Starting phenix.real_space_refine on Tue Mar 3 15:18:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7met_23803/03_2026/7met_23803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7met_23803/03_2026/7met_23803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7met_23803/03_2026/7met_23803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7met_23803/03_2026/7met_23803.map" model { file = "/net/cci-nas-00/data/ceres_data/7met_23803/03_2026/7met_23803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7met_23803/03_2026/7met_23803.cif" } resolution = 3.97 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 2 4.86 5 C 4121 2.51 5 N 1169 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6521 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 3643 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 222} Link IDs: {'PTRANS': 13, 'TRANS': 550} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 799 Unresolved non-hydrogen angles: 1029 Unresolved non-hydrogen dihedrals: 635 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 22, 'TYR:plan': 9, 'ASP:plan': 19, 'ASN:plan1': 14, 'HIS:plan': 9, 'GLU:plan': 15, 'ARG:plan': 16, 'PHE:plan': 7} Unresolved non-hydrogen planarities: 477 Chain: "B" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 2834 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'PTRANS': 10, 'TRANS': 444} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 756 Unresolved non-hydrogen angles: 972 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'ASP:plan': 18, 'GLU:plan': 15, 'GLN:plan1': 21, 'ASN:plan1': 13, 'ARG:plan': 16, 'PHE:plan': 7, 'HIS:plan': 8, 'TYR:plan': 7} Unresolved non-hydrogen planarities: 448 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'Z5G': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.35, per 1000 atoms: 0.21 Number of scatterers: 6521 At special positions: 0 Unit cell: (80.56, 81.62, 136.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 20 16.00 O 1209 8.00 N 1169 7.00 C 4121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 295.3 milliseconds 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 68.6% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 removed outlier: 3.733A pdb=" N SER A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 52 removed outlier: 3.664A pdb=" N LEU A 23 " --> pdb=" O TRP A 19 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLY A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 103 Proline residue: A 62 - end of helix removed outlier: 4.334A pdb=" N LEU A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 removed outlier: 3.825A pdb=" N TYR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 158 Processing helix chain 'A' and resid 167 through 207 removed outlier: 4.201A pdb=" N ILE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 216 through 265 removed outlier: 4.471A pdb=" N GLU A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Proline residue: A 247 - end of helix removed outlier: 3.630A pdb=" N LEU A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 removed outlier: 3.921A pdb=" N THR A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 274' Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 288 through 309 removed outlier: 4.274A pdb=" N ASN A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.961A pdb=" N LEU A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 removed outlier: 4.040A pdb=" N SER A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.508A pdb=" N ILE A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 451 through 458 removed outlier: 3.801A pdb=" N LEU A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.915A pdb=" N SER A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'A' and resid 507 through 522 removed outlier: 3.687A pdb=" N GLN A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 554 through 560 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'B' and resid 8 through 16 removed outlier: 3.786A pdb=" N ILE B 12 " --> pdb=" O TYR B 8 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 53 removed outlier: 3.692A pdb=" N LEU B 23 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 25 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 105 Proline residue: B 62 - end of helix removed outlier: 3.677A pdb=" N ARG B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.832A pdb=" N LEU B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 158 removed outlier: 3.623A pdb=" N MET B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR B 157 " --> pdb=" O TYR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 316 removed outlier: 