Starting phenix.real_space_refine on Sat Jun 14 05:51:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8brj_16217/06_2025/8brj_16217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8brj_16217/06_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_16217/06_2025/8brj_16217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8brj_16217/06_2025/8brj_16217.map" model { file = "/net/cci-nas-00/data/ceres_data/8brj_16217/06_2025/8brj_16217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8brj_16217/06_2025/8brj_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.80, per 1000 atoms: 0.67 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: 2.88 Conformation dependent library (CDL) restraints added in 1.6 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: 1.49 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: 3.88 Time building geometry restraints manager: 3.30 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.140 Find NCS groups from input model: 0.480 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.210 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.27694 ( 543) hydrogen bonds : angle 8.62592 ( 1665) covalent geometry : bond 0.00274 (11824) covalent geometry : angle 0.64474 (16057) *********************** 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 : 1.373 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: 0.2639 time to fit residues: 119.0663 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 : 1.255 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.113265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.086955 restraints weight = 43031.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.088786 restraints weight = 30890.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.090226 restraints weight = 24524.984| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 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= 0.203 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 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 543) hydrogen bonds : angle 5.94612 ( 1665) covalent geometry : bond 0.00434 (11824) covalent geometry : angle 0.77567 (16057) *********************** 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 : 1.285 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 23 THR cc_start: 0.7390 (m) cc_final: 0.6856 (p) REVERT: A 91 ASP cc_start: 0.8424 (m-30) cc_final: 0.7874 (m-30) REVERT: A 291 LYS cc_start: 0.8832 (tmtt) cc_final: 0.8474 (pttm) REVERT: A 317 LEU cc_start: 0.8326 (mt) cc_final: 0.8040 (tp) REVERT: A 321 TRP cc_start: 0.6825 (m100) cc_final: 0.6587 (m100) REVERT: A 392 HIS cc_start: 0.8059 (t70) cc_final: 0.7615 (t70) REVERT: A 400 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7820 (tmm-80) REVERT: A 401 MET cc_start: 0.8268 (ptp) cc_final: 0.8024 (ptp) REVERT: B 108 ASN cc_start: 0.9012 (m-40) cc_final: 0.8398 (m-40) REVERT: B 314 ASP cc_start: 0.5789 (m-30) cc_final: 0.5207 (m-30) REVERT: B 401 MET cc_start: 0.6615 (ptp) cc_final: 0.6069 (ptp) REVERT: B 436 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7498 (mt-10) REVERT: C 135 VAL cc_start: 0.5340 (p) cc_final: 0.5110 (p) REVERT: C 264 SER cc_start: 0.7981 (m) cc_final: 0.7591 (p) REVERT: C 337 ILE cc_start: 0.6651 (mt) cc_final: 0.6423 (mt) REVERT: C 643 ARG cc_start: 0.5927 (ppt170) cc_final: 0.4565 (mmt-90) outliers start: 8 outliers final: 1 residues processed: 243 average time/residue: 0.2473 time to fit residues: 84.7016 Evaluate side-chains 181 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 72 optimal weight: 0.0980 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 0.0170 chunk 30 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 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 373 GLN ** 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 = 0.4057 r_free = 0.4057 target = 0.114224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.086555 restraints weight = 43340.