Starting phenix.real_space_refine on Fri Feb 16 22:42:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brj_16217/02_2024/8brj_16217.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brj_16217/02_2024/8brj_16217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brj_16217/02_2024/8brj_16217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brj_16217/02_2024/8brj_16217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brj_16217/02_2024/8brj_16217.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brj_16217/02_2024/8brj_16217.pdb" } 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 Residue "A ASP 314": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.37, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 4.90 Conformation dependent library (CDL) restraints added in 2.4 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: 1.47 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: 3.66 Time building geometry restraints manager: 5.26 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: 98.14 - 105.31: 271 105.31 - 112.47: 6220 112.47 - 119.63: 3807 119.63 - 126.80: 5635 126.80 - 133.96: 124 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 2.440 nonbonded pdb=" OD2 ASP A 377 " pdb=" OG SER A 379 " model vdw 2.137 2.440 nonbonded pdb=" O LEU B 384 " pdb=" OH TYR B 390 " model vdw 2.154 2.440 nonbonded pdb=" O GLU C 166 " pdb=" OG1 THR C 170 " model vdw 2.193 2.440 nonbonded pdb=" OG SER C 310 " pdb=" O HIS C 388 " model vdw 2.194 2.440 ... (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 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 9.910 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.100 Find NCS groups from input model: 0.500 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: 50.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11824 Z= 0.184 Angle : 0.645 7.910 16057 Z= 0.353 Chirality : 0.041 0.273 1888 Planarity : 0.005 0.056 2103 Dihedral : 13.328 89.691 4278 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.85 % Favored : 92.70 % Rotamer: Outliers : 0.17 % Allowed : 0.86 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1576 helix: 0.28 (0.20), residues: 658 sheet: -0.23 (0.38), residues: 180 loop : -1.57 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 217 HIS 0.003 0.001 HIS B 407 PHE 0.012 0.001 PHE C 655 TYR 0.014 0.001 TYR A 93 ARG 0.009 0.001 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 327 time to evaluate : 1.213 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: 0.2532 time to fit residues: 114.3681 Evaluate side-chains 195 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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: 3.9990 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4850 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11824 Z= 0.241 Angle : 0.714 13.172 16057 Z= 0.367 Chirality : 0.045 0.194 1888 Planarity : 0.006 0.063 2103 Dihedral : 5.140 64.368 1701 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.90 % Favored : 93.59 % Rotamer: Outliers : 0.17 % Allowed : 6.52 % Favored : 93.30 % 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: -0.90 (0.21), residues: 1576 helix: 0.31 (0.19), residues: 686 sheet: -0.07 (0.42), residues: 