3.770A pdb=" N LYS B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 374 through 382 removed outlier: 4.037A pdb=" N LEU B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 424 through 430 removed outlier: 3.720A pdb=" N ALA B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 451 through 458 removed outlier: 4.280A pdb=" N LEU B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 490 removed outlier: 3.826A pdb=" N ASN B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 520 Processing helix chain 'B' and resid 530 through 537 Processing helix chain 'B' and resid 553 through 561 removed outlier: 3.761A pdb=" N LEU B 557 " --> pdb=" O THR B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 570 removed outlier: 3.804A pdb=" N TYR B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN B 566 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 340 through 343 removed outlier: 7.605A pdb=" N LEU A 342 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS A 352 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 367 removed outlier: 3.598A pdb=" N VAL A 367 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 540 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 552 " --> pdb=" O ILE A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA4, first strand: chain 'B' and resid 335 through 338 removed outlier: 3.621A pdb=" N ILE B 335 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 342 through 344 removed outlier: 6.744A pdb=" N LEU B 342 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 348 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 411 through 414 removed outlier: 3.580A pdb=" N ILE B 495 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA B 365 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET B 543 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 367 " --> pdb=" O MET B 543 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL B 542 " --> pdb=" O VAL B 549 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1413 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: 0.86 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1129 1.32 - 1.44: 1588 1.44 - 1.56: 3840 1.56 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 6596 Sorted by residual: bond pdb=" C08 Z5G A 601 " pdb=" N10 Z5G A 601 " ideal model delta sigma weight residual 1.345 1.456 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C08 Z5G A 602 " pdb=" N10 Z5G A 602 " ideal model delta sigma weight residual 1.345 1.454 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C11 Z5G A 601 " pdb=" N10 Z5G A 601 " ideal model delta sigma weight residual 1.375 1.454 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C11 Z5G A 602 " pdb=" N10 Z5G A 602 " ideal model delta sigma weight residual 1.375 1.448 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C02 Z5G A 601 " pdb="CL01 Z5G A 601 " ideal model delta sigma weight residual 1.729 1.786 -0.057 2.00e-02 2.50e+03 8.05e+00 ... (remaining 6591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 8830 1.69 - 3.37: 135 3.37 - 5.06: 49 5.06 - 6.75: 13 6.75 - 8.44: 6 Bond angle restraints: 9033 Sorted by residual: angle pdb=" CA PRO B 17 " pdb=" N PRO B 17 " pdb=" CD PRO B 17 " ideal model delta sigma weight residual 112.00 107.68 4.32 1.40e+00 5.10e-01 9.51e+00 angle pdb=" C14 Z5G A 602 " pdb=" C13 Z5G A 602 " pdb=" S12 Z5G A 602 " ideal model delta sigma weight residual 121.23 129.67 -8.44 3.00e+00 1.11e-01 7.91e+00 angle pdb=" C14 Z5G A 601 " pdb=" C13 Z5G A 601 " pdb=" S12 Z5G A 601 " ideal model delta sigma weight residual 121.23 129.50 -8.27 3.00e+00 1.11e-01 7.59e+00 angle pdb=" C MET A 166 " pdb=" N VAL A 167 " pdb=" CA VAL A 167 " ideal model delta sigma weight residual 121.97 126.64 -4.67 1.80e+00 3.09e-01 6.74e+00 angle pdb=" N ILE A 429 " pdb=" CA ILE A 429 " pdb=" C ILE A 429 " ideal model delta sigma weight residual 111.91 109.62 2.29 8.90e-01 1.26e+00 6.63e+00 ... (remaining 9028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 3618 15.90 - 31.81: 204 31.81 - 47.71: 52 47.71 - 63.61: 7 63.61 - 79.51: 7 Dihedral angle restraints: 3888 sinusoidal: 947 harmonic: 2941 Sorted by residual: dihedral pdb=" CA PRO B 17 " pdb=" C PRO B 17 " pdb=" N TYR B 18 " pdb=" CA TYR B 18 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLN A 268 " pdb=" C GLN A 268 " pdb=" N ILE A 269 " pdb=" CA ILE A 269 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA VAL A 167 " pdb=" C VAL A 167 " pdb=" N PHE A 168 " pdb=" CA PHE A 168 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 634 0.027 - 0.053: 304 0.053 - 0.080: 114 0.080 - 0.106: 50 0.106 - 0.133: 30 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CB VAL A 167 " pdb=" CA VAL A 167 " pdb=" CG1 VAL A 167 " pdb=" CG2 VAL A 167 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CB VAL A 239 " pdb=" CA VAL A 239 " pdb=" CG1 VAL A 239 " pdb=" CG2 VAL A 239 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA PRO A 106 " pdb=" N PRO A 106 " pdb=" C PRO A 106 " pdb=" CB PRO A 106 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1129 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 16 " 0.076 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO B 17 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 17 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 17 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 290 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO B 291 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 121 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C LYS B 121 " 0.030 2.00e-02 2.50e+03 pdb=" O LYS B 121 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE B 122 " -0.010 2.00e-02 2.50e+03 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1238 2.77 - 3.30: 6738 3.30 - 3.83: 10450 3.83 - 4.37: 10126 4.37 - 4.90: 18212 Nonbonded interactions: 46764 Sorted by model distance: nonbonded pdb=" OH TYR B 18 " pdb=" OG SER B 89 " model vdw 2.236 3.040 nonbonded pdb=" ND2 ASN B 125 " pdb=" OG SER B 311 " model vdw 2.238 3.120 nonbonded pdb=" O ALA A 132 " pdb=" OG SER A 136 " model vdw 2.285 3.040 nonbonded pdb=" O ALA B 308 " pdb=" OG SER B 311 " model vdw 2.286 3.040 nonbonded pdb=" NE2 GLN A 96 " pdb=" O GLY A 432 " model vdw 2.345 3.120 ... (remaining 46759 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.480 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 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 0.111 6596 Z= 0.205 Angle : 0.643 8.435 9033 Z= 0.326 Chirality : 0.041 0.133 1132 Planarity : 0.005 0.113 1185 Dihedral : 12.062 79.515 1986 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.24 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 1.22 (0.27), residues: 1013 helix: 1.90 (0.21), residues: 624 sheet: 1.11 (0.98), residues: 34 loop : -1.27 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 160 TYR 0.017 0.001 TYR B 110 PHE 0.011 0.001 PHE A 71 TRP 0.010 0.001 TRP A 262 HIS 0.002 0.000 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6596) covalent geometry : angle 0.64319 ( 9033) hydrogen bonds : bond 0.13882 ( 476) hydrogen bonds : angle 5.34575 ( 1413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8635 (t0) cc_final: 0.8320 (t0) REVERT: A 61 PHE cc_start: 0.8276 (t80) cc_final: 0.8033 (t80) REVERT: A 127 GLU cc_start: 0.7651 (tp30) cc_final: 0.7431 (tp30) REVERT: B 90 LEU cc_start: 0.7958 (tp) cc_final: 0.7676 (tp) REVERT: B 140 ILE cc_start: 0.9026 (tp) cc_final: 0.8824 (tp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0681 time to fit residues: 17.2802 Evaluate side-chains 167 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 40.0000 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 40.0000 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 50.0000 chunk 61 optimal weight: 0.7980 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 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.211091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.173262 restraints weight = 9581.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.178610 restraints weight = 9412.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.179174 restraints weight = 4837.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.180198 restraints weight = 3603.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.180412 restraints weight = 3351.911| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6596 Z= 0.190 Angle : 0.628 9.254 9033 Z= 0.329 Chirality : 0.044 0.162 1132 Planarity : 0.004 0.073 1185 Dihedral : 4.759 35.686 1093 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.13 % Favored : 94.37 % Rotamer: Outliers : 2.39 % Allowed : 20.53 % Favored : 77.09 % 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: 0.88 (0.27), residues: 1013 helix: 1.57 (0.20), residues: 651 sheet: 0.76 (0.94), residues: 34 loop : -1.49 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 160 TYR 0.019 0.002 TYR B 18 PHE 0.013 0.001 PHE A 214 TRP 0.011 0.001 TRP A 19 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 6596) covalent geometry : angle 0.62836 ( 9033) hydrogen bonds : bond 0.03898 ( 476) hydrogen bonds : angle 4.57049 ( 1413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8958 (t0) cc_final: 0.8587 (t0) REVERT: A 101 LYS cc_start: 0.8708 (tttm) cc_final: 0.8213 (tttm) REVERT: A 127 GLU cc_start: 0.7811 (tp30) cc_final: 0.7489 (tp30) REVERT: B 47 ILE cc_start: 0.7444 (mm) cc_final: 0.7243 (mm) REVERT: B 72 ARG cc_start: 0.8297 (ttm170) cc_final: 0.7812 (ptp-170) REVERT: B 90 LEU cc_start: 0.8354 (tp) cc_final: 0.8114 (tp) REVERT: B 121 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7283 (ttmm) outliers start: 10 outliers final: 8 residues processed: 192 average time/residue: 0.0687 time to fit residues: 17.9146 Evaluate side-chains 185 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 279 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 76 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 35 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.216238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.182442 restraints weight = 9518.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.182933 restraints weight = 5772.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.183939 restraints weight = 4584.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.185571 restraints weight = 2891.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.185357 restraints weight = 2527.039| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6596 Z= 0.111 Angle : 0.547 8.956 9033 Z= 0.282 Chirality : 0.042 0.157 1132 Planarity : 0.004 0.056 1185 Dihedral : 4.425 36.781 1093 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.49 % Allowed : 3.95 % Favored : 95.56 % Rotamer: Outliers : 2.15 % Allowed : 24.82 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.14 (0.27), residues: 1013 helix: 1.71 (0.21), residues: 659 sheet: 0.84 (0.92), residues: 34 loop : -1.30 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.013 0.001 TYR B 18 PHE 0.010 0.001 PHE A 214 TRP 0.007 0.001 TRP A 262 HIS 0.001 0.000 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 6596) covalent geometry : angle 0.54722 ( 9033) hydrogen bonds : bond 0.03308 ( 476) hydrogen bonds : angle 4.10478 ( 1413) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.189 Fit side-chains REVERT: A 32 ASN cc_start: 0.8730 (t0) cc_final: 0.8323 (t0) REVERT: A 101 LYS cc_start: 0.8743 (tttm) cc_final: 0.8226 (tttm) REVERT: A 127 GLU cc_start: 0.7571 (tp30) cc_final: 0.7272 (tp30) REVERT: A 238 MET cc_start: 0.8171 (tmm) cc_final: 0.7274 (ttt) REVERT: A 287 LEU cc_start: 0.8939 (mp) cc_final: 0.8145 (mp) REVERT: A 314 GLU cc_start: 0.8739 (pp20) cc_final: 0.8514 (pp20) REVERT: B 47 ILE cc_start: 0.7449 (mm) cc_final: 0.7244 (mm) REVERT: B 72 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7986 (ptm160) REVERT: B 123 MET cc_start: 0.8762 (mtp) cc_final: 0.8440 (ttm) outliers start: 9 outliers final: 5 residues processed: 191 average time/residue: 0.0665 time to fit residues: 17.4295 Evaluate side-chains 183 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 134 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 79 optimal weight: 50.0000 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.204379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.169345 restraints weight = 9564.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.169087 restraints weight = 5709.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.170568 restraints weight = 4253.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.171208 restraints weight = 2821.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.171892 restraints weight = 2701.747| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6596 Z= 0.244 Angle : 0.679 7.285 9033 Z= 0.364 Chirality : 0.046 0.191 1132 Planarity : 0.004 0.057 1185 Dihedral : 5.214 40.251 1093 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.73 % Favored : 93.68 % Rotamer: Outliers : 6.21 % Allowed : 26.25 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.57 (0.26), residues: 1013 helix: 1.30 (0.20), residues: 656 sheet: 0.66 (0.89), residues: 34 loop : -1.60 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.024 0.003 TYR A 281 PHE 0.016 0.002 PHE A 214 TRP 0.013 0.002 TRP A 19 HIS 0.007 0.002 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 6596) covalent geometry : angle 0.67913 ( 9033) hydrogen bonds : bond 0.04450 ( 476) hydrogen bonds : angle 4.79212 ( 1413) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.151 Fit side-chains REVERT: A 32 ASN cc_start: 0.9052 (t0) cc_final: 0.8738 (t0) REVERT: A 101 LYS cc_start: 0.8775 (tttm) cc_final: 0.8344 (tttm) REVERT: A 127 GLU cc_start: 0.7962 (tp30) cc_final: 0.7641 (tp30) REVERT: B 16 LYS cc_start: 0.8887 (pttp) cc_final: 0.8669 (pptt) REVERT: B 121 LYS cc_start: 0.8186 (ttmm) cc_final: 0.7687 (ttmm) REVERT: B 140 ILE cc_start: 0.9142 (tp) cc_final: 0.8904 (tp) REVERT: B 161 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6673 (pt) outliers start: 26 outliers final: 20 residues processed: 196 average time/residue: 0.0666 time to fit residues: 17.9433 Evaluate side-chains 200 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 40.0000 chunk 58 optimal weight: 0.5980 chunk 96 optimal weight: 30.0000 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.200589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.164411 restraints weight = 9730.