Starting phenix.real_space_refine on Tue Nov 18 07:52:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fe8_4241/11_2025/6fe8_4241.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fe8_4241/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/6fe8_4241/11_2025/6fe8_4241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fe8_4241/11_2025/6fe8_4241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6fe8_4241/11_2025/6fe8_4241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fe8_4241/11_2025/6fe8_4241.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG: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: {'ASN:plan1': 3, 'ASP:plan': 3, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG: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: {'ASN:plan1': 12, 'GLU:plan': 16, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 175 Time building chain proxies: 3.39, per 1000 atoms: 0.27 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: 1.00 Conformation dependent library (CDL) restraints added in 615.1 milliseconds 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: 0.46 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: 2.05 Time building geometry restraints manager: 1.27 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: 0.500 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.100 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.001 ARG D 128 TYR 0.032 0.002 TYR D 21 PHE 0.030 0.003 PHE B 398 TRP 0.040 0.004 TRP B 346 HIS 0.004 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00447 (12766) covalent geometry : angle 0.90025 (17315) SS BOND : bond 0.00462 ( 2) SS BOND : angle 2.10006 ( 4) hydrogen bonds : bond 0.14660 ( 669) hydrogen bonds : angle 6.45673 ( 1971) *********************** 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 : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8540 (pt) cc_final: 0.8205 (mt) REVERT: A 137 TYR cc_start: 0.6828 (m-10) cc_final: 0.5697 (m-10) REVERT: A 179 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7288 (tm) REVERT: A 307 ARG cc_start: 0.8503 (mmp80) cc_final: 0.8211 (mmp-170) REVERT: B 96 THR cc_start: 0.8413 (m) cc_final: 0.8074 (p) REVERT: B 126 TYR cc_start: 0.7354 (p90) cc_final: 0.7127 (p90) REVERT: B 133 ILE cc_start: 0.7500 (tt) cc_final: 0.6620 (tt) REVERT: B 534 TYR cc_start: 0.7738 (m-80) cc_final: 0.7421 (m-80) REVERT: B 608 SER cc_start: 0.8035 (m) cc_final: 0.7540 (p) REVERT: C 88 GLN cc_start: 0.7991 (tt0) cc_final: 0.7584 (tm-30) REVERT: C 92 GLU cc_start: 0.7133 (tt0) cc_final: 0.6788 (tm-30) REVERT: C 107 ASP cc_start: 0.8207 (t0) cc_final: 0.7873 (t0) REVERT: C 157 MET cc_start: 0.8261 (mtp) cc_final: 0.7788 (mtp) REVERT: D 141 TRP cc_start: 0.7927 (p-90) cc_final: 0.7526 (p-90) REVERT: D 275 LYS cc_start: 0.8375 (mttp) cc_final: 0.8115 (mtpp) REVERT: D 399 PHE cc_start: 0.7206 (t80) cc_final: 0.6966 (t80) outliers start: 6 outliers final: 1 residues processed: 452 average time/residue: 0.1311 time to fit residues: 82.4555 Evaluate side-chains 242 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 543 ASN A 598 GLN B 67 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.136335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115524 restraints weight = 21980.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118364 restraints weight = 13040.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120212 restraints weight = 9366.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121449 restraints weight = 7586.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122033 restraints weight = 6606.272| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2984 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= 0.146 Angle : 0.634 10.018 17319 Z= 0.328 Chirality : 0.043 0.247 1968 Planarity : 0.005 0.049 2161 Dihedral : 5.291 36.689 1685 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.35 % Allowed : 11.39 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.20), residues: 1523 helix: 0.02 (0.16), residues: 959 sheet: -1.45 (0.69), residues: 57 loop : -2.71 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 375 TYR 0.021 0.002 TYR A 301 PHE 0.022 0.002 PHE A 264 TRP 0.019 0.002 TRP A 346 HIS 0.007 0.001 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00328 (12766) covalent geometry : angle 0.63289 (17315) SS BOND : bond 0.00339 ( 2) SS BOND : angle 2.56389 ( 4) hydrogen bonds : bond 0.04669 ( 669) hydrogen bonds : angle 4.53343 ( 1971) *********************** 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 302 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6295 (mmm160) cc_final: 0.6086 (mmm160) REVERT: A 119 MET cc_start: 0.6921 (ttp) cc_final: 0.6611 (ttp) REVERT: A 130 ILE cc_start: 0.8399 (pt) cc_final: 0.8124 (mt) REVERT: A 179 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7088 (tm) REVERT: A 307 ARG cc_start: 0.8655 (mmp80) cc_final: 0.8425 (mmp-170) REVERT: A 554 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6554 (mm-30) REVERT: B 96 THR cc_start: 0.8267 (m) cc_final: 0.7978 (p) REVERT: B 444 ASN cc_start: 0.7761 (t0) cc_final: 0.7547 (t0) REVERT: B 474 GLN cc_start: 0.7257 (tp-100) cc_final: 0.6661 (tm-30) REVERT: B 498 THR cc_start: 0.8476 (p) cc_final: 0.8268 (p) REVERT: B 516 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8257 (mmtp) REVERT: B 534 TYR cc_start: 0.7666 (m-80) cc_final: 0.7318 (m-80) REVERT: B 592 THR cc_start: 0.7382 (OUTLIER) cc_final: 0.7044 (p) REVERT: B 608 SER cc_start: 0.7999 (m) cc_final: 0.7494 (p) REVERT: C 88 GLN cc_start: 0.7960 (tt0) cc_final: 0.7606 (tm-30) REVERT: C 157 MET cc_start: 0.8292 (mtp) cc_final: 0.7864 (mtp) REVERT: D 102 ASP cc_start: 0.7413 (t70) cc_final: 0.7175 (t70) REVERT: D 141 TRP cc_start: 0.8014 (p-90) cc_final: 0.7438 (p-90) REVERT: D 275 LYS cc_start: 0.8517 (mttp) cc_final: 0.8178 (mtpp) REVERT: D 325 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5689 (tm) outliers start: 45 outliers final: 32 residues processed: 290 average time/residue: 0.1042 time to fit residues: 44.8668 Evaluate side-chains 251 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 208 MET 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 443 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 THR 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 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 B residue 592 THR Chi-restraints excluded: chain C residue 86 VAL 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 349 SER 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 27 optimal weight: 0.0470 chunk 43 optimal weight: 5.9990 chunk 121 optimal weight: 0.2980 chunk 105 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS A 598 GLN B 67 ASN B 303 GLN D 169 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.139845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119696 restraints weight = 21989.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122424 restraints weight = 13270.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124255 restraints weight = 9634.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125331 restraints weight = 7847.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.125886 restraints weight = 6931.040| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12768 Z= 0.105 Angle : 0.568 9.740 17319 Z= 0.289 Chirality : 0.040 0.238 1968 Planarity : 0.004 0.048 2161 Dihedral : 4.824 36.196 1685 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.20 % Allowed : 13.85 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1523 helix: 0.81 (0.17), residues: 960 sheet: -0.80 (0.66), residues: 73 loop : -2.44 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 147 TYR 0.021 0.001 TYR D 21 PHE 0.018 0.001 PHE A 101 TRP 0.014 0.001 TRP A 65 HIS 0.005 0.001 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00223 (12766) covalent geometry : angle 0.56702 (17315) SS BOND : bond 0.00388 ( 2) SS BOND : angle 1.68260 ( 4) hydrogen bonds : bond 0.03737 ( 669) hydrogen bonds : angle 4.08610 ( 1971) *********************** 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 305 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 262 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8404 (pt) cc_final: 0.8040 (mt) REVERT: A 179 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7018 (tm) REVERT: A 402 ILE cc_start: 0.9140 (mm) cc_final: 0.8922 (mt) REVERT: B 96 THR cc_start: 0.8350 (m) cc_final: 0.7986 (p) REVERT: B 126 TYR cc_start: 0.7452 (p90) cc_final: 0.7135 (p90) REVERT: B 444 ASN cc_start: 0.7812 (t0) cc_final: 0.7582 (t0) REVERT: B 474 GLN cc_start: 0.7086 (tp-100) cc_final: 0.6577 (tm-30) REVERT: B 608 SER cc_start: 0.7991 (m) cc_final: 0.7475 (p) REVERT: C 88 GLN cc_start: 0.7930 (tt0) cc_final: 0.7615 (tm-30) REVERT: D 141 TRP cc_start: 0.7915 (p-90) cc_final: 0.7452 (p-90) REVERT: D 275 LYS cc_start: 0.8474 (mttp) cc_final: 0.8118 (mtpp) REVERT: D 325 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5575 (tm) outliers start: 43 outliers final: 28 residues processed: 287 average time/residue: 0.0971 time to fit residues: 42.2204 Evaluate side-chains 236 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 387 LEU 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 208 MET Chi-restraints excluded: chain B residue 209 CYS 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 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 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 118 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3823 r_free = 0.3823 target = 0.139148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118050 restraints weight = 22136.