149 loop : -1.58 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 353 HIS 0.011 0.002 HIS C 109 PHE 0.030 0.002 PHE C 229 TYR 0.015 0.002 TYR A 93 ARG 0.005 0.000 ARG B 14 *********************** 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 238 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 236 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.4257 (ttp80) cc_final: 0.3810 (ptm-80) REVERT: A 40 LEU cc_start: 0.5810 (mt) cc_final: 0.4914 (mt) REVERT: A 108 ASN cc_start: 0.7411 (m-40) cc_final: 0.6925 (t0) REVERT: A 113 LEU cc_start: 0.8876 (tt) cc_final: 0.8634 (mp) REVERT: A 114 MET cc_start: 0.8276 (mmp) cc_final: 0.7684 (mmm) REVERT: A 118 ILE cc_start: 0.5745 (mm) cc_final: 0.5294 (mm) REVERT: A 291 LYS cc_start: 0.8741 (tmtt) cc_final: 0.8290 (pttm) REVERT: A 314 ASP cc_start: 0.7310 (p0) cc_final: 0.6648 (t0) REVERT: A 315 MET cc_start: 0.5265 (pmm) cc_final: 0.4245 (ptm) REVERT: A 334 MET cc_start: 0.8445 (tpt) cc_final: 0.8233 (tmm) REVERT: A 392 HIS cc_start: 0.7789 (t70) cc_final: 0.7577 (t70) REVERT: A 431 MET cc_start: 0.7810 (tmm) cc_final: 0.7484 (tmm) REVERT: B 9 THR cc_start: 0.6005 (t) cc_final: 0.5774 (t) REVERT: B 35 ILE cc_start: 0.6373 (pt) cc_final: 0.5983 (pt) REVERT: B 103 PHE cc_start: 0.6867 (m-10) cc_final: 0.6303 (m-10) REVERT: B 314 ASP cc_start: 0.6670 (m-30) cc_final: 0.6289 (m-30) REVERT: B 341 ASP cc_start: 0.7161 (t70) cc_final: 0.6780 (t70) REVERT: B 401 MET cc_start: 0.7332 (ptp) cc_final: 0.6831 (ptp) REVERT: B 419 VAL cc_start: 0.7005 (t) cc_final: 0.6644 (t) REVERT: C 73 MET cc_start: 0.9303 (mmp) cc_final: 0.8956 (ptt) REVERT: C 98 HIS cc_start: 0.6973 (t70) cc_final: 0.6385 (t70) REVERT: C 319 MET cc_start: 0.8175 (ptt) cc_final: 0.7760 (tpt) REVERT: C 643 ARG cc_start: 0.6145 (ppt170) cc_final: 0.4578 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 237 average time/residue: 0.2384 time to fit residues: 80.5451 Evaluate side-chains 175 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 142 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 48 optimal weight: 0.0050 chunk 114 optimal weight: 3.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- 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 382 ASN B 108 ASN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS C 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5037 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 11824 Z= 0.259 Angle : 0.700 10.511 16057 Z= 0.361 Chirality : 0.045 0.307 1888 Planarity : 0.005 0.054 2103 Dihedral : 5.043 56.272 1701 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.54 % Favored : 92.96 % Rotamer: Outliers : 0.09 % Allowed : 6.27 % 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: -1.03 (0.21), residues: 1576 helix: 0.15 (0.19), residues: 695 sheet: -0.14 (0.42), residues: 148 loop : -1.61 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 321 HIS 0.009 0.001 HIS C 109 PHE 0.024 0.002 PHE A 260 TYR 0.024 0.002 TYR A 93 ARG 0.011 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: -0.3917 (ttp) cc_final: -0.4397 (ttp) REVERT: A 113 LEU cc_start: 0.8944 (tt) cc_final: 0.8704 (mp) REVERT: A 114 MET cc_start: 0.8338 (mmp) cc_final: 0.7966 (mmm) REVERT: A 118 ILE cc_start: 