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.165769 restraints weight = 5558.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.166483 restraints weight = 4060.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.166909 restraints weight = 2604.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.167226 restraints weight = 2328.848| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6596 Z= 0.211 Angle : 0.640 10.682 9033 Z= 0.342 Chirality : 0.045 0.177 1132 Planarity : 0.004 0.058 1185 Dihedral : 5.042 37.366 1093 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.23 % Favored : 94.18 % Rotamer: Outliers : 6.68 % Allowed : 30.07 % Favored : 63.25 % 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: 0.56 (0.26), residues: 1013 helix: 1.37 (0.20), residues: 639 sheet: 0.55 (0.88), residues: 34 loop : -1.61 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.020 0.002 TYR A 281 PHE 0.013 0.001 PHE A 214 TRP 0.014 0.002 TRP A 159 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 6596) covalent geometry : angle 0.64023 ( 9033) hydrogen bonds : bond 0.04108 ( 476) hydrogen bonds : angle 4.67579 ( 1413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.187 Fit side-chains REVERT: A 32 ASN cc_start: 0.9014 (t0) cc_final: 0.8701 (t0) REVERT: A 52 ASN cc_start: 0.7495 (m-40) cc_final: 0.7234 (m-40) REVERT: A 101 LYS cc_start: 0.8861 (tttm) cc_final: 0.8300 (tttm) REVERT: A 127 GLU cc_start: 0.7880 (tp30) cc_final: 0.7187 (tp30) REVERT: B 72 ARG cc_start: 0.8342 (ttm170) cc_final: 0.7965 (ptm160) REVERT: B 121 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7679 (ttmm) REVERT: B 140 ILE cc_start: 0.9193 (tp) cc_final: 0.8969 (tp) REVERT: B 161 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6694 (pt) outliers start: 28 outliers final: 22 residues processed: 188 average time/residue: 0.0638 time to fit residues: 16.4933 Evaluate side-chains 197 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 94 optimal weight: 0.5980 chunk 32 optimal weight: 50.0000 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.210119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.175610 restraints weight = 9658.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.175039 restraints weight = 5817.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176906 restraints weight = 4446.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177858 restraints weight = 2716.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.178368 restraints weight = 2503.674| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6596 Z= 0.115 Angle : 0.572 10.195 9033 Z= 0.295 Chirality : 0.043 0.188 1132 Planarity : 0.003 0.058 1185 Dihedral : 4.606 33.218 1093 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.34 % Favored : 95.06 % Rotamer: Outliers : 3.58 % Allowed : 32.94 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.00 (0.27), residues: 1013 helix: 1.63 (0.21), residues: 657 sheet: 0.67 (0.89), residues: 34 loop : -1.41 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.012 0.001 TYR B 18 PHE 0.009 0.001 PHE A 214 TRP 0.010 0.001 TRP A 262 HIS 0.001 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 6596) covalent geometry : angle 0.57212 ( 9033) hydrogen bonds : bond 0.03339 ( 476) hydrogen bonds : angle 4.10540 ( 1413) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.214 Fit side-chains REVERT: A 32 ASN cc_start: 0.8886 (t0) cc_final: 0.8558 (t0) REVERT: A 52 ASN cc_start: 0.7382 (m-40) cc_final: 0.7126 (m110) REVERT: A 101 LYS cc_start: 0.8777 (tttm) cc_final: 0.8178 (tttm) REVERT: A 103 LEU cc_start: 0.5680 (OUTLIER) cc_final: 0.5028 (pp) REVERT: A 127 GLU cc_start: 0.7638 (tp30) cc_final: 0.7241 (tp30) REVERT: A 287 LEU cc_start: 0.8807 (mp) cc_final: 0.8507 (mp) REVERT: B 72 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7899 (ptm160) REVERT: B 121 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7541 (ttmm) REVERT: B 123 MET cc_start: 0.8658 (mtp) cc_final: 0.8360 (ttm) outliers start: 15 outliers final: 9 residues processed: 186 average time/residue: 0.0707 time to fit residues: 17.7919 Evaluate side-chains 185 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 20.0000 chunk 34 optimal weight: 50.