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.088469 restraints weight = 31135.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.090070 restraints weight = 24616.043| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.4670 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= 0.141 Angle : 0.670 10.520 16057 Z= 0.341 Chirality : 0.044 0.181 1888 Planarity : 0.005 0.053 2103 Dihedral : 5.012 60.932 1701 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.77 % Favored : 93.72 % Rotamer: Outliers : 0.17 % Allowed : 5.41 % Favored : 94.42 % 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: 0.18 (0.19), residues: 688 sheet: -0.30 (0.39), residues: 163 loop : -1.55 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 706 HIS 0.006 0.001 HIS B 392 PHE 0.016 0.002 PHE A 362 TYR 0.021 0.002 TYR C 325 ARG 0.007 0.001 ARG A 411 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 543) hydrogen bonds : angle 5.43281 ( 1665) covalent geometry : bond 0.00304 (11824) covalent geometry : angle 0.67012 (16057) *********************** 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 235 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 1.297 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: 0.7665 (m) cc_final: 0.7132 (p) REVERT: A 59 ILE cc_start: 0.9203 (mm) cc_final: 0.8996 (pt) REVERT: A 114 MET cc_start: 0.8746 (mmp) cc_final: 0.8403 (mmm) REVERT: A 291 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8596 (ptpp) REVERT: A 315 MET cc_start: 0.8238 (ppp) cc_final: 0.7536 (ppp) REVERT: A 381 PHE cc_start: 0.8227 (t80) cc_final: 0.7710 (t80) REVERT: A 382 ASN cc_start: 0.7447 (m-40) cc_final: 0.6770 (m-40) REVERT: A 392 HIS cc_start: 0.8076 (t70) cc_final: 0.7436 (t70) REVERT: A 400 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7871 (tmm-80) REVERT: A 401 MET cc_start: 0.8440 (ptp) cc_final: 0.8208 (ptp) REVERT: B 30 THR cc_start: 0.7359 (p) cc_final: 0.7127 (p) REVERT: B 114 MET cc_start: 0.8182 (tmm) cc_final: 0.7764 (ptm) REVERT: B 342 MET cc_start: 0.7962 (ttp) cc_final: 0.7695 (ttp) REVERT: C 264 SER cc_start: 0.8038 (m) cc_final: 0.7676 (p) REVERT: C 643 ARG cc_start: 0.6295 (ppt170) cc_final: 0.4704 (tpp80) outliers start: 2 outliers final: 0 residues processed: 235 average time/residue: 0.2380 time to fit residues: 80.1603 Evaluate side-chains 179 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 110 optimal weight: 0.3980 chunk 124 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 B 349 GLN B 353 ASN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN C 373 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.110732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.082519 restraints weight = 42770.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.084295 restraints weight = 31171.