0.5708 (mm) cc_final: 0.5228 (mm) REVERT: A 315 MET cc_start: 0.6188 (pmm) cc_final: 0.5363 (ppp) REVERT: A 341 ASP cc_start: 0.6366 (p0) cc_final: 0.5811 (p0) REVERT: B 59 ILE cc_start: 0.8628 (mm) cc_final: 0.8413 (mm) REVERT: B 70 MET cc_start: 0.7594 (tmm) cc_final: 0.7337 (tmm) REVERT: B 86 MET cc_start: 0.2401 (tpt) cc_final: 0.1940 (tpt) REVERT: B 128 SER cc_start: -0.3103 (t) cc_final: -0.3450 (p) REVERT: B 227 MET cc_start: 0.6774 (ppp) cc_final: 0.6383 (ppp) REVERT: B 277 ASP cc_start: 0.2472 (m-30) cc_final: 0.1924 (m-30) REVERT: B 306 PHE cc_start: 0.0445 (m-80) cc_final: -0.0075 (m-80) REVERT: B 315 MET cc_start: 0.5650 (ttt) cc_final: 0.5382 (tpt) REVERT: B 341 ASP cc_start: 0.7224 (t70) cc_final: 0.6803 (t70) REVERT: C 73 MET cc_start: 0.9303 (mmp) cc_final: 0.8956 (ptt) REVERT: C 145 LEU cc_start: 0.4300 (tp) cc_final: 0.4070 (tp) REVERT: C 319 MET cc_start: 0.8228 (ptt) cc_final: 0.7784 (tpt) REVERT: C 325 TYR cc_start: 0.6791 (t80) cc_final: 0.6556 (t80) REVERT: C 355 GLN cc_start: 0.7229 (mm110) cc_final: 0.6877 (mp10) REVERT: C 411 GLU cc_start: 0.7839 (tp30) cc_final: 0.7169 (mt-10) REVERT: C 431 ASP cc_start: 0.8088 (t70) cc_final: 0.7831 (t70) REVERT: C 643 ARG cc_start: 0.6672 (ppt170) cc_final: 0.4683 (tpp80) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.2119 time to fit residues: 72.8854 Evaluate side-chains 186 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 50.0000 chunk 68 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 151 optimal weight: 0.3980 chunk 135 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5118 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11824 Z= 0.190 Angle : 0.652 11.543 16057 Z= 0.331 Chirality : 0.043 0.198 1888 Planarity : 0.005 0.064 2103 Dihedral : 5.052 85.382 1701 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.71 % Favored : 93.78 % Rotamer: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1576 helix: 0.41 (0.20), residues: 697 sheet: 0.10 (0.41), residues: 154 loop : -1.67 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 321 HIS 0.005 0.001 HIS A 210 PHE 0.015 0.002 PHE A 362 TYR 0.013 0.001 TYR A 93 ARG 0.006 0.000 ARG A 400 *********************** 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 234 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8939 (tt) cc_final: 0.8689 (mt) REVERT: A 114 MET cc_start: 0.8360 (mmp) cc_final: 0.7997 (mmm) REVERT: A 118 ILE cc_start: 0.5928 (mm) cc_final: 0.5494 (mm) REVERT: A 183 ARG cc_start: 0.7618 (tmm-80) cc_final: 0.7296 (tpt170) REVERT: A 264 HIS cc_start: 0.7515 (m90) cc_final: 0.7249 (m90) REVERT: A 291 LYS cc_start: 0.9028 (tmtt) cc_final: 0.8665 (ptpt) REVERT: A 315 MET cc_start: 0.5900 (pmm) cc_final: 0.5512 (ppp) REVERT: A 328 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8471 (pt0) REVERT: B 35 ILE cc_start: 0.5962 (pt) cc_final: 0.5655 (pt) REVERT: B 40 LEU cc_start: 0.6943 (mt) cc_final: 0.6628 (mt) REVERT: B 70 MET cc_start: 0.7672 (tmm) cc_final: 0.7450 (tmm) REVERT: B 128 SER cc_start: -0.3249 (t) cc_final: -0.3779 (p) REVERT: B 191 MET cc_start: 0.7089 (mmt) cc_final: 0.6790 (mmt) REVERT: B 227 MET cc_start: 0.6866 (ppp) cc_final: 0.6406 (ppp) REVERT: B 306 PHE cc_start: 0.1003 (m-80) cc_final: 0.0258 (m-80) REVERT: B 341 ASP cc_start: 0.6611 (t70) cc_final: 0.6331 (t70) REVERT: C 73 MET cc_start: 0.9287 (mmp) cc_final: 0.8960 (ptt) REVERT: C 149 SER cc_start: 0.2600 (t) cc_final: 0.2228 (m) REVERT: C 188 VAL cc_start: 0.1261 (m) cc_final: 0.1022 (m) REVERT: C 248 GLU cc_start: 0.7895 (pm20) cc_final: 0.7011 (tp30) REVERT: C 319 MET cc_start: 0.8143 (ptt) cc_final: 0.7728 (tpt) REVERT: C 355 GLN cc_start: 0.7358 (mm110) cc_final: 0.7072 (mp10) REVERT: C 411 GLU cc_start: 0.8319 (tp30) cc_final: 0.7420 (mt-10) REVERT: C 460 ILE cc_start: 0.2023 (mt) cc_final: 0.1628 (mt) REVERT: C 643 ARG cc_start: 0.6862 (ppt170) cc_final: 0.5086 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.2383 time to fit residues: 83.6809 Evaluate side-chains 178 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 496 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.8113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 11824 Z= 0.317 Angle : 0.811 10.834 16057 Z= 0.416 Chirality : 0.048 0.244 1888 Planarity : 0.007 0.138 2103 Dihedral : 5.296 62.990 1701 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.11 % Favored : 92.39 % Rotamer: Outliers : 0.26 % Allowed : 4.12 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.21 (0.21), residues: 1576 helix: 0.01 (0.19), residues: 695 sheet: 0.16 (0.44), residues: 149 loop : -1.83 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 321 HIS 0.008 0.002 HIS A 407 PHE 0.034 0.003 PHE C 65 TYR 0.023 0.003 TYR B 300 ARG 0.029 0.001 ARG A 410 *********************** 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 238 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9150 (tt) cc_final: 0.8944 (mt) REVERT: A 114 MET cc_start: 0.8322 (mmp) cc_final: 0.7913 (mmm) REVERT: A 264 HIS cc_start: 0.7617 (m90) cc_final: 0.7223 (m90) REVERT: A 291 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8919 (ptpt) REVERT: A 315 MET cc_start: 0.6215 (pmm) cc_final: 0.5801 (ppp) REVERT: A 328 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8634 (pt0) REVERT: A 334 MET cc_start: 0.8634 (tpt) cc_final: 0.8124 (tpt) REVERT: A 400 ARG cc_start: 0.7988 (tmm-80) cc_final: 0.7232 (tpm170) REVERT: B 21 LEU cc_start: 0.4570 (tt) cc_final: 0.4211 (tt) REVERT: B 33 HIS cc_start: 0.8291 (t70) cc_final: 0.7995 (t70) REVERT: B 40 LEU cc_start: 0.7853 (mt) cc_final: 0.7467 (mt) REVERT: B 70 MET cc_start: 0.7751 (tmm) cc_final: 0.7540 (tmm) REVERT: B 223 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7604 (tptp) REVERT: B 306 PHE cc_start: 0.2247 (m-80) cc_final: 0.1339 (m-80) REVERT: B 388 ILE cc_start: 0.5811 (mm) cc_final: 0.5116 (mm) REVERT: C 43 ILE cc_start: 0.8368 (tp) cc_final: 0.8106 (tt) REVERT: C 73 MET cc_start: 0.9284 (mmp) cc_final: 0.8956 (ptt) REVERT: C 149 SER cc_start: 0.3725 (t) cc_final: 0.3500 (m) REVERT: C 248 GLU cc_start: 0.8113 (pm20) cc_final: 0.7508 (pm20) REVERT: C 319 MET cc_start: 0.8464 (ptt) cc_final: 0.7772 (tpp) REVERT: C 323 ILE cc_start: 0.7204 (tp) cc_final: 0.6957 (tt) REVERT: C 454 MET cc_start: 0.6999 (tpt) cc_final: 0.6046 (ptp) REVERT: C 473 THR cc_start: 0.7817 (m) cc_final: 0.7543 (p) outliers start: 3 outliers final: 0 residues processed: 237 average time/residue: 0.2233 