cg_exo) REVERT: B 419 VAL cc_start: 0.8008 (t) cc_final: 0.7748 (p) REVERT: C 73 MET cc_start: 0.9132 (mmp) cc_final: 0.8888 (ptt) REVERT: C 319 MET cc_start: 0.8491 (ptt) cc_final: 0.7624 (tpp) REVERT: C 398 GLU cc_start: 0.8412 (pm20) cc_final: 0.7530 (mt-10) REVERT: C 406 MET cc_start: 0.8339 (mmp) cc_final: 0.8024 (mmt) REVERT: C 454 MET cc_start: 0.7300 (tpt) cc_final: 0.6857 (pmm) REVERT: C 456 LEU cc_start: 0.8849 (tp) cc_final: 0.8183 (tp) REVERT: C 533 ILE cc_start: 0.6220 (pt) cc_final: 0.5954 (pt) REVERT: C 655 PHE cc_start: 0.7173 (t80) cc_final: 0.6545 (t80) REVERT: C 656 PRO cc_start: 0.5680 (Cg_exo) cc_final: 0.4946 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2294 time to fit residues: 66.3733 Evaluate side-chains 141 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 127 optimal weight: 0.0870 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 243 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 1.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11824 Z= 0.270 Angle : 0.757 11.980 16057 Z= 0.386 Chirality : 0.047 0.181 1888 Planarity : 0.005 0.067 2103 Dihedral : 5.161 47.824 1701 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.92 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1576 helix: 0.02 (0.20), residues: 707 sheet: -0.93 (0.38), residues: 195 loop : -1.79 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 321 HIS 0.004 0.001 HIS C 518 PHE 0.020 0.002 PHE C 583 TYR 0.025 0.002 TYR A 93 ARG 0.006 0.001 ARG B 78 *********************** 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 176 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8889 (ttt) cc_final: 0.8680 (mmt) REVERT: A 315 MET cc_start: 0.6338 (pmm) cc_final: 0.5411 (ppp) REVERT: A 341 ASP cc_start: 0.7306 (p0) cc_final: 0.6574 (p0) REVERT: A 342 MET cc_start: 0.7925 (tpp) cc_final: 0.7678 (mmm) REVERT: A 420 THR cc_start: 0.7523 (p) cc_final: 0.7205 (t) REVERT: B 47 GLU cc_start: 0.8339 (tp30) cc_final: 0.8125 (mm-30) REVERT: B 113 LEU cc_start: 0.9164 (tp) cc_final: 0.8912 (mm) REVERT: B 118 ILE cc_start: 0.5065 (pt) cc_final: 0.3894 (pt) REVERT: B 285 MET cc_start: 0.6851 (tmm) cc_final: 0.6649 (ppp) REVERT: B 304 TYR cc_start: 0.6801 (p90) cc_final: 0.6591 (p90) REVERT: B 315 MET cc_start: 0.4190 (ttt) cc_final: 0.3679 (tpp) REVERT: C 73 MET cc_start: 0.9128 (mmp) cc_final: 0.8878 (ptt) REVERT: C 319 MET cc_start: 0.8406 (ptt) cc_final: 0.7536 (tpp) REVERT: C 398 GLU cc_start: 0.8439 (pm20) cc_final: 0.7496 (mt-10) REVERT: C 406 MET cc_start: 0.8436 (mmp) cc_final: 0.8083 (mmt) REVERT: C 454 MET cc_start: 0.7814 (tpt) cc_final: 0.7018 (ptp) REVERT: C 456 LEU cc_start: 0.8719 (tp) cc_final: 0.8162 (tp) REVERT: C 655 PHE cc_start: 0.6889 (t80) cc_final: 0.6230 (t80) REVERT: C 656 PRO cc_start: 0.5799 (Cg_exo) cc_final: 0.5135 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2467 time to fit residues: 62.0693 Evaluate side-chains 135 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 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 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 243 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 1.3222 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= 0.220 Angle : 0.721 11.796 16057 Z= 0.366 Chirality : 0.046 0.177 1888 Planarity : 0.005 0.078 2103 Dihedral : 5.055 55.170 1701 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.39 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1576 