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.085613 restraints weight = 24950.131| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 11824 Z= 0.193 Angle : 0.786 17.743 16057 Z= 0.397 Chirality : 0.047 0.223 1888 Planarity : 0.006 0.069 2103 Dihedral : 5.254 77.577 1701 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.35 % Favored : 93.15 % Rotamer: Outliers : 0.26 % Allowed : 6.09 % Favored : 93.65 % 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: -1.11 (0.21), residues: 1576 helix: 0.15 (0.19), residues: 690 sheet: -0.57 (0.38), residues: 181 loop : -1.65 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 353 HIS 0.008 0.001 HIS C 109 PHE 0.019 0.002 PHE C 658 TYR 0.016 0.002 TYR C 351 ARG 0.023 0.001 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 543) hydrogen bonds : angle 5.20115 ( 1665) covalent geometry : bond 0.00412 (11824) covalent geometry : angle 0.78567 (16057) *********************** 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 231 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 228 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ASP cc_start: 0.8249 (m-30) cc_final: 0.7990 (m-30) REVERT: A 114 MET cc_start: 0.8884 (mmp) cc_final: 0.8445 (mmm) REVERT: A 264 HIS cc_start: 0.7554 (m90) cc_final: 0.7274 (m90) REVERT: A 291 LYS cc_start: 0.9080 (tmtt) cc_final: 0.8877 (ptpt) REVERT: A 315 MET cc_start: 0.8410 (ppp) cc_final: 0.7728 (ppp) REVERT: A 334 MET cc_start: 0.7911 (tpt) cc_final: 0.7709 (tmm) REVERT: A 381 PHE cc_start: 0.8239 (t80) cc_final: 0.7859 (t80) REVERT: A 382 ASN cc_start: 0.7800 (m-40) cc_final: 0.7259 (m-40) REVERT: A 392 HIS cc_start: 0.8407 (t70) cc_final: 0.7546 (t70) REVERT: A 400 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7936 (tmm-80) REVERT: B 43 MET cc_start: 0.8025 (ptm) cc_final: 0.7651 (ptp) REVERT: B 102 SER cc_start: 0.8093 (m) cc_final: 0.7519 (t) REVERT: B 191 MET cc_start: 0.7471 (mmt) cc_final: 0.6909 (mmt) REVERT: B 223 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7671 (tptp) REVERT: B 234 TYR cc_start: 0.6438 (m-80) cc_final: 0.5360 (m-10) REVERT: B 388 ILE cc_start: 0.5340 (mm) cc_final: 0.4813 (mm) REVERT: B 436 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6318 (mm-30) REVERT: C 43 ILE cc_start: 0.7460 (tp) cc_final: 0.7160 (tt) REVERT: C 248 GLU cc_start: 0.6983 (pm20) cc_final: 0.6475 (tp30) REVERT: C 252 GLU cc_start: 0.8395 (mp0) cc_final: 0.7843 (mp0) outliers start: 3 outliers final: 0 residues processed: 230 average time/residue: 0.2251 time to fit residues: 75.3811 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 : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 147 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 210 HIS ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.111262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.082903 restraints weight = 42596.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.084703 restraints weight = 31073.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.085903 restraints weight = 24925.110| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.7301 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= 0.143 Angle : 0.683 12.080 16057 Z= 0.344 Chirality : 0.044 0.171 1888 Planarity : 0.005 0.050 2103 Dihedral : 5.070 80.976 1701 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.08 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % 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: -0.93 (0.21), residues: 1576 helix: 0.34 (0.20), residues: 687 sheet: -0.69 (0.37), residues: 192 loop : -1.54 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 HIS 0.005 0.001 HIS A 210 PHE 0.030 0.002 PHE C 65 TYR 0.015 0.002 TYR A 93 ARG 0.004 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 543) hydrogen bonds : angle 5.01020 ( 1665) covalent geometry : bond 0.00312 (11824) covalent geometry : angle 0.68316 (16057) *********************** 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 216 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8824 (mmp) cc_final: 0.8354 (mmm) REVERT: A 315 MET cc_start: 0.8210 (ppp) cc_final: 0.7817 (ppp) REVERT: A 381 PHE cc_start: 0.8393 (t80) cc_final: 0.7747 (t80) REVERT: A 382 ASN cc_start: 0.7913 (m-40) cc_final: 0.7244 (m-40) REVERT: A 392 HIS cc_start: 0.8325 (t70) cc_final: 0.7634 (t70) REVERT: B 86 MET cc_start: 0.8385 (tpp) cc_final: 0.8009 (tpp) REVERT: B 102 SER cc_start: 0.8469 (m) cc_final: 0.7876 (t) REVERT: B 223 LYS cc_start: 0.8314 (pttp) cc_final: 0.7937 (tptp) REVERT: B 339 LEU cc_start: 0.8317 (tt) cc_final: 0.7636 (tt) REVERT: B 388 ILE cc_start: 0.5721 (mm) cc_final: 0.5254 (mm) REVERT: B 436 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6417 (mm-30) REVERT: C 43 ILE cc_start: 0.7505 (tp) cc_final: 0.7198 (tt) REVERT: C 248 GLU cc_start: 0.6980 (pm20) cc_final: 0.6571 (tp30) REVERT: C 252 GLU cc_start: 0.8406 (mp0) cc_final: 0.7834 (mp0) REVERT: C 341 ASN cc_start: 0.8308 (m-40) cc_final: 0.7934 (m-40) REVERT: C 512 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7932 (tm-30) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2204 time to fit residues: 70.3132 Evaluate side-chains 155 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 135 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 88 optimal weight: 0.0970 chunk 100 optimal weight: 0.9990 chunk 92 optimal weight: 0.0870 chunk 20 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 210 HIS ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS B 343 HIS ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.111371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082485 restraints weight = 44015.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.084128 restraints weight = 32243.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.085451 restraints weight = 26004.784| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.7730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11824 Z= 0.125 Angle : 0.669 10.935 16057 Z= 0.337 Chirality : 0.044 0.187 1888 Planarity : 0.005 0.054 2103 Dihedral : 5.023 87.532 1701 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.52 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % 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 (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: -0.88 (0.21), residues: 1576 helix: 0.33 (0.20), residues: 688 sheet: -0.46 (0.39), residues: 178 loop : -1.52 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 HIS 0.006 0.001 HIS A 210 PHE 0.020 0.002 PHE A 362 TYR 0.015 0.001 TYR A 93 ARG 0.007 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 543) hydrogen bonds : angle 4.92022 ( 1665) covalent geometry : bond 0.00271 (11824) covalent geometry : angle 0.66924 (16057) *********************** 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 214 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8847 (mmp) cc_final: 0.8413 (mmm) REVERT: A 315 MET cc_start: 0.8080 (ppp) cc_final: 0.7705 (ppp) REVERT: A 341 ASP cc_start: 0.8252 (p0) cc_final: 0.7729 (p0) REVERT: A 381 PHE cc_start: 0.8420 (t80) cc_final: 0.7841 (t80) REVERT: A 382 ASN cc_start: 0.7962 (m-40) cc_final: 0.7261 (m-40) REVERT: A 392 HIS cc_start: 0.8366 (t70) cc_final: 0.7694 (t70) REVERT: B 75 ASN cc_start: 0.6583 (t0) cc_final: 0.6022 (p0) REVERT: B 79 GLU cc_start: 0.7776 (mp0) cc_final: 0.7348 (mp0) REVERT: B 102 SER cc_start: 0.8628 (m) cc_final: 0.7999 (t) REVERT: B 223 LYS cc_start: 0.8319 (pttp) cc_final: 0.7855 (tptp) REVERT: B 339 LEU cc_start: 0.8244 (tt) cc_final: 0.7729 (tt) REVERT: B 388 ILE cc_start: 0.6047 (mm) cc_final: 0.5553 (mm) REVERT: C 43 ILE cc_start: 0.7598 (tp) cc_final: 0.7281 (tt) REVERT: C 248 GLU cc_start: 0.7016 (pm20) cc_final: 0.6219 (tp30) REVERT: C 252 GLU