Starting phenix.real_space_refine on Wed Jul 30 11:23:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fe8_4241/07_2025/6fe8_4241.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fe8_4241/07_2025/6fe8_4241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6fe8_4241/07_2025/6fe8_4241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fe8_4241/07_2025/6fe8_4241.map" model { file = "/net/cci-nas-00/data/ceres_data/6fe8_4241/07_2025/6fe8_4241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fe8_4241/07_2025/6fe8_4241.cif" } resolution = 3.7 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 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 55 5.16 5 C 8120 2.51 5 N 2055 2.21 5 O 2249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12479 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4320 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 4249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4249 Classifications: {'peptide': 512} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 495} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1137 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2773 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain breaks: 3 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 10, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 175 Time building chain proxies: 7.83, per 1000 atoms: 0.63 Number of scatterers: 12479 At special positions: 0 Unit cell: (103.88, 117.66, 127.2, 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 55 16.00 O 2249 8.00 N 2055 7.00 C 8120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 215 " distance=2.04 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 215 " distance=2.04 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: 3.00 Conformation dependent library (CDL) restraints added in 1.7 seconds 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3010 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 7 sheets defined 64.0% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.778A pdb=" N GLN A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.818A pdb=" N TYR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.855A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 147 removed outlier: 4.045A pdb=" N ARG A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 173 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.684A pdb=" N HIS A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 193 " --> pdb=" O HIS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.685A pdb=" N GLY A 203 " --> pdb=" O TRP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 222 Processing helix chain 'A' and resid 230 through 241 removed outlier: 4.484A pdb=" N VAL A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 249 through 266 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 340 through 356 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.518A pdb=" N PHE A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.837A pdb=" N HIS A 456 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 477 removed outlier: 3.870A pdb=" N ILE A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.894A pdb=" N LYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 524 removed outlier: 3.795A pdb=" N LEU A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 551 removed outlier: 3.536A pdb=" N LYS A 539 " --> pdb=" O HIS A 535 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 Processing helix chain 'A' and resid 589 through 601 Processing helix chain 'A' and resid 602 through 607 removed outlier: 3.609A pdb=" N ASP A 605 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 72 removed outlier: 4.461A pdb=" N ASP B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.576A pdb=" N TYR B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 105 removed outlier: 3.821A pdb=" N PHE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.665A pdb=" N TYR B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 153 through 173 removed outlier: 3.520A pdb=" N TYR B 173 " --> pdb=" O MET B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.579A pdb=" N HIS B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.572A pdb=" N LEU B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.687A pdb=" N GLU B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 266 Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 393 through 421 removed outlier: 3.798A pdb=" N ARG B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.572A pdb=" N PHE B 453 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.902A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 495 removed outlier: 3.629A pdb=" N ALA B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 524 Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.730A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 563 Processing helix chain 'B' and resid 589 through 601 Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.616A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 28 through 33 Processing helix chain 'C' and resid 83 through 97 Processing helix chain 'C' and resid 107 through 113 removed outlier: 3.709A pdb=" N LYS C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 124 Processing helix chain 'C' and resid 127 through 141 Processing helix chain 'C' and resid 143 through 160 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.662A pdb=" N GLU D 11 " --> pdb=" O VAL D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 removed outlier: 3.893A pdb=" N HIS D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 111 removed outlier: 3.622A pdb=" N LEU D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 Processing helix chain 'D' and resid 176 through 190 removed outlier: 4.071A pdb=" N LYS D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 removed outlier: 3.757A pdb=" N SER D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 288 removed outlier: 3.902A pdb=" N TYR D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 381 removed outlier: 3.645A pdb=" N LYS D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 Processing helix chain 'D' and resid 419 through 432 Processing helix chain 'D' and resid 457 through 459 No H-bonds generated for 'chain 'D' and resid 457 through 459' Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 removed outlier: 4.007A pdb=" N TYR A 534 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AA4, first strand: chain 'C' and resid 15 through 19 removed outlier: 8.685A pdb=" N MET C 77 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 7 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 118 through 123 removed outlier: 6.517A pdb=" N LEU D 129 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TRP D 141 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR D 131 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 198 through 200 removed outlier: 6.616A pdb=" N VAL D 199 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE D 276 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE D 312 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU D 337 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE D 440 " --> pdb=" O GLU D 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 391 through 392 removed outlier: 6.096A pdb=" N ARG D 409 " --> pdb=" O VAL D 475 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL D 477 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS D 411 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE D 452 " --> pdb=" O GLN D 474 " (cutoff:3.500A) 669 hydrogen bonds defined for protein. 1971 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: 3.93 Time building geometry restraints manager: 3.59 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: 3865 1.34 - 1.46: 2375 1.46 - 1.58: 6437 1.58 - 1.69: 1 1.69 - 1.81: 88 Bond restraints: 12766 Sorted by residual: bond pdb=" C LEU A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.60e+00 bond pdb=" C TYR A 186 " pdb=" N PRO A 187 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.25e-02 6.40e+03 2.52e+00 bond pdb=" CB ASN A 394 " pdb=" CG ASN A 394 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.52e+00 bond pdb=" CA LEU A 302 " pdb=" C LEU A 302 " ideal model delta sigma weight residual 1.518 1.580 -0.062 4.01e-02 6.22e+02 2.40e+00 bond pdb=" CA ASN A 394 " pdb=" CB ASN A 394 " ideal model delta sigma weight residual 1.533 1.558 -0.025 1.66e-02 3.63e+03 2.27e+00 ... (remaining 12761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 16994 2.74 - 5.48: 266 5.48 - 8.21: 49 8.21 - 10.95: 3 10.95 - 13.69: 3 Bond angle restraints: 17315 Sorted by residual: angle pdb=" N ASN D 451 " pdb=" CA ASN D 451 " pdb=" C ASN D 451 " ideal model delta sigma weight residual 110.91 116.55 -5.64 1.17e+00 7.31e-01 2.33e+01 angle pdb=" C VAL D 445 " pdb=" N SER D 446 " pdb=" CA SER D 446 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C SER A 393 " pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 123.91 130.52 -6.61 1.66e+00 3.63e-01 1.59e+01 angle pdb=" CA LEU D 12 " pdb=" CB LEU D 12 " pdb=" CG LEU D 12 " ideal model delta sigma weight residual 116.30 129.99 -13.69 3.50e+00 8.16e-02 1.53e+01 angle pdb=" N TYR A 335 " pdb=" CA TYR A 335 " pdb=" C TYR A 335 " ideal model delta sigma weight residual 114.64 108.81 5.83 1.52e+00 4.33e-01 1.47e+01 ... (remaining 17310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 7158 15.29 - 30.58: 364 30.58 - 45.86: 70 45.86 - 61.15: 9 61.15 - 76.44: 8 Dihedral angle restraints: 7609 sinusoidal: 2991 harmonic: 4618 Sorted by residual: dihedral pdb=" CA ASN D 450 " pdb=" C ASN D 450 " pdb=" N ASN D 451 " pdb=" CA ASN D 451 " ideal model delta harmonic sigma weight residual 180.00 147.94 32.06 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CA PHE C 170 " pdb=" C PHE C 170 " pdb=" N ASN C 171 " pdb=" CA ASN C 171 " ideal model delta harmonic sigma weight residual -180.00 -153.07 -26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PHE D 434 " pdb=" C PHE D 434 " pdb=" N ARG D 435 " pdb=" CA ARG D 435 " ideal model delta harmonic sigma weight residual 180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 7606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1743 0.078 - 0.156: 207 0.156 - 0.234: 13 0.234 - 0.312: 1 0.312 - 0.390: 4 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CB ILE D 453 " pdb=" CA ILE D 453 " pdb=" CG1 ILE D 453 " pdb=" CG2 ILE D 453 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB VAL D 454 " pdb=" CA VAL D 454 " pdb=" CG1 VAL D 454 " pdb=" CG2 VAL D 454 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB ILE C 172 " pdb=" CA ILE C 172 " pdb=" CG1 ILE C 172 " pdb=" CG2 ILE C 172 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1965 not shown) Planarity restraints: 2161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 508 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.58e+00 pdb=" C VAL A 508 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 508 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR A 509 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 510 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C LEU A 510 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU A 510 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 511 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 346 " 0.022 2.00e-02 2.50e+03 1.52e-02 5.77e+00 pdb=" CG TRP B 346 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 346 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 346 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 346 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 346 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 346 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 346 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 346 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 346 " 0.004 2.00e-02 2.50e+03 ... (remaining 2158 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3447 2.81 - 3.33: 11373 3.33 - 3.85: 20249 3.85 - 4.38: 23229 4.38 - 4.90: 39733 Nonbonded interactions: 98031 Sorted by model distance: nonbonded pdb=" O PRO B 365 " pdb=" OH TYR B 422 " model vdw 2.283 3.040 nonbonded pdb=" O LYS B 108 " pdb=" OG SER B 111 " model vdw 2.307 3.040 nonbonded pdb=" OH TYR B 158 " pdb=" O HIS B 228 " model vdw 2.316 3.040 nonbonded pdb=" O GLU A 512 " pdb=" OG SER A 515 " model vdw 2.323 3.040 nonbonded pdb=" O LYS A 108 " pdb=" OG SER A 111 " model vdw 2.326 3.040 ... (remaining 98026 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 54 through 316 or (resid 317 and (name N or name CA or nam \ e C or name O or name CB )) or resid 339 through 608)) selection = (chain 'B' and (resid 54 through 388 or (resid 389 and (name N or name CA or nam \ e C or name O or name CB )) or resid 390 or (resid 391 through 392 and (name N o \ r name CA or name C or name O or name CB )) or resid 393 through 608)) } 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=0.00 max=1.00 mean=0.99 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 30.990 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12768 Z= 0.214 Angle : 0.901 13.688 17319 Z= 0.499 Chirality : 0.053 0.390 1968 Planarity : 0.007 0.056 2161 Dihedral : 10.187 76.440 4593 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.52 % Favored : 94.42 % Rotamer: Outliers : 0.45 % Allowed : 3.35 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.46 (0.17), residues: 1523 helix: -1.78 (0.13), residues: 930 sheet: -2.19 (0.61), residues: 65 loop : -3.05 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP B 346 HIS 0.004 0.001 HIS D 108 PHE 0.030 0.003 PHE B 398 TYR 0.032 0.002 TYR D 21 ARG 0.006 0.001 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.14660 ( 669) hydrogen bonds : angle 6.45673 ( 1971) SS BOND : bond 0.00462 ( 2) SS BOND : angle 2.10006 ( 4) covalent geometry : bond 0.00447 (12766) covalent geometry : angle 0.90025 (17315) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 448 time to evaluate : 1.585 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 130 ILE cc_start: 0.8540 (pt) cc_final: 0.8205 (mt) REVERT: A 137 TYR cc_start: 0.6828 (m-10) cc_final: 0.5795 (m-10) REVERT: A 179 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7290 (tm) REVERT: A 307 ARG cc_start: 0.8503 (mmp80) cc_final: 0.8213 (mmp-170) REVERT: B 96 THR cc_start: 0.8413 (m) cc_final: 0.8073 (p) REVERT: B 126 TYR cc_start: 0.7354 (p90) cc_final: 0.7132 (p90) REVERT: B 133 ILE cc_start: 0.7500 (tt) cc_final: 0.6603 (tt) REVERT: B 534 TYR cc_start: 0.7738 (m-80) cc_final: 0.7420 (m-80) REVERT: B 608 SER cc_start: 0.8035 (m) cc_final: 0.7539 (p) REVERT: C 88 GLN cc_start: 0.7991 (tt0) cc_final: 0.7583 (tm-30) REVERT: C 92 GLU cc_start: 0.7133 (tt0) cc_final: 0.6778 (tm-30) REVERT: C 107 ASP cc_start: 0.8207 (t0) cc_final: 0.7880 (t0) REVERT: C 157 MET cc_start: 