time to fit residues: 76.8479 Evaluate side-chains 169 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 A 382 ASN A 407 HIS B 343 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.8839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11824 Z= 0.196 Angle : 0.665 13.787 16057 Z= 0.335 Chirality : 0.044 0.159 1888 Planarity : 0.005 0.066 2103 Dihedral : 4.892 59.521 1701 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.89 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: -0.86 (0.21), residues: 1576 helix: 0.41 (0.20), residues: 704 sheet: -0.03 (0.41), residues: 160 loop : -1.72 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 321 HIS 0.010 0.001 HIS C 347 PHE 0.016 0.002 PHE A 394 TYR 0.019 0.002 TYR A 93 ARG 0.008 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7515 (p0) cc_final: 0.7100 (t0) REVERT: A 113 LEU cc_start: 0.9117 (tt) cc_final: 0.8915 (mt) REVERT: A 114 MET cc_start: 0.8377 (mmp) cc_final: 0.7958 (mmm) REVERT: A 264 HIS cc_start: 0.7597 (m90) cc_final: 0.7222 (m90) REVERT: A 291 LYS cc_start: 0.9194 (tmtt) cc_final: 0.8958 (ptpt) REVERT: A 328 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8537 (pt0) REVERT: A 334 MET cc_start: 0.8609 (tpt) cc_final: 0.8310 (tpt) REVERT: A 400 ARG cc_start: 0.7891 (tmm-80) cc_final: 0.7185 (tpm170) REVERT: B 21 LEU cc_start: 0.4064 (tt) cc_final: 0.2381 (tt) REVERT: B 23 THR cc_start: 0.7334 (m) cc_final: 0.6253 (m) REVERT: B 33 HIS cc_start: 0.8202 (t70) cc_final: 0.7910 (t70) REVERT: B 47 GLU cc_start: 0.7587 (tp30) cc_final: 0.7148 (mm-30) REVERT: B 114 MET cc_start: 0.8108 (ptm) cc_final: 0.7894 (ptm) REVERT: B 315 MET cc_start: 0.3697 (tpp) cc_final: 0.3369 (tpp) REVERT: B 341 ASP cc_start: 0.7053 (m-30) cc_final: 0.6493 (m-30) REVERT: B 344 GLU cc_start: 0.6362 (mt-10) cc_final: 0.6004 (mp0) REVERT: C 43 ILE cc_start: 0.8455 (tp) cc_final: 0.8178 (tt) REVERT: C 73 MET cc_start: 0.9262 (mmp) cc_final: 0.8953 (ptt) REVERT: C 248 GLU cc_start: 0.7979 (pm20) cc_final: 0.7562 (pm20) REVERT: C 319 MET cc_start: 0.8294 (ptt) cc_final: 0.7698 (tpp) REVERT: C 454 MET cc_start: 0.7275 (tpt) cc_final: 0.6369 (ptp) REVERT: C 473 THR cc_start: 0.8094 (m) cc_final: 0.7830 (p) REVERT: C 533 ILE cc_start: 0.5789 (pt) cc_final: 0.5566 (pt) REVERT: C 624 MET cc_start: 0.5084 (mtt) cc_final: 0.4701 (mmp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2126 time to fit residues: 69.0964 Evaluate side-chains 170 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN A 382 ASN A 407 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 moved from start: 1.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 11824 Z= 0.326 Angle : 0.802 9.911 16057 Z= 0.416 Chirality : 0.048 0.275 1888 Planarity : 0.006 0.066 2103 Dihedral : 5.463 76.330 1701 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.44 % Favored : 90.99 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: -1.12 (0.21), residues: 1576 helix: 0.14 (0.20), residues: 704 sheet: -0.45 (0.40), residues: 191 loop : -1.76 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 321 HIS 0.005 0.001 HIS C 98 PHE 0.024 0.003 PHE B 306 TYR 0.036 0.003 TYR A 93 ARG 0.013 0.001 ARG B 78 *********************** 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 