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.208851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.173524 restraints weight = 9542.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175842 restraints weight = 5967.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.176151 restraints weight = 4225.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.176755 restraints weight = 2673.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176949 restraints weight = 2569.784| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6596 Z= 0.133 Angle : 0.586 9.501 9033 Z= 0.301 Chirality : 0.043 0.189 1132 Planarity : 0.003 0.059 1185 Dihedral : 4.659 34.952 1093 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.64 % Favored : 94.77 % Rotamer: Outliers : 4.30 % Allowed : 34.61 % Favored : 61.10 % 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: 1.02 (0.27), residues: 1013 helix: 1.67 (0.21), residues: 656 sheet: 0.65 (0.89), residues: 34 loop : -1.45 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.012 0.002 TYR A 225 PHE 0.010 0.001 PHE A 214 TRP 0.018 0.002 TRP A 262 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6596) covalent geometry : angle 0.58563 ( 9033) hydrogen bonds : bond 0.03480 ( 476) hydrogen bonds : angle 4.14873 ( 1413) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.163 Fit side-chains REVERT: A 32 ASN cc_start: 0.8957 (t0) cc_final: 0.8652 (t0) REVERT: A 52 ASN cc_start: 0.7301 (m-40) cc_final: 0.6990 (m110) REVERT: A 101 LYS cc_start: 0.8798 (tttm) cc_final: 0.8188 (tttm) REVERT: A 103 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5282 (pp) REVERT: A 127 GLU cc_start: 0.7571 (tp30) cc_final: 0.7365 (tp30) REVERT: B 41 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8234 (mmtt) REVERT: B 72 ARG cc_start: 0.8307 (ttm170) cc_final: 0.7934 (ptm160) REVERT: B 121 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7538 (ttmm) REVERT: B 123 MET cc_start: 0.8671 (mtp) cc_final: 0.8244 (ttm) outliers start: 18 outliers final: 12 residues processed: 189 average time/residue: 0.0619 time to fit residues: 16.0368 Evaluate side-chains 189 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.0170 chunk 4 optimal weight: 0.1980 chunk 55 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 50.0000 chunk 18 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 79 optimal weight: 40.0000 chunk 19 optimal weight: 6.9990 chunk 54 optimal weight: 40.0000 chunk 50 optimal weight: 10.0000 overall best weight: 2.6424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.204482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.169497 restraints weight = 9522.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.169951 restraints weight = 5531.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.171181 restraints weight = 4145.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.171421 restraints weight = 2605.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.171884 restraints weight = 2564.981| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6596 Z= 0.166 Angle : 0.624 8.458 9033 Z= 0.327 Chirality : 0.044 0.197 1132 Planarity : 0.003 0.059 1185 Dihedral : 4.840 36.048 1093 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.03 % Favored : 94.37 % Rotamer: Outliers : 5.01 % Allowed : 33.41 % Favored : 61.58 % 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: 0.86 (0.27), residues: 1013 helix: 1.53 (0.20), residues: 654 sheet: 0.65 (0.88), residues: 34 loop : -1.47 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.014 0.002 TYR A 281 PHE 0.011 0.001 PHE A 214 TRP 0.020 0.002 TRP A 262 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6596) covalent geometry : angle 0.62370 ( 9033) hydrogen bonds : bond 0.03749 ( 476) hydrogen bonds : angle 4.33349 ( 1413) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.182 Fit side-chains REVERT: A 32 ASN cc_start: 0.9015 (t0) cc_final: 0.8693 (t0) REVERT: A 52 ASN cc_start: 0.7339 (m-40) cc_final: 0.7095 (m-40) REVERT: A 101 LYS cc_start: 0.8874 (tttm) cc_final: 0.8268 (tttm) REVERT: A 103 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5252 (pp) REVERT: A 127 GLU cc_start: 0.7687 (tp30) cc_final: 0.7332 (tp30) REVERT: A 306 LEU cc_start: 0.7182 (mt) cc_final: 0.6421 (tt) REVERT: B 41 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8247 (mmtt) REVERT: B 72 ARG cc_start: 0.8340 (ttm170) cc_final: 0.7963 (ptm160) REVERT: B 121 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7618 (ttmm) REVERT: B 123 MET cc_start: 0.8704 (mtp) cc_final: 0.8419 (mtt) REVERT: B 315 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8359 (tt) outliers start: 21 outliers final: 16 residues processed: 191 average time/residue: 0.0662 time to fit residues: 17.2036 Evaluate side-chains 194 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.204665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.165696 restraints weight = 9646.