0.8261 (mtp) cc_final: 0.7898 (mtp) REVERT: D 141 TRP cc_start: 0.7927 (p-90) cc_final: 0.7531 (p-90) REVERT: D 275 LYS cc_start: 0.8375 (mttp) cc_final: 0.8117 (mtpp) REVERT: D 399 PHE cc_start: 0.7206 (t80) cc_final: 0.6969 (t80) outliers start: 6 outliers final: 1 residues processed: 452 average time/residue: 0.2771 time to fit residues: 172.2869 Evaluate side-chains 243 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain D residue 476 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 0.0670 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 399 GLN A 406 GLN A 433 HIS A 474 GLN A 543 ASN B 67 ASN B 82 GLN B 394 ASN B 543 ASN C 142 ASN D 310 ASN D 355 ASN D 404 ASN D 443 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119606 restraints weight = 21731.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122398 restraints weight = 13093.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124273 restraints weight = 9497.160| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12768 Z= 0.119 Angle : 0.608 9.811 17319 Z= 0.313 Chirality : 0.042 0.233 1968 Planarity : 0.005 0.048 2161 Dihedral : 5.170 35.664 1685 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.05 % Allowed : 11.24 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.40 (0.20), residues: 1523 helix: 0.02 (0.16), residues: 960 sheet: -1.23 (0.71), residues: 57 loop : -2.71 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 346 HIS 0.008 0.001 HIS C 96 PHE 0.021 0.001 PHE A 101 TYR 0.022 0.001 TYR D 21 ARG 0.008 0.001 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 669) hydrogen bonds : angle 4.44479 ( 1971) SS BOND : bond 0.00599 ( 2) SS BOND : angle 2.44177 ( 4) covalent geometry : bond 0.00253 (12766) covalent geometry : angle 0.60720 (17315) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 283 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6311 (mmm160) cc_final: 0.6102 (mmm160) REVERT: A 109 ASP cc_start: 0.6179 (m-30) cc_final: 0.5948 (t70) REVERT: A 130 ILE cc_start: 0.8449 (pt) cc_final: 0.8046 (mt) REVERT: A 137 TYR cc_start: 0.6785 (m-10) cc_final: 0.6469 (m-10) REVERT: A 179 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7019 (tm) REVERT: A 295 ARG cc_start: 0.8276 (tpt-90) cc_final: 0.7928 (tpt90) REVERT: A 307 ARG cc_start: 0.8534 (mmp80) cc_final: 0.8070 (mmp-170) REVERT: A 343 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.7734 (t) REVERT: A 459 VAL cc_start: 0.9168 (m) cc_final: 0.8922 (p) REVERT: B 96 THR cc_start: 0.8258 (m) cc_final: 0.7803 (p) REVERT: B 163 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8361 (mt) REVERT: B 474 GLN cc_start: 0.7098 (tp-100) cc_final: 0.6506 (tm-30) REVERT: B 498 THR cc_start: 0.8465 (p) cc_final: 0.8248 (p) REVERT: B 534 TYR cc_start: 0.7618 (m-80) cc_final: 0.7224 (m-80) REVERT: B 608 SER cc_start: 0.8000 (m) cc_final: 0.7517 (p) REVERT: C 24 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7045 (mt-10) REVERT: C 88 GLN cc_start: 0.7986 (tt0) cc_final: 0.7618 (tm-30) REVERT: D 141 TRP cc_start: 0.7965 (p-90) cc_final: 0.7430 (p-90) REVERT: D 275 LYS cc_start: 0.8467 (mttp) cc_final: 0.8172 (mtpp) REVERT: D 325 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5739 (tm) outliers start: 41 outliers final: 23 residues processed: 314 average time/residue: 0.2243 time to fit residues: 103.5359 Evaluate side-chains 242 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 20.0000 chunk 127 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 118 optimal weight: 0.0070 chunk 22 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN B 303 GLN ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.139861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119216 restraints weight = 22032.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121984 restraints weight = 13263.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123851 restraints weight = 9659.970| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12768 Z= 0.109 Angle : 0.572 9.951 17319 Z= 0.291 Chirality : 0.041 0.217 1968 Planarity : 0.004 0.047 2161 Dihedral : 4.811 35.898 1685 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.43 % Allowed : 14.22 % Favored : 82.35 % 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: -0.47 (0.21), residues: 1523 helix: 0.79 (0.17), residues: 955 sheet: -0.63 (0.66), residues: 72 loop : -2.50 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 370 HIS 0.004 0.001 HIS D 439 PHE 0.029 0.001 PHE B 64 TYR 0.016 0.001 TYR A 301 ARG 0.007 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 669) hydrogen bonds : angle 4.09776 ( 1971) SS BOND : bond 0.00490 ( 2) SS BOND : angle 1.67247 ( 4) covalent geometry : bond 0.00236 (12766) covalent geometry : angle 0.57176 (17315) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.6126 (m-30) cc_final: 0.5890 (t70) REVERT: A 179 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7033 (tm) REVERT: A 295 ARG cc_start: 0.8342 (tpt-90) cc_final: 0.7932 (tpt90) REVERT: A 459 VAL cc_start: 0.9133 (m) cc_final: 0.8921 (p) REVERT: B 96 THR cc_start: 0.8393 (m) cc_final: 0.8000 (p) REVERT: B 126 TYR cc_start: 0.7398 (p90) cc_final: 0.7054 (p90) REVERT: B 163 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8335 (mt) REVERT: B 474 GLN cc_start: 0.7132 (tp-100) cc_final: 0.6698 (tm-30) REVERT: B 534 TYR cc_start: 0.7779 (m-80) cc_final: 0.7373 (m-80) REVERT: B 608 SER cc_start: 0.8032 (m) cc_final: 0.7519 (p) REVERT: C 88 GLN cc_start: 0.7953 (tt0) cc_final: 0.7613 (tm-30) REVERT: C 92 GLU cc_start: 0.6503 (tm-30) cc_final: 0.6256 (tm-30) REVERT: C 95 GLU cc_start: 0.7981 (pt0) cc_final: 0.7759 (tp30) REVERT: D 141 TRP cc_start: 0.7831 (p-90) cc_final: 0.7502 (p-90) REVERT: D 275 LYS cc_start: 0.8391 (mttp) cc_final: 0.8044 (mtpp) REVERT: D 325 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5646 (tm) REVERT: D 370 TRP cc_start: 0.6962 (m-90) cc_final: 0.6743 (m-90) REVERT: D 396 ASP cc_start: 0.3565 (m-30) cc_final: 0.3357 (m-30) outliers start: 46 outliers final: 30 residues processed: 276 average time/residue: 0.3022 time to fit residues: 126.7754 Evaluate side-chains 247 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 46 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 444 ASN D 169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113140 restraints weight = 21935.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115969 restraints weight = 13223.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117824 restraints weight = 9639.452| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12768 Z= 0.183 Angle : 0.645 12.730 17319 Z= 0.327 Chirality : 0.044 0.273 1968 Planarity : 0.004 0.048 2161 Dihedral : 4.913 38.911 1685 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.02 % Allowed : 15.12 % Favored : 80.86 % 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: -0.21 (0.22), residues: 1523 helix: 0.99 (0.17), residues: 954 sheet: -0.72 (0.66), residues: 71 loop : -2.31 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 346 HIS 0.006 0.001 HIS B 313 PHE 0.023 0.002 PHE B 500 TYR 0.018 0.002 TYR B 143 ARG 0.004 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 669) hydrogen bonds : angle 4.24971 ( 1971) SS BOND : bond 0.00525 ( 2) SS BOND : angle 1.18034 ( 4) covalent geometry : bond 0.00422 (12766) covalent geometry : angle 0.64479 (17315) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7235 (tm) REVERT: A 343 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8004 (t) REVERT: A 459 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8876 (p) REVERT: B 96 THR cc_start: 0.8398 (m) cc_final: 0.8027 (p) REVERT: B 136 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 204 MET cc_start: 0.8803 (tpp) cc_final: 0.8272 (tpp) REVERT: B 474 GLN cc_start: 0.7402 (tp-100) cc_final: 0.6869 (tm-30) REVERT: B 534 TYR cc_start: 0.7834 (m-80) cc_final: 0.7446 (m-80) REVERT: C 88 GLN cc_start: 0.7858 (tt0) cc_final: 0.7565 (tm-30) REVERT: C 92 GLU cc_start: 0.6441 (tm-30) cc_final: 0.6073 (tm-30) REVERT: C 95 GLU cc_start: 0.8029 (pt0) cc_final: 0.7665 (tp30) REVERT: C 133 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7180 (mt-10) REVERT: D 141 TRP cc_start: 0.7969 (p-90) cc_final: 0.7464 (p-90) REVERT: D 275 LYS cc_start: 0.8582 (mttp) cc_final: 0.8143 (mtpp) REVERT: D 325 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5604 (tm) REVERT: D 396 ASP cc_start: 0.3682 (m-30) cc_final: 0.3481 (m-30) outliers start: 54 outliers final: 41 residues processed: 254 average time/residue: 0.2103 time to fit residues: 81.1513 Evaluate side-chains 244 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 56 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN D 169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114753 restraints weight = 21962.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117670 restraints weight = 13155.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119543 restraints weight = 9422.251| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12768 Z= 0.135 Angle : 0.600 11.767 17319 Z= 0.302 Chirality : 0.042 0.254 1968 Planarity : 0.004 0.046 2161 Dihedral : 4.786 40.284 1685 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.39 % Allowed : 15.41 % Favored : 80.19 % 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: 0.09 (0.22), residues: 1523 helix: 1.25 (0.17), residues: 954 sheet: -0.67 (0.65), residues: 71 loop : -2.23 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 346 HIS 0.004 0.001 HIS D 439 PHE 0.026 0.002 PHE B 500 TYR 0.017 0.001 TYR A 301 ARG 0.003 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 669) hydrogen bonds : angle 4.05115 ( 1971) SS BOND : bond 0.00351 ( 2) SS BOND : angle 1.84008 ( 4) covalent geometry : bond 0.00309 (12766) covalent geometry : angle 0.59988 (17315) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.6983 (mmt) cc_final: 0.6648 (mmt) REVERT: A 130 