202 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 VAL cc_start: 0.7936 (p) cc_final: 0.7615 (t) REVERT: A 264 HIS cc_start: 0.7843 (m90) cc_final: 0.7527 (m90) REVERT: A 315 MET cc_start: 0.7268 (ppp) cc_final: 0.6946 (ptm) REVERT: A 334 MET cc_start: 0.8689 (tpt) cc_final: 0.8375 (tpt) REVERT: A 341 ASP cc_start: 0.8306 (m-30) cc_final: 0.7133 (m-30) REVERT: A 400 ARG cc_start: 0.7945 (tmm-80) cc_final: 0.7725 (tmm-80) REVERT: A 401 MET cc_start: 0.8177 (ptm) cc_final: 0.7328 (ptm) REVERT: B 35 ILE cc_start: 0.6951 (pt) cc_final: 0.6567 (pt) REVERT: B 63 VAL cc_start: 0.6576 (t) cc_final: 0.6241 (m) REVERT: B 79 GLU cc_start: 0.7990 (mp0) cc_final: 0.7772 (mp0) REVERT: B 339 LEU cc_start: 0.8288 (tt) cc_final: 0.7925 (tt) REVERT: C 73 MET cc_start: 0.9207 (mmp) cc_final: 0.8920 (ptt) REVERT: C 252 GLU cc_start: 0.8160 (mp0) cc_final: 0.7924 (mp0) REVERT: C 319 MET cc_start: 0.8467 (ptt) cc_final: 0.7666 (tpp) REVERT: C 398 GLU cc_start: 0.8424 (pm20) cc_final: 0.7507 (mm-30) REVERT: C 454 MET cc_start: 0.7559 (tpt) cc_final: 0.6884 (ptp) REVERT: C 456 LEU cc_start: 0.8609 (tp) cc_final: 0.8378 (tp) REVERT: C 624 MET cc_start: 0.6404 (mtt) cc_final: 0.6194 (mmp) REVERT: C 655 PHE cc_start: 0.6924 (t80) cc_final: 0.6545 (t80) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2067 time to fit residues: 62.4853 Evaluate side-chains 157 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 190 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 moved from start: 1.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11824 Z= 0.203 Angle : 0.688 10.709 16057 Z= 0.345 Chirality : 0.044 0.178 1888 Planarity : 0.005 0.073 2103 Dihedral : 5.048 74.527 1701 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.71 % Favored : 93.78 % Rotamer: Outliers : 0.09 % Allowed : 1.37 % Favored : 98.54 % 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: -0.87 (0.22), residues: 1576 helix: 0.40 (0.20), residues: 712 sheet: -0.44 (0.40), residues: 190 loop : -1.67 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 321 HIS 0.005 0.001 HIS C 435 PHE 0.031 0.002 PHE A 362 TYR 0.024 0.002 TYR A 93 ARG 0.011 0.000 ARG A 183 *********************** 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 211 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: -0.3497 (ttp) cc_final: -0.3752 (ttp) REVERT: A 194 THR cc_start: 0.8230 (p) cc_final: 0.7989 (p) REVERT: A 195 TYR cc_start: 0.7621 (m-80) cc_final: 0.7396 (m-80) REVERT: A 264 HIS cc_start: 0.7503 (m90) cc_final: 0.7150 (m90) REVERT: A 315 MET cc_start: 0.7162 (ppp) cc_final: 0.6484 (ptm) REVERT: A 328 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8654 (pt0) REVERT: A 334 MET cc_start: 0.8666 (tpt) cc_final: 0.8377 (tpt) REVERT: A 341 ASP cc_start: 0.8275 (m-30) cc_final: 0.7452 (m-30) REVERT: A 401 MET cc_start: 0.7814 (ptm) cc_final: 0.7471 (ptm) REVERT: A 404 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8647 (tm-30) REVERT: B 35 ILE cc_start: 0.6709 (pt) cc_final: 0.6481 (pt) REVERT: B 59 ILE cc_start: 0.8393 (mm) cc_final: 0.8065 (tp) REVERT: B 63 VAL cc_start: 0.6416 (t) cc_final: 0.6181 (m) REVERT: B 70 MET cc_start: 0.7403 (tmm) cc_final: 0.7108 (tmm) REVERT: B 75 