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121005 restraints weight = 13097.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122934 restraints weight = 9386.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124194 restraints weight = 7581.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124710 restraints weight = 6595.260| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12768 Z= 0.111 Angle : 0.572 10.434 17319 Z= 0.290 Chirality : 0.041 0.248 1968 Planarity : 0.004 0.047 2161 Dihedral : 4.678 38.118 1685 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.43 % Allowed : 15.41 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.22), residues: 1523 helix: 1.25 (0.17), residues: 949 sheet: -0.54 (0.66), residues: 71 loop : -2.31 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 87 TYR 0.021 0.001 TYR D 21 PHE 0.029 0.001 PHE B 64 TRP 0.014 0.001 TRP C 119 HIS 0.004 0.001 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00245 (12766) covalent geometry : angle 0.57213 (17315) SS BOND : bond 0.00356 ( 2) SS BOND : angle 1.27790 ( 4) hydrogen bonds : bond 0.03787 ( 669) hydrogen bonds : angle 3.98487 ( 1971) *********************** 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 263 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6719 (ttp) cc_final: 0.6504 (ttp) REVERT: A 130 ILE cc_start: 0.8508 (pt) cc_final: 0.8089 (mt) REVERT: A 179 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7144 (tm) REVERT: A 343 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.7763 (t) REVERT: A 428 LEU cc_start: 0.7989 (tt) cc_final: 0.7453 (tt) REVERT: B 96 THR cc_start: 0.8316 (m) cc_final: 0.7929 (p) REVERT: B 126 TYR cc_start: 0.7488 (p90) cc_final: 0.7065 (p90) REVERT: B 353 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.8082 (ttp-170) REVERT: B 444 ASN cc_start: 0.7877 (t0) cc_final: 0.7619 (t0) REVERT: B 474 GLN cc_start: 0.6991 (tp-100) cc_final: 0.6575 (tm-30) REVERT: B 608 SER cc_start: 0.7959 (m) cc_final: 0.7423 (p) REVERT: C 87 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7869 (tt) REVERT: C 88 GLN cc_start: 0.7828 (tt0) cc_final: 0.7563 (tm-30) REVERT: C 133 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7116 (mt-10) REVERT: D 141 TRP cc_start: 0.7887 (p-90) cc_final: 0.7440 (p-90) REVERT: D 275 LYS cc_start: 0.8482 (mttp) cc_final: 0.8092 (mtpp) REVERT: D 325 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5545 (tm) outliers start: 46 outliers final: 34 residues processed: 249 average time/residue: 0.0933 time to fit residues: 36.1155 Evaluate side-chains 227 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 520 LEU Chi-restraints excluded: chain A residue 526 LEU 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 209 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 356 ASP 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 87 LEU 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 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 359 LEU 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 74 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 21 optimal weight: 0.0370 chunk 55 optimal weight: 7.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.138787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118078 restraints weight = 22043.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120945 restraints weight = 13168.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122807 restraints weight = 9495.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123876 restraints weight = 7699.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124557 restraints weight = 6785.980| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12768 Z= 0.112 Angle : 0.578 11.680 17319 Z= 0.289 Chirality : 0.041 0.219 1968 Planarity : 0.004 0.045 2161 Dihedral : 4.558 39.291 1685 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.43 % Allowed : 16.16 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.22), residues: 1523 helix: 1.46 (0.17), residues: 952 sheet: -0.47 (0.65), residues: 71 loop : -2.20 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 83 TYR 0.023 0.001 TYR D 21 PHE 0.024 0.001 PHE B 64 TRP 0.016 0.001 TRP C 119 HIS 0.008 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00247 (12766) covalent geometry : angle 0.57730 (17315) SS BOND : bond 0.01026 ( 2) SS BOND : angle 1.83582 ( 4) hydrogen bonds : bond 0.03729 ( 669) hydrogen bonds : angle 3.90674 ( 1971) *********************** 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 260 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8450 (pt) cc_final: 0.8083 (mt) REVERT: A 179 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7240 (tm) REVERT: A 343 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.7886 (t) REVERT: A 428 LEU cc_start: 0.7940 (tt) cc_final: 0.7699 (mt) REVERT: B 96 THR cc_start: 0.8111 (m) cc_final: 0.7776 (p) REVERT: B 126 TYR cc_start: 0.7477 (p90) cc_final: 0.7047 (p90) REVERT: B 353 ARG cc_start: 0.8311 (ttp-170) cc_final: 0.7939 (ttp-170) REVERT: B 444 ASN cc_start: 0.7833 (t0) cc_final: 0.7556 (t0) REVERT: B 474 GLN cc_start: 0.6914 (tp-100) cc_final: 0.6592 (tm-30) REVERT: C 87 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7917 (tt) REVERT: D 141 TRP cc_start: 0.7846 (p-90) cc_final: 0.7469 (p-90) REVERT: D 275 LYS cc_start: 0.8463 (mttp) cc_final: 0.8071 (mtpp) REVERT: D 325 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5410 (tm) outliers start: 46 outliers final: 35 residues processed: 244 average time/residue: 0.0942 time to fit residues: 35.2110 Evaluate side-chains 225 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 443 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 163 ILE 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 463 ILE Chi-restraints excluded: chain C residue 87 LEU 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 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 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 76 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 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 = 0.3789 r_free = 0.3789 target = 0.136494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116105 restraints weight = 22010.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118818 restraints weight = 13633.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120594 restraints weight = 9993.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121760 restraints weight = 8177.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122224 restraints weight = 7161.702| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12768 Z= 0.131 Angle : 0.579 12.187 17319 Z= 0.293 Chirality : 0.041 0.206 1968 Planarity : 0.004 0.042 2161 Dihedral : 4.603 41.447 1685 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.80 % Allowed : 16.90 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1523 helix: 1.49 (0.17), residues: 961 sheet: -0.53 (0.62), residues: 71 loop : -2.12 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 295 TYR 0.023 0.001 TYR D 21 PHE 0.020 0.001 PHE B 64 TRP 0.017 0.002 TRP A 164 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00297 (12766) covalent geometry : angle 0.57866 (17315) SS BOND : bond 0.00430 ( 2) SS BOND : angle 1.44122 ( 4) hydrogen bonds : bond 0.03885 ( 669) hydrogen bonds : angle 3.93290 ( 1971) *********************** 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 253 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.6814 (mmp) cc_final: 0.6564 (mmp) REVERT: A 130 ILE cc_start: 0.8425 (pt) cc_final: 0.8127 (mt) REVERT: A 179 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7319 (tm) REVERT: A 343 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.7910 (t) REVERT: B 96 THR cc_start: 0.8091 (m) cc_final: 0.7764 (p) REVERT: B 204 MET cc_start: 0.8582 (tpp) cc_final: 0.8190 (tpp) REVERT: B 353 ARG cc_start: 0.8367 (ttp-170) cc_final: 0.7943 (ttp-170) REVERT: B 444 ASN cc_start: 0.7840 (t0) cc_final: 0.7555 (t0) REVERT: B 458 MET cc_start: 0.7315 (ptp) cc_final: 0.6951 (ptp) REVERT: B 474 GLN cc_start: 0.6933 (tp-100) cc_final: 0.6566 (tm-30) REVERT: D 123 LEU cc_start: 0.8327 (mm) cc_final: 0.8117 (mp) REVERT: D 141 TRP cc_start: 0.7814 (p-90) cc_final: 0.7505 (p-90) REVERT: D 275 LYS cc_start: 0.8492 (mttp) cc_final: 0.8107 (mtpp) REVERT: D 325 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5318 (tm) outliers start: 51 outliers final: 39 residues processed: 236 average time/residue: 0.0938 time to fit residues: 34.1806 Evaluate side-chains 229 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 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 100 MET 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 463 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LEU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** D 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.132028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110756 restraints weight = 22174.