cc_start: 0.8434 (mp0) cc_final: 0.7495 (mp0) REVERT: C 341 ASN cc_start: 0.8314 (m-40) cc_final: 0.7939 (m-40) REVERT: C 470 ILE cc_start: 0.8322 (mt) cc_final: 0.8080 (mm) REVERT: C 512 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7918 (tm-30) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2095 time to fit residues: 66.6172 Evaluate side-chains 158 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 32 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 0.0020 chunk 29 optimal weight: 0.0670 chunk 90 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.3728 ------------------------------------------------------------------------------- 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 A 243 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN C 496 ASN ** 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 = 0.3902 r_free = 0.3902 target = 0.105787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.077073 restraints weight = 43113.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.078762 restraints weight = 30879.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.079964 restraints weight = 24715.331| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 1.0116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11824 Z= 0.219 Angle : 0.838 13.538 16057 Z= 0.432 Chirality : 0.049 0.224 1888 Planarity : 0.006 0.056 2103 Dihedral : 5.489 81.369 1701 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.73 % Favored : 92.77 % Rotamer: Outliers : 0.17 % Allowed : 3.00 % Favored : 96.82 % 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: -1.34 (0.21), residues: 1576 helix: -0.07 (0.19), residues: 693 sheet: -0.95 (0.37), residues: 189 loop : -1.67 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 217 HIS 0.012 0.002 HIS B 33 PHE 0.051 0.003 PHE C 663 TYR 0.045 0.003 TYR C 584 ARG 0.008 0.001 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.04687 ( 543) hydrogen bonds : angle 5.33860 ( 1665) covalent geometry : bond 0.00465 (11824) covalent geometry : angle 0.83814 (16057) *********************** 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 223 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7298 (t0) cc_final: 0.6400 (p0) REVERT: A 114 MET cc_start: 0.8893 (mmp) cc_final: 0.8378 (mmm) REVERT: A 175 VAL cc_start: 0.7990 (m) cc_final: 0.7715 (p) REVERT: A 315 MET cc_start: 0.8082 (ppp) cc_final: 0.7851 (ppp) REVERT: A 321 TRP cc_start: 0.7569 (m100) cc_final: 0.7241 (m100) REVERT: A 341 ASP cc_start: 0.8455 (p0) cc_final: 0.7458 (p0) REVERT: A 382 ASN cc_start: 0.8452 (m-40) cc_final: 0.8026 (m110) REVERT: A 392 HIS cc_start: 0.8686 (t70) cc_final: 0.8047 (t70) REVERT: A 401 MET cc_start: 0.8775 (ptp) cc_final: 0.8465 (ptp) REVERT: A 436 GLU cc_start: 0.7324 (mp0) cc_final: 0.6961 (mp0) REVERT: B 39 ASP cc_start: 0.8928 (m-30) cc_final: 0.8623 (m-30) REVERT: B 75 ASN cc_start: 0.6802 (t0) cc_final: 0.5723 (t0) REVERT: B 79 GLU cc_start: 0.7855 (mp0) cc_final: 0.7354 (mp0) REVERT: B 90 THR cc_start: 0.7552 (t) cc_final: 0.7260 (p) REVERT: B 99 CYS cc_start: 0.8999 (m) cc_final: 0.8797 (m) REVERT: B 223 LYS cc_start: 0.8617 (pttp) cc_final: 0.8246 (tptp) REVERT: B 344 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6935 (tt0) REVERT: C 252 GLU cc_start: 0.8597 (mp0) cc_final: 0.8161 (mp0) REVERT: C 281 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8092 (pp30) REVERT: C 341 ASN cc_start: 0.8595 (m-40) cc_final: 0.8335 (m-40) REVERT: C 374 LEU cc_start: 0.8080 (pp) cc_final: 0.7436 (mt) REVERT: C 616 PRO cc_start: 0.8441 (Cg_exo) cc_final: 0.8119 (Cg_endo) REVERT: C 624 MET cc_start: 0.5911 (mtt) cc_final: 0.5655 (mmp) REVERT: C 655 PHE cc_start: 0.7424 (t80) cc_final: 0.6930 (t80) REVERT: C 656 PRO cc_start: 0.8667 (Cg_exo) cc_final: 0.7774 (Cg_endo) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.2153 time to fit residues: 70.9341 Evaluate side-chains 173 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 95 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 243 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.103800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.074811 restraints weight = 44417.