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8108 (mt) REVERT: A 179 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7329 (tm) REVERT: A 343 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.7905 (t) REVERT: A 376 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: B 96 THR cc_start: 0.8115 (m) cc_final: 0.7756 (p) REVERT: B 353 ARG cc_start: 0.8320 (ttp-170) cc_final: 0.8067 (ttp-110) REVERT: B 474 GLN cc_start: 0.7217 (tp-100) cc_final: 0.6858 (tm-30) REVERT: B 608 SER cc_start: 0.8069 (m) cc_final: 0.7533 (p) REVERT: C 88 GLN cc_start: 0.7960 (tt0) cc_final: 0.7657 (tm-30) REVERT: C 92 GLU cc_start: 0.6483 (tm-30) cc_final: 0.6124 (tm-30) REVERT: C 95 GLU cc_start: 0.8042 (pt0) cc_final: 0.7581 (tp30) REVERT: D 123 LEU cc_start: 0.8408 (mm) cc_final: 0.8199 (mp) REVERT: D 141 TRP cc_start: 0.7899 (p-90) cc_final: 0.7456 (p-90) REVERT: D 275 LYS cc_start: 0.8578 (mttp) cc_final: 0.8132 (mtpp) REVERT: D 325 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5440 (tm) REVERT: D 408 THR cc_start: 0.6145 (OUTLIER) cc_final: 0.5705 (p) outliers start: 59 outliers final: 43 residues processed: 250 average time/residue: 0.2072 time to fit residues: 78.8022 Evaluate side-chains 247 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 4 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 chunk 79 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.134143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113671 restraints weight = 22142.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116252 restraints weight = 13865.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117952 restraints weight = 10309.437| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12768 Z= 0.145 Angle : 0.600 12.408 17319 Z= 0.303 Chirality : 0.042 0.241 1968 Planarity : 0.004 0.046 2161 Dihedral : 4.776 42.692 1685 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.77 % Allowed : 16.16 % Favored : 79.08 % 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: 0.23 (0.22), residues: 1523 helix: 1.35 (0.17), residues: 954 sheet: -0.75 (0.63), residues: 71 loop : -2.15 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 119 HIS 0.005 0.001 HIS B 313 PHE 0.017 0.002 PHE B 64 TYR 0.017 0.001 TYR B 534 ARG 0.003 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 669) hydrogen bonds : angle 4.07464 ( 1971) SS BOND : bond 0.00508 ( 2) SS BOND : angle 1.42305 ( 4) covalent geometry : bond 0.00333 (12766) covalent geometry : angle 0.59933 (17315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 208 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8121 (mt) REVERT: A 179 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7306 (tm) REVERT: A 343 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8046 (t) REVERT: A 376 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: A 476 PHE cc_start: 0.8485 (m-80) cc_final: 0.8007 (m-10) REVERT: B 96 THR cc_start: 0.8142 (m) cc_final: 0.7781 (p) REVERT: B 353 ARG cc_start: 0.8351 (ttp-170) cc_final: 0.7970 (ttp-110) REVERT: B 474 GLN cc_start: 0.7235 (tp-100) cc_final: 0.6825 (tm-30) REVERT: C 88 GLN cc_start: 0.7934 (tt0) cc_final: 0.7672 (tm-30) REVERT: C 92 GLU cc_start: 0.6543 (tm-30) cc_final: 0.6080 (tm-30) REVERT: C 95 GLU cc_start: 0.8010 (pt0) cc_final: 0.7507 (tp30) REVERT: D 123 LEU cc_start: 0.8367 (mm) cc_final: 0.8149 (mp) REVERT: D 141 TRP cc_start: 0.7919 (p-90) cc_final: 0.7523 (p-90) REVERT: D 325 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5632 (tm) REVERT: D 408 THR cc_start: 0.6174 (OUTLIER) cc_final: 0.5756 (p) REVERT: D 460 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.6964 (t70) outliers start: 64 outliers final: 48 residues processed: 247 average time/residue: 0.3081 time to fit residues: 116.7950 Evaluate side-chains 253 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115602 restraints weight = 22068.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118056 restraints weight = 13676.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119954 restraints weight = 10207.859| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12768 Z= 0.122 Angle : 0.579 11.183 17319 Z= 0.293 Chirality : 0.042 0.265 1968 Planarity : 0.004 0.043 2161 Dihedral : 4.680 42.795 1685 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.32 % Allowed : 16.83 % Favored : 78.85 % 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: 0.37 (0.22), residues: 1523 helix: 1.44 (0.17), residues: 954 sheet: -0.70 (0.62), residues: 71 loop : -2.05 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 119 HIS 0.004 0.001 HIS D 439 PHE 0.022 0.001 PHE B 476 TYR 0.015 0.001 TYR D 21 ARG 0.003 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 669) hydrogen bonds : angle 4.00857 ( 1971) SS BOND : bond 0.00437 ( 2) SS BOND : angle 1.22773 ( 4) covalent geometry : bond 0.00275 (12766) covalent geometry : angle 0.57828 (17315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8455 (pt) cc_final: 