ASN cc_start: 0.5998 (p0) cc_final: 0.5760 (p0) REVERT: B 339 LEU cc_start: 0.8062 (tt) cc_final: 0.7822 (tt) REVERT: C 73 MET cc_start: 0.9200 (mmp) cc_final: 0.8917 (ptt) REVERT: C 319 MET cc_start: 0.8406 (ptt) cc_final: 0.7636 (tpp) REVERT: C 325 TYR cc_start: 0.6967 (t80) cc_final: 0.6674 (t80) REVERT: C 398 GLU cc_start: 0.8488 (pm20) cc_final: 0.7430 (mm-30) REVERT: C 454 MET cc_start: 0.7530 (tpt) cc_final: 0.6957 (ptp) REVERT: C 646 ASP cc_start: 0.6178 (t0) cc_final: 0.5962 (t70) REVERT: C 655 PHE cc_start: 0.6696 (t80) cc_final: 0.6050 (t80) REVERT: C 656 PRO cc_start: 0.5295 (Cg_exo) cc_final: 0.4895 (Cg_endo) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.2134 time to fit residues: 67.8262 Evaluate side-chains 159 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN A 210 HIS A 243 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 1.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11824 Z= 0.207 Angle : 0.700 10.314 16057 Z= 0.351 Chirality : 0.045 0.197 1888 Planarity : 0.005 0.072 2103 Dihedral : 5.055 82.788 1701 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.41 % Favored : 93.08 % 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: -0.87 (0.21), residues: 1576 helix: 0.42 (0.20), residues: 701 sheet: -0.51 (0.39), residues: 191 loop : -1.64 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 321 HIS 0.004 0.001 HIS A 210 PHE 0.025 0.002 PHE A 362 TYR 0.027 0.002 TYR A 93 ARG 0.006 0.000 ARG B 410 *********************** 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 201 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.7625 (m-80) cc_final: 0.7415 (m-80) REVERT: A 315 MET cc_start: 0.7063 (ppp) cc_final: 0.6352 (ptm) REVERT: A 334 MET cc_start: 0.8648 (tpt) cc_final: 0.8387 (tpt) REVERT: A 341 ASP cc_start: 0.8306 (m-30) cc_final: 0.7581 (t0) REVERT: A 401 MET cc_start: 0.7840 (ptm) cc_final: 0.7375 (ptp) REVERT: A 420 THR cc_start: 0.7458 (p) cc_final: 0.7105 (t) REVERT: B 59 ILE cc_start: 0.8350 (mm) cc_final: 0.7987 (tp) REVERT: B 63 VAL cc_start: 0.6681 (t) cc_final: 0.6242 (m) REVERT: B 70 MET cc_start: 0.7376 (tmm) cc_final: 0.7056 (tmm) REVERT: B 75 ASN cc_start: 0.6432 (p0) cc_final: 0.5898 (p0) REVERT: B 113 LEU cc_start: 0.9029 (tp) cc_final: 0.8658 (mm) REVERT: B 118 ILE cc_start: 0.5221 (pt) cc_final: 0.4050 (pt) REVERT: B 227 MET cc_start: 0.5604 (ptm) cc_final: 0.5401 (ptm) REVERT: C 73 MET cc_start: 0.9197 (mmp) cc_final: 0.8907 (ptt) REVERT: C 319 MET cc_start: 0.8385 (ptt) cc_final: 0.7529 (tpp) REVERT: C 398 GLU cc_start: 0.8553 (pm20) cc_final: 0.7425 (mm-30) REVERT: C 454 MET cc_start: 0.7601 (tpt) cc_final: 0.7091 (mpp) REVERT: C 456 LEU cc_start: 0.8802 (tp) cc_final: 0.8429 (tp) REVERT: C 655 PHE cc_start: 0.6792 (t80) cc_final: 0.6080 (t80) REVERT: C 656 PRO cc_start: 0.5704 (Cg_exo) cc_final: 0.4963 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1988 time to fit residues: 60.8423 Evaluate side-chains 153 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN A 382 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 1.