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.076234 restraints weight = 32008.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.077488 restraints weight = 26194.950| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 1.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11824 Z= 0.198 Angle : 0.778 15.313 16057 Z= 0.396 Chirality : 0.047 0.205 1888 Planarity : 0.006 0.098 2103 Dihedral : 5.296 73.073 1701 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.15 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: -0.04 (0.19), residues: 706 sheet: -1.13 (0.37), residues: 190 loop : -1.63 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 312 HIS 0.014 0.002 HIS C 347 PHE 0.019 0.002 PHE B 32 TYR 0.029 0.003 TYR A 93 ARG 0.009 0.001 ARG C 88 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 543) hydrogen bonds : angle 5.23596 ( 1665) covalent geometry : bond 0.00445 (11824) covalent geometry : angle 0.77845 (16057) *********************** 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 204 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: -0.3524 (ttp) cc_final: -0.3802 (ttp) REVERT: A 75 ASN cc_start: 0.7674 (t0) cc_final: 0.7323 (t0) REVERT: A 114 MET cc_start: 0.8888 (mmp) cc_final: 0.8329 (mmm) REVERT: A 175 VAL cc_start: 0.8040 (m) cc_final: 0.7755 (p) REVERT: A 195 TYR cc_start: 0.7532 (m-80) cc_final: 0.7248 (m-80) REVERT: A 341 ASP cc_start: 0.8523 (p0) cc_final: 0.8279 (p0) REVERT: A 382 ASN cc_start: 0.8629 (m-40) cc_final: 0.8199 (m110) REVERT: A 392 HIS cc_start: 0.8603 (t70) cc_final: 0.7934 (t70) REVERT: A 436 GLU cc_start: 0.7274 (mp0) cc_final: 0.6891 (mp0) REVERT: B 39 ASP cc_start: 0.9161 (m-30) cc_final: 0.8874 (m-30) REVERT: B 75 ASN cc_start: 0.7317 (t0) cc_final: 0.6665 (p0) REVERT: B 79 GLU cc_start: 0.8058 (mp0) cc_final: 0.7621 (mp0) REVERT: B 223 LYS cc_start: 0.8648 (pttp) cc_final: 0.8372 (tptp) REVERT: B 342 MET cc_start: 0.8444 (ttp) cc_final: 0.8045 (ttp) REVERT: B 344 GLU cc_start: 0.7799 (mt-10) cc_final: 0.6563 (mp0) REVERT: C 248 GLU cc_start: 0.8015 (pm20) cc_final: 0.7795 (pm20) REVERT: C 406 MET cc_start: 0.8904 (mmp) cc_final: 0.8517 (mmm) REVERT: C 454 MET cc_start: 0.8181 (pmm) cc_final: 0.7916 (pmm) REVERT: C 552 GLU cc_start: 0.6361 (mp0) cc_final: 0.5595 (mp0) REVERT: C 646 ASP cc_start: 0.5575 (t0) cc_final: 0.5265 (t0) REVERT: C 655 PHE cc_start: 0.8082 (t80) cc_final: 0.7652 (t80) REVERT: C 656 PRO cc_start: 0.9093 (Cg_exo) cc_final: 0.8534 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2006 time to fit residues: 63.1374 Evaluate side-chains 150 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 124 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 57 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN B 207 HIS ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.100605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.072123 restraints weight = 43583.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.073738 restraints weight = 31028.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.074636 restraints weight = 24705.123| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 1.