0.8108 (mt) REVERT: A 179 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7304 (tm) REVERT: A 343 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.7990 (t) REVERT: A 376 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: B 353 ARG cc_start: 0.8318 (ttp-170) cc_final: 0.7892 (ttp-110) REVERT: B 608 SER cc_start: 0.8017 (m) cc_final: 0.7500 (p) REVERT: C 88 GLN cc_start: 0.7977 (tt0) cc_final: 0.7730 (tm-30) REVERT: C 92 GLU cc_start: 0.6543 (tm-30) cc_final: 0.6076 (tm-30) REVERT: C 95 GLU cc_start: 0.7972 (pt0) cc_final: 0.7489 (tp30) REVERT: C 133 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7160 (mt-10) REVERT: D 123 LEU cc_start: 0.8404 (mm) cc_final: 0.8156 (mp) REVERT: D 141 TRP cc_start: 0.7896 (p-90) cc_final: 0.7514 (p-90) REVERT: D 325 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5541 (tm) REVERT: D 408 THR cc_start: 0.6150 (OUTLIER) cc_final: 0.5679 (p) REVERT: D 460 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.6921 (t70) outliers start: 58 outliers final: 43 residues processed: 247 average time/residue: 0.2027 time to fit residues: 77.0012 Evaluate side-chains 245 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 30 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114001 restraints weight = 22224.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116652 restraints weight = 13845.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118422 restraints weight = 10213.950| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12768 Z= 0.150 Angle : 0.616 11.803 17319 Z= 0.312 Chirality : 0.043 0.242 1968 Planarity : 0.004 0.043 2161 Dihedral : 4.708 38.419 1685 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.17 % Allowed : 17.50 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.36 (0.22), residues: 1523 helix: 1.42 (0.17), residues: 955 sheet: -0.72 (0.62), residues: 71 loop : -2.02 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 412 HIS 0.007 0.001 HIS B 456 PHE 0.021 0.002 PHE A 476 TYR 0.016 0.001 TYR A 301 ARG 0.003 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 669) hydrogen bonds : angle 4.07023 ( 1971) SS BOND : bond 0.00468 ( 2) SS BOND : angle 1.11807 ( 4) covalent geometry : bond 0.00347 (12766) covalent geometry : angle 0.61603 (17315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6540 (ttp) cc_final: 0.6265 (mtp) REVERT: A 130 ILE cc_start: 0.8446 (pt) cc_final: 0.8117 (mt) REVERT: A 137 TYR cc_start: 0.6606 (m-80) cc_final: 0.6273 (m-80) REVERT: A 179 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7316 (tm) REVERT: A 343 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8064 (t) REVERT: A 376 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: A 476 PHE cc_start: 0.8484 (m-80) cc_final: 0.8227 (m-10) REVERT: B 353 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.7818 (ttp-110) REVERT: B 474 GLN cc_start: 0.7301 (tm-30) cc_final: 0.7081 (tm-30) REVERT: B 608 SER cc_start: 0.7948 (m) cc_final: 0.7437 (p) REVERT: C 92 GLU cc_start: 0.6552 (tm-30) cc_final: 0.6090 (tm-30) REVERT: C 95 GLU cc_start: 0.7990 (pt0) cc_final: 0.7457 (tp30) REVERT: C 133 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7169 (mt-10) REVERT: D 123 LEU cc_start: 0.8414 (mm) cc_final: 0.8203 (mp) REVERT: D 141 TRP cc_start: 0.7841 (p-90) cc_final: 0.7590 (p-90) REVERT: D 325 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5590 (tm) REVERT: D 335 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.6735 (mp10) REVERT: D 408 THR cc_start: 0.6058 (OUTLIER) cc_final: 0.5601 (p) REVERT: D 460 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.6956 (t70) outliers start: 56 outliers final: 48 residues processed: 238 average time/residue: 0.2075 time to fit residues: 74.4638 Evaluate side-chains 251 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 140 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.137182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.116964 restraints weight = 21966.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119674 restraints weight = 13565.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121501 restraints weight = 9951.460| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12768 Z= 0.117 Angle : 0.595 10.655 17319 Z= 0.301 Chirality : 0.042 0.255 1968 Planarity : 0.004 0.057 2161 Dihedral : 4.590 39.015 1685 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.43 % Allowed : 18.39 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.45 (0.22), residues: 1523 helix: 1.43 (0.17), residues: 963 sheet: -0.56 (0.62), residues: 71 loop : -1.90 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 412 HIS 0.004 0.001 HIS D 439 PHE 0.020 0.001 PHE A 101 TYR 0.026 0.001 TYR D 21 ARG 0.014 0.000 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 669) hydrogen bonds : angle 3.98319 ( 1971) SS BOND : bond 0.00371 ( 2) SS BOND : angle 1.16877 ( 4) covalent geometry : bond 0.00265 (12766) covalent geometry : angle 0.59478 (17315) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6580 (ttp) cc_final: 0.6143 (mtp) REVERT: A 130 ILE cc_start: 0.8456 (pt) cc_final: 0.8112 (mt) REVERT: A 137 TYR cc_start: 0.6475 (m-80) cc_final: 0.6263 (m-80) REVERT: A 179 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7309 (tm) REVERT: A 343 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.7975 (t) REVERT: B 126 TYR cc_start: 0.7374 (p90) cc_final: 0.7015 (p90) REVERT: B 204 MET cc_start: 0.8620 (tpp) cc_final: 0.8131 (tpp) REVERT: B 353 ARG cc_start: 0.8256 (ttp-170) cc_final: 0.7737 (ttp-110) REVERT: B 608 SER cc_start: 0.8018 (m) cc_final: 0.7504 (p) REVERT: C 20 LYS cc_start: 0.7647 (tptm) cc_final: 0.7429 (tppt) REVERT: C 92 GLU cc_start: 0.6447 (tm-30) cc_final: 0.6017 (tm-30) REVERT: C 95 GLU cc_start: 0.7965 (pt0) cc_final: 0.7435 (tp30) REVERT: C 133 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7194 (mt-10) REVERT: D 325 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5570 (tm) REVERT: D 408 THR cc_start: 0.5973 (OUTLIER) cc_final: 0.5443 (p) REVERT: D 460 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.6922 (t70) outliers start: 46 outliers final: 38 residues processed: 235 average time/residue: 0.2061 time to fit residues: 74.0570 Evaluate side-chains 236 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 88 optimal weight: 0.0670 chunk 83 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 41 optimal weight: 0.0770 chunk 122 optimal weight: 1.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118195 restraints weight = 21757.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120897 restraints weight = 13558.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122687 restraints weight = 9952.777| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12768 Z= 0.114 Angle : 0.604 13.155 17319 Z= 0.305 Chirality : 0.042 0.253 1968 Planarity : 0.004 0.055 2161 Dihedral : 4.558 38.390 1685 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.43 % Allowed : 19.06 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.54 (0.22), residues: 1523 helix: 1.50 (0.17), residues: 959 sheet: -0.35 (0.61), residues: 69 loop : -1.88 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 141 HIS 0.007 0.001 HIS B 456 PHE 0.060 0.002 PHE A 476 TYR 0.025 0.001 TYR D 21 ARG 0.013 0.000 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 669) hydrogen bonds : angle 3.96066 ( 1971) SS BOND : bond 0.00359 ( 2) SS BOND : angle 1.14479 ( 4) covalent geometry : bond 0.00252 (12766) covalent geometry : angle 0.60362 (17315) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7179 (tm) REVERT: A 343 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8048 (t) REVERT: B 126 TYR cc_start: 0.7355 (p90) cc_final: 0.7024 (p90) REVERT: B 204 MET cc_start: 0.8662 (tpp) cc_final: 0.8211 (tpp) REVERT: B 222 GLN cc_start: 0.8605 (mt0) cc_final: 0.8370 (tt0) REVERT: B 353 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7675 (ttp-110) REVERT: B 418 TYR cc_start: 0.6633 (OUTLIER) cc_final: 0.6416 (t80) REVERT: B 608 SER cc_start: 0.8012 (m) cc_final: 0.7492 (p) REVERT: C 92 GLU cc_start: 0.6631 (tm-30) cc_final: 0.6196 (tm-30) REVERT: C 95 GLU cc_start: 0.7937 (pt0) cc_final: 0.7422 (tp30) REVERT: D 325 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5505 (tm) REVERT: D 460 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.6891 (t70) outliers start: 46 outliers final: 37 residues processed: 233 average time/residue: 0.1983 time to fit residues: 70.6211 Evaluate side-chains 235 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 82 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 98 optimal weight: 0.0040 chunk 87 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.139287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119166 restraints weight = 21776.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121883 restraints weight = 13464.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123637 restraints weight = 9878.465| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12768 Z= 0.113 Angle : 0.599 13.404 17319 Z= 0.303 Chirality : 0.042 0.233 1968 Planarity : 0.004 0.053 2161 Dihedral : 4.490 38.620 1685 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.28 % Allowed : 18.99 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.62 (0.22), residues: 1523 helix: 1.56 (0.17), residues: 957 sheet: -0.31 (0.60), residues: 69 loop : -1.81 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 346 HIS 0.006 0.001 HIS A 189 PHE 0.026 0.001 PHE A 476 TYR 0.025 0.001 TYR D 21 ARG 0.013 0.000 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 669) hydrogen bonds : angle 3.95656 ( 1971) SS BOND : bond 0.00366 ( 2) SS BOND : angle 1.13432 ( 4) covalent geometry : bond 0.00248 (12766) covalent geometry : angle 0.59885 (17315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4073.90 seconds wall clock time: 72 minutes 46.31 seconds (4366.31 seconds total)