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 11824 Z= 0.341 Angle : 0.820 13.235 16057 Z= 0.421 Chirality : 0.050 0.317 1888 Planarity : 0.006 0.080 2103 Dihedral : 5.641 84.139 1701 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.55 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -1.21 (0.21), residues: 1576 helix: 0.03 (0.19), residues: 716 sheet: -0.71 (0.38), residues: 202 loop : -1.72 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 321 HIS 0.010 0.002 HIS A 407 PHE 0.049 0.003 PHE A 362 TYR 0.035 0.003 TYR A 93 ARG 0.011 0.001 ARG B 78 ********************** 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 fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8970 (ttt) cc_final: 0.8729 (mmt) REVERT: A 226 VAL cc_start: 0.8549 (t) cc_final: 0.6621 (t) REVERT: A 341 ASP cc_start: 0.8176 (m-30) cc_final: 0.7049 (m-30) REVERT: A 401 MET cc_start: 0.7896 (ptm) cc_final: 0.7352 (ptm) REVERT: A 404 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 63 VAL cc_start: 0.6806 (t) cc_final: 0.6491 (m) REVERT: B 70 MET cc_start: 0.7407 (tmm) cc_final: 0.6839 (tmm) REVERT: B 113 LEU cc_start: 0.9233 (tp) cc_final: 0.8990 (mm) REVERT: B 118 ILE cc_start: 0.5037 (pt) cc_final: 0.3997 (pt) REVERT: B 315 MET cc_start: 0.2716 (tpp) cc_final: 0.2447 (tpp) REVERT: B 393 PRO cc_start: 0.5852 (Cg_exo) cc_final: 0.5384 (Cg_endo) REVERT: C 73 MET cc_start: 0.9149 (mmp) cc_final: 0.8896 (ptt) REVERT: C 319 MET cc_start: 0.8343 (ptt) cc_final: 0.7512 (tpp) REVERT: C 398 GLU cc_start: 0.8618 (pm20) cc_final: 0.7652 (mt-10) REVERT: C 406 MET cc_start: 0.7935 (mmm) cc_final: 0.7726 (tpp) REVERT: C 456 LEU cc_start: 0.8937 (tp) cc_final: 0.8606 (mt) REVERT: C 646 ASP cc_start: 0.7023 (t0) cc_final: 0.6650 (t70) REVERT: C 655 PHE cc_start: 0.6771 (t80) cc_final: 0.6167 (t80) REVERT: C 656 PRO cc_start: 0.5681 (Cg_exo) cc_final: 0.5120 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2084 time to fit residues: 56.6023 Evaluate side-chains 142 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 50.0000 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 210 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 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 = 0.3787 r_free = 0.3787 target = 0.100190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.071223 restraints weight = 43325.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.072635 restraints weight = 30886.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.073759 restraints weight = 25096.916| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 1.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11824 Z= 0.210 Angle : 0.720 12.762 16057 Z= 0.363 Chirality : 0.046 0.191 1888 Planarity : 0.005 0.069 2103 Dihedral : 5.229 82.870 1701 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.96 % Favored : 93.53 % Rotamer: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.40 % 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: -1.02 (0.22), residues: 1576 helix: 0.22 (0.20), residues: 711 sheet: -0.82 (0.38), residues: 200 loop : -1.57 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 321 HIS 0.004 0.001 HIS A 210 PHE 0.027 0.002 PHE A 362 TYR 0.029 0.002 TYR A 93 ARG 0.010 0.000 ARG A 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2515.02 seconds wall clock time: 46 minutes 30.49 seconds (2790.49 seconds total)