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 11824 Z= 0.215 Angle : 0.780 10.223 16057 Z= 0.401 Chirality : 0.047 0.219 1888 Planarity : 0.006 0.076 2103 Dihedral : 5.321 62.244 1701 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.98 % Favored : 92.58 % 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: -1.51 (0.21), residues: 1576 helix: -0.19 (0.19), residues: 717 sheet: -1.04 (0.38), residues: 198 loop : -1.84 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 217 HIS 0.005 0.001 HIS B 264 PHE 0.024 0.002 PHE B 306 TYR 0.030 0.003 TYR A 93 ARG 0.008 0.001 ARG C 88 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 543) hydrogen bonds : angle 5.30721 ( 1665) covalent geometry : bond 0.00468 (11824) covalent geometry : angle 0.77958 (16057) *********************** 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 195 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8894 (mmp) cc_final: 0.8440 (mmm) REVERT: A 175 VAL cc_start: 0.8194 (m) cc_final: 0.7874 (p) REVERT: A 341 ASP cc_start: 0.8519 (p0) cc_final: 0.7774 (p0) REVERT: A 382 ASN cc_start: 0.8711 (m-40) cc_final: 0.8313 (m110) REVERT: A 392 HIS cc_start: 0.8588 (t70) cc_final: 0.7887 (t70) REVERT: B 39 ASP cc_start: 0.9143 (m-30) cc_final: 0.8819 (m-30) REVERT: B 75 ASN cc_start: 0.7465 (t0) cc_final: 0.6520 (p0) REVERT: B 76 ILE cc_start: 0.8026 (pt) cc_final: 0.6913 (pt) REVERT: B 78 ARG cc_start: 0.8449 (tpp-160) cc_final: 0.7770 (tpp-160) REVERT: B 79 GLU cc_start: 0.7901 (mp0) cc_final: 0.7381 (mp0) REVERT: B 99 CYS cc_start: 0.9164 (m) cc_final: 0.8961 (m) REVERT: B 113 LEU cc_start: 0.9106 (tp) cc_final: 0.8870 (mm) REVERT: B 223 LYS cc_start: 0.8637 (pttp) cc_final: 0.8427 (tptp) REVERT: B 344 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7440 (tt0) REVERT: B 354 ILE cc_start: 0.9267 (pt) cc_final: 0.8920 (tt) REVERT: C 406 MET cc_start: 0.9027 (mmp) cc_final: 0.8750 (mmt) REVERT: C 454 MET cc_start: 0.8367 (pmm) cc_final: 0.7959 (pmm) REVERT: C 552 GLU cc_start: 0.7218 (mp0) cc_final: 0.6448 (mp0) REVERT: C 646 ASP cc_start: 0.6655 (t0) cc_final: 0.6032 (t70) REVERT: C 656 PRO cc_start: 0.9310 (Cg_exo) cc_final: 0.8962 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2173 time to fit residues: 62.7481 Evaluate side-chains 138 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS A 243 ASN B 207 HIS ** C 91 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.101894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073098 restraints weight = 43429.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.074697 restraints weight = 30843.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.075926 restraints weight = 24512.162| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 1.2759 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= 0.146 Angle : 0.732 11.829 16057 Z= 0.371 Chirality : 0.046 0.194 1888 Planarity : 0.006 0.089 2103 Dihedral : 5.042 55.097 1701 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.27 % Favored : 94.29 % 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: -1.22 (0.21), residues: 1576 helix: 0.12 (0.19), residues: 703 sheet: -1.01 (0.38), residues: 197 loop : -1.70 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 312 HIS 0.005 0.001 HIS A 210 PHE 0.033 0.002 PHE A 64 TYR 0.025 0.002 TYR A 93 ARG 0.005 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 543) hydrogen bonds : angle 5.09592 ( 1665) covalent geometry : bond 0.00332 (11824) covalent geometry : angle 0.73220 (16057) ********************** 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 