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113484 restraints weight = 13529.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115288 restraints weight = 9853.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116334 restraints weight = 8057.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.116774 restraints weight = 7137.801| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12768 Z= 0.209 Angle : 0.666 13.258 17319 Z= 0.339 Chirality : 0.044 0.207 1968 Planarity : 0.004 0.044 2161 Dihedral : 4.938 43.188 1685 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.47 % Allowed : 16.60 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.22), residues: 1523 helix: 1.26 (0.17), residues: 957 sheet: -0.95 (0.60), residues: 71 loop : -2.15 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 295 TYR 0.018 0.002 TYR B 143 PHE 0.023 0.002 PHE A 264 TRP 0.018 0.002 TRP A 164 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00489 (12766) covalent geometry : angle 0.66595 (17315) SS BOND : bond 0.00468 ( 2) SS BOND : angle 1.30529 ( 4) hydrogen bonds : bond 0.04746 ( 669) hydrogen bonds : angle 4.27611 ( 1971) *********************** 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 259 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8467 (pt) cc_final: 0.8186 (mt) REVERT: A 179 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7635 (tm) REVERT: A 256 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8821 (mp) REVERT: A 476 PHE cc_start: 0.8661 (m-80) cc_final: 0.8151 (m-10) REVERT: B 96 THR cc_start: 0.8217 (m) cc_final: 0.7872 (p) REVERT: B 204 MET cc_start: 0.8784 (tpp) cc_final: 0.8365 (tpp) REVERT: B 444 ASN cc_start: 0.7849 (t0) cc_final: 0.7597 (t0) REVERT: B 474 GLN cc_start: 0.7382 (tp-100) cc_final: 0.7059 (tm-30) REVERT: C 87 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.7936 (tt) REVERT: D 96 TYR cc_start: 0.8151 (m-80) cc_final: 0.7649 (m-80) REVERT: D 123 LEU cc_start: 0.8410 (mm) cc_final: 0.8184 (mp) REVERT: D 141 TRP cc_start: 0.7954 (p-90) cc_final: 0.7514 (p-90) REVERT: D 325 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5696 (tm) REVERT: D 460 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7026 (t70) outliers start: 60 outliers final: 42 residues processed: 239 average time/residue: 0.0933 time to fit residues: 34.6262 Evaluate side-chains 241 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 243 THR Chi-restraints excluded: chain A residue 256 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 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 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 188 LEU Chi-restraints excluded: chain B residue 209 CYS 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 463 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LEU 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 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 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 42 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 61 optimal weight: 0.0270 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.3844 ------------------------------------------------------------------------------- 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** D 23 HIS D 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115158 restraints weight = 22063.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118075 restraints weight = 13145.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119970 restraints weight = 9426.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121071 restraints weight = 7661.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121919 restraints weight = 6753.547| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12768 Z= 0.123 Angle : 0.593 11.017 17319 Z= 0.302 Chirality : 0.042 0.260 1968 Planarity : 0.003 0.041 2161 Dihedral : 4.734 43.932 1685 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.65 % Allowed : 17.80 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1523 helix: 1.43 (0.17), residues: 959 sheet: -0.86 (0.60), residues: 71 loop : -2.01 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.035 0.001 TYR D 21 PHE 0.018 0.001 PHE B 64 TRP 0.022 0.002 TRP B 412 HIS 0.004 0.001 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00278 (12766) covalent geometry : angle 0.59301 (17315) SS BOND : bond 0.00356 ( 2) SS BOND : angle 1.27232 ( 4) hydrogen bonds : bond 0.03959 ( 669) hydrogen bonds : angle 4.05439 ( 1971) *********************** 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: 