helix: 0.19 (0.20), residues: 697 sheet: -0.95 (0.39), residues: 192 loop : -1.69 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 321 HIS 0.006 0.001 HIS C 435 PHE 0.035 0.002 PHE A 362 TYR 0.025 0.002 TYR A 93 ARG 0.006 0.000 ARG C 249 ********************** 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 177 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 THR cc_start: 0.7399 (m) cc_final: 0.7154 (p) REVERT: A 70 MET cc_start: -0.3862 (ttp) cc_final: -0.4162 (ttp) REVERT: A 111 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8669 (tt0) REVERT: A 257 ARG cc_start: 0.8700 (ttp-110) cc_final: 0.8482 (mtm110) REVERT: A 262 ARG cc_start: 0.8516 (tpp-160) cc_final: 0.8199 (mmm160) REVERT: A 315 MET cc_start: 0.6311 (pmm) cc_final: 0.5409 (ppp) REVERT: A 341 ASP cc_start: 0.7212 (p0) cc_final: 0.6567 (p0) REVERT: A 420 THR cc_start: 0.7645 (p) cc_final: 0.7257 (p) REVERT: B 59 ILE cc_start: 0.8373 (mm) cc_final: 0.8080 (tp) REVERT: B 70 MET cc_start: 0.7918 (tmm) cc_final: 0.7689 (tmm) REVERT: B 113 LEU cc_start: 0.9109 (tp) cc_final: 0.8843 (mm) REVERT: B 118 ILE cc_start: 0.4940 (pt) cc_final: 0.3636 (pt) REVERT: B 219 ASP cc_start: 0.7551 (t0) cc_final: 0.6999 (m-30) REVERT: B 253 TYR cc_start: 0.6748 (m-10) cc_final: 0.6162 (m-10) REVERT: B 285 MET cc_start: 0.7110 (tmm) cc_final: 0.6894 (ppp) REVERT: B 315 MET cc_start: 0.3918 (ttt) cc_final: 0.3471 (tpp) REVERT: C 73 MET cc_start: 0.9105 (mmp) cc_final: 0.8817 (ptt) REVERT: C 319 MET cc_start: 0.8404 (ptt) cc_final: 0.7523 (tpp) REVERT: C 398 GLU cc_start: 0.8480 (pm20) cc_final: 0.7542 (mt-10) REVERT: C 406 MET cc_start: 0.8432 (mmp) cc_final: 0.8210 (tpp) REVERT: C 454 MET cc_start: 0.8011 (tpt) cc_final: 0.7564 (ptp) REVERT: C 655 PHE cc_start: 0.6771 (t80) cc_final: 0.6090 (t80) REVERT: C 656 PRO cc_start: 0.5783 (Cg_exo) cc_final: 0.5147 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2502 time to fit residues: 64.3914 Evaluate side-chains 144 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 114 optimal weight: 0.0670 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 50.0000 chunk 22 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 108 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS ** C 435 HIS ** 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 = 0.3743 r_free = 0.3743 target = 0.098195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.068900 restraints weight = 44148.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.070511 restraints weight = 31025.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.071756 restraints weight = 24608.868| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 1.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11824 Z= 0.280 Angle : 0.772 10.893 16057 Z= 0.392 Chirality : 0.048 0.328 1888 Planarity : 0.006 0.079 2103 Dihedral : 5.183 50.618 1701 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.36 % Favored : 92.20 % Rotamer: Outliers : 0.09 % Allowed : 0.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.21), residues: 1576 helix: 0.06 (0.20), residues: 707 sheet: -1.25 (0.37), residues: 196 loop : -1.70 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 217 HIS 0.005 0.001 HIS C 435 PHE 0.029 0.002 PHE A 394 TYR 0.030 0.002 TYR A 93 ARG 0.007 0.001 ARG C 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2652.85 seconds wall clock time: 50 minutes 19.44 seconds (3019.44 seconds total)