182 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.9021 (tp30) cc_final: 0.8811 (mm-30) REVERT: A 114 MET cc_start: 0.8849 (mmp) cc_final: 0.8390 (mmm) REVERT: A 175 VAL cc_start: 0.8196 (m) cc_final: 0.7940 (p) REVERT: A 315 MET cc_start: 0.8373 (tmm) cc_final: 0.8145 (tmm) REVERT: A 382 ASN cc_start: 0.8656 (m-40) cc_final: 0.8242 (m110) REVERT: A 392 HIS cc_start: 0.8500 (t70) cc_final: 0.7794 (t70) REVERT: B 39 ASP cc_start: 0.9005 (m-30) cc_final: 0.8752 (m-30) REVERT: B 75 ASN cc_start: 0.7311 (t0) cc_final: 0.6481 (p0) REVERT: B 78 ARG cc_start: 0.8532 (tpp-160) cc_final: 0.7814 (tpp-160) REVERT: B 79 GLU cc_start: 0.7938 (mp0) cc_final: 0.7503 (mp0) REVERT: B 86 MET cc_start: 0.8630 (tpt) cc_final: 0.8412 (tpt) REVERT: B 99 CYS cc_start: 0.9132 (m) cc_final: 0.8891 (m) REVERT: B 223 LYS cc_start: 0.8682 (pttp) cc_final: 0.8409 (tptp) REVERT: B 342 MET cc_start: 0.8463 (ttp) cc_final: 0.8165 (ttp) REVERT: B 344 GLU cc_start: 0.8006 (mt-10) cc_final: 0.6797 (mp0) REVERT: B 354 ILE cc_start: 0.9287 (pt) cc_final: 0.8937 (tt) REVERT: C 454 MET cc_start: 0.8427 (pmm) cc_final: 0.8016 (pmm) REVERT: C 552 GLU cc_start: 0.7216 (mp0) cc_final: 0.6295 (mp0) REVERT: C 560 SER cc_start: 0.8114 (p) cc_final: 0.7765 (p) REVERT: C 655 PHE cc_start: 0.7928 (t80) cc_final: 0.7555 (t80) REVERT: C 656 PRO cc_start: 0.9298 (Cg_exo) cc_final: 0.9025 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2205 time to fit residues: 59.4375 Evaluate side-chains 139 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.8796 > 50: distance: 31 - 105: 26.802 distance: 58 - 63: 9.721 distance: 63 - 64: 16.156 distance: 64 - 65: 16.608 distance: 64 - 67: 28.155 distance: 65 - 66: 5.828 distance: 67 - 68: 23.150 distance: 68 - 69: 20.825 distance: 68 - 70: 25.450 distance: 71 - 72: 19.624 distance: 72 - 73: 16.389 distance: 72 - 75: 13.918 distance: 73 - 74: 11.512 distance: 73 - 79: 24.666 distance: 75 - 76: 9.110 distance: 76 - 77: 28.116 distance: 76 - 78: 21.953 distance: 79 - 80: 9.217 distance: 79 - 85: 21.771 distance: 80 - 81: 17.362 distance: 80 - 83: 17.873 distance: 81 - 82: 12.713 distance: 81 - 86: 12.009 distance: 83 - 84: 32.541 distance: 84 - 85: 29.465 distance: 86 - 87: 18.891 distance: 87 - 88: 25.014 distance: 87 - 90: 19.434 distance: 88 - 89: 19.282 distance: 88 - 95: 23.371 distance: 90 - 91: 29.854 distance: 91 - 92: 28.530 distance: 92 - 93: 29.083 distance: 93 - 94: 16.850 distance: 95 - 96: 30.071 distance: 96 - 97: 12.440 distance: 96 - 99: 35.714 distance: 97 - 98: 21.088 distance: 97 - 102: 10.372 distance: 99 - 100: 22.235 distance: 99 - 101: 44.708 distance: 102 - 103: 28.761 distance: 103 - 104: 20.373 distance: 103 - 106: 12.519 distance: 104 - 105: 10.699 distance: 104 - 109: 33.471 distance: 106 - 107: 27.473 distance: 106 - 108: 22.680 distance: 109 - 110: 27.887 distance: 110 - 111: 22.040 distance: 110 - 113: 19.441 distance: 111 - 112: 17.311 distance: 111 - 117: 38.964 distance: 113 - 114: 12.765 distance: 114 - 115: 44.197 distance: 114 - 116: 40.775 distance: 117 - 118: 24.865 distance: 118 - 119: 23.537 distance: 119 - 120: 35.847 distance: 119 - 121: 12.903 distance: 121 - 122: 34.757 distance: 122 - 123: 27.062 distance: 122 - 125: 26.325 distance: 123 - 124: 21.155 distance: 123 - 129: 11.529 distance: 125 - 126: 16.909 distance: 126 - 127: 36.399 distance: 126 - 128: 42.416 distance: 129 - 130: 18.962 distance: 129 - 135: 11.882 distance: 130 - 131: 14.402 distance: 130 - 133: 18.384 distance: 131 - 132: 23.833 distance: 131 - 136: 18.897 distance: 133 - 134: 15.604 distance: 134 - 135: 20.585