49 poor density : 207 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6439 (ttp) cc_final: 0.6157 (mtp) REVERT: A 130 ILE cc_start: 0.8447 (pt) cc_final: 0.8209 (mt) REVERT: A 137 TYR cc_start: 0.6523 (m-80) cc_final: 0.6107 (m-80) REVERT: A 179 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7602 (tm) REVERT: B 444 ASN cc_start: 0.7927 (t0) cc_final: 0.7668 (t0) REVERT: B 474 GLN cc_start: 0.7216 (tp-100) cc_final: 0.6887 (tm-30) REVERT: B 608 SER cc_start: 0.8055 (m) cc_final: 0.7504 (p) REVERT: D 123 LEU cc_start: 0.8394 (mm) cc_final: 0.8142 (mp) REVERT: D 141 TRP cc_start: 0.7809 (p-90) cc_final: 0.7547 (p-90) REVERT: D 325 LEU cc_start: 0.6115 (OUTLIER) cc_final: 0.5662 (tm) REVERT: D 460 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6948 (t70) outliers start: 49 outliers final: 38 residues processed: 239 average time/residue: 0.0971 time to fit residues: 35.5655 Evaluate side-chains 231 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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 383 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 607 LEU 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 302 LEU Chi-restraints excluded: chain B residue 347 LYS 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 463 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LEU 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 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 334 LEU Chi-restraints excluded: chain D residue 349 SER 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 12 optimal weight: 0.2980 chunk 107 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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** D 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111645 restraints weight = 22261.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114396 restraints weight = 13445.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116009 restraints weight = 9782.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117369 restraints weight = 8072.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117696 restraints weight = 7003.407| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12768 Z= 0.185 Angle : 0.648 12.224 17319 Z= 0.330 Chirality : 0.044 0.262 1968 Planarity : 0.004 0.043 2161 Dihedral : 4.834 43.466 1685 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.65 % Allowed : 18.09 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1523 helix: 1.34 (0.17), residues: 959 sheet: -1.04 (0.60), residues: 71 loop : -2.06 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.033 0.002 TYR D 21 PHE 0.020 0.002 PHE A 264 TRP 0.023 0.002 TRP B 412 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00435 (12766) covalent geometry : angle 0.64727 (17315) SS BOND : bond 0.00427 ( 2) SS BOND : angle 1.32967 ( 4) hydrogen bonds : bond 0.04481 ( 669) hydrogen bonds : angle 4.22367 ( 1971) *********************** 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 245 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.6737 (mmp) cc_final: 0.6508 (mmp) REVERT: A 119 MET cc_start: 0.6641 (ttp) cc_final: 0.6235 (ttp) REVERT: A 130 ILE cc_start: 0.8490 (pt) cc_final: 0.8164 (mt) REVERT: A 179 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7640 (tm) REVERT: A 476 PHE cc_start: 0.8589 (m-80) cc_final: 0.8320 (m-10) REVERT: B 96 THR cc_start: 0.8207 (m) cc_final: 0.7612 (p) REVERT: B 444 ASN cc_start: 0.7835 (t0) cc_final: 0.7587 (t0) REVERT: B 474 GLN cc_start: 0.7358 (tp-100) cc_final: 0.7038 (tm-30) REVERT: C 87 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.7905 (tt) REVERT: D 123 LEU cc_start: 0.8428 (mm) cc_final: 0.8203 (mp) REVERT: D 325 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5590 (tm) REVERT: D 335 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.6666 (mp10) REVERT: D 460 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.6986 (t70) outliers start: 49 outliers final: 44 residues processed: 229 average time/residue: 0.0961 time to fit residues: 33.6369 Evaluate side-chains 240 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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 492 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 302 LEU Chi-restraints excluded: chain B residue 347 LYS 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 463 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 87 LEU 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 15 ASP 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 334 LEU Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 349 SER 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 38 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 123 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 D 427 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114833 restraints weight = 22043.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117668 restraints weight = 13259.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119542 restraints weight = 9604.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120642 restraints weight = 7797.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121536 restraints weight = 6855.650| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 12768 Z= 0.129 Angle : 0.633 14.220 17319 Z= 0.323 Chirality : 0.043 0.343 1968 Planarity : 0.004 0.040 2161 Dihedral : 4.810 43.740 1685 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.35 % Allowed : 18.47 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.22), residues: 1523 helix: 1.46 (0.17), residues: 956 sheet: -0.98 (0.59), residues: 71 loop : -1.95 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.035 0.001 TYR D 21 PHE 0.019 0.001 PHE B 476 TRP 0.042 0.002 TRP D 141 HIS 0.008 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00298 (12766) covalent geometry : angle 0.62776 (17315) SS BOND : bond 0.01242 ( 2) SS BOND : angle 5.35426 ( 4) hydrogen bonds : bond 0.04097 ( 669) hydrogen bonds : angle 4.15417 ( 1971) ********************** 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 247 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.6391 (mmp) cc_final: 0.6110 (mmp) REVERT: A 130 ILE cc_start: 0.8477 (pt) cc_final: 0.8199 (mt) REVERT: A 476 PHE cc_start: 0.8558 (m-80) cc_final: 0.8133 (m-10) REVERT: B 96 THR cc_start: 0.8369 (m) cc_final: 0.8133 (p) REVERT: B 444 ASN cc_start: 0.7882 (t0) cc_final: 0.7645 (t0) REVERT: B 474 GLN cc_start: 0.7317 (tp-100) cc_final: 0.7049 (tm-30) REVERT: B 608 SER cc_start: 0.8044 (m) cc_final: 0.7497 (p) REVERT: C 87 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8199 (tt) REVERT: D 325 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5651 (tm) REVERT: D 460 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6928 (t70) outliers start: 45 outliers final: 40 residues processed: 231 average time/residue: 0.0908 time to fit residues: 32.7080 Evaluate side-chains 234 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 223 CYS 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 383 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 526 LEU 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 302 LEU Chi-restraints excluded: chain B residue 347 LYS 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 87 LEU 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 15 ASP 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 334 LEU Chi-restraints excluded: chain D residue 349 SER 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 113 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.0770 chunk 87 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.0000 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.0020 chunk 130 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.4150 ------------------------------------------------------------------------------- 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** D 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120327 restraints weight = 21967.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123070 restraints weight = 13500.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124892 restraints weight = 9879.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126050 restraints weight = 8050.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126581 restraints weight = 7056.943| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 12768 Z= 0.110 Angle : 0.599 10.572 17319 Z= 0.306 Chirality : 0.042 0.267 1968 Planarity : 0.004 0.040 2161 Dihedral : 4.499 40.454 1683 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.68 % Allowed : 19.51 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.22), residues: 1523 helix: 1.65 (0.17), residues: 946 sheet: -0.76 (0.58), residues: 71 loop : -1.88 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.036 0.001 TYR D 21 PHE 0.019 0.001 PHE B 64 TRP 0.039 0.002 TRP D 141 HIS 0.004 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00241 (12766) covalent geometry : angle 0.59696 (17315) SS BOND : bond 0.00782 ( 2) SS BOND : angle 3.54459 ( 4) hydrogen bonds : bond 0.03577 ( 669) hydrogen bonds : angle 3.99742 ( 1971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1967.65 seconds wall clock time: 34 minutes 54.44 seconds (2094.44 seconds total)