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.172185 restraints weight = 8500.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.171857 restraints weight = 3928.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.172700 restraints weight = 3299.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.172894 restraints weight = 3093.318| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6596 Z= 0.173 Angle : 0.633 8.385 9033 Z= 0.331 Chirality : 0.045 0.214 1132 Planarity : 0.004 0.059 1185 Dihedral : 4.891 35.931 1093 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.13 % Favored : 94.27 % Rotamer: Outliers : 5.25 % Allowed : 34.61 % Favored : 60.14 % 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: 0.75 (0.27), residues: 1013 helix: 1.45 (0.20), residues: 653 sheet: 0.64 (0.88), residues: 34 loop : -1.51 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.015 0.002 TYR A 14 PHE 0.011 0.001 PHE A 214 TRP 0.022 0.002 TRP A 262 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6596) covalent geometry : angle 0.63318 ( 9033) hydrogen bonds : bond 0.03843 ( 476) hydrogen bonds : angle 4.42651 ( 1413) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.196 Fit side-chains REVERT: A 32 ASN cc_start: 0.8970 (t0) cc_final: 0.8686 (t0) REVERT: A 52 ASN cc_start: 0.7381 (m-40) cc_final: 0.7022 (m110) REVERT: A 101 LYS cc_start: 0.8850 (tttm) cc_final: 0.8255 (tttm) REVERT: A 127 GLU cc_start: 0.7662 (tp30) cc_final: 0.7261 (tp30) REVERT: B 41 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8256 (mmtt) REVERT: B 72 ARG cc_start: 0.8381 (ttm170) cc_final: 0.8024 (ptm160) REVERT: B 121 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7590 (ttmm) REVERT: B 123 MET cc_start: 0.8732 (mtp) cc_final: 0.8464 (mtt) REVERT: B 315 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8327 (tt) outliers start: 22 outliers final: 19 residues processed: 191 average time/residue: 0.0642 time to fit residues: 16.7327 Evaluate side-chains 197 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.7980 chunk 81 optimal weight: 50.0000 chunk 32 optimal weight: 50.0000 chunk 36 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.220436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.181408 restraints weight = 9590.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.185911 restraints weight = 5503.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.189016 restraints weight = 3624.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.190877 restraints weight = 2644.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.192567 restraints weight = 2111.594| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6596 Z= 0.124 Angle : 0.609 9.372 9033 Z= 0.312 Chirality : 0.043 0.207 1132 Planarity : 0.003 0.058 1185 Dihedral : 4.604 33.478 1093 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.74 % Favored : 94.67 % Rotamer: Outliers : 4.06 % Allowed : 35.56 % Favored : 60.38 % 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: 0.97 (0.27), residues: 1013 helix: 1.59 (0.21), residues: 661 sheet: 0.75 (0.89), residues: 34 loop : -1.41 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.018 0.001 TYR A 14 PHE 0.009 0.001 PHE A 214 TRP 0.023 0.002 TRP A 262 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6596) covalent geometry : angle 0.60885 ( 9033) hydrogen bonds : bond 0.03455 ( 476) hydrogen bonds : angle 4.17744 ( 1413) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8836 (t0) cc_final: 0.8558 (t0) REVERT: A 52 ASN cc_start: 0.7182 (m-40) cc_final: 0.6874 (m110) REVERT: A 101 LYS cc_start: 0.8803 (tttm) cc_final: 0.8172 (tttm) REVERT: A 127 GLU cc_start: 0.7575 (tp30) cc_final: 0.7301 (tp30) REVERT: B 41 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8067 (mmtt) REVERT: B 72 ARG cc_start: 0.8290 (ttm170) cc_final: 0.7912 (ptm160) REVERT: B 113 ASN cc_start: 0.8144 (m110) cc_final: 0.7933 (m110) REVERT: B 123 MET cc_start: 0.8696 (mtp) cc_final: 0.8475 (mtt) REVERT: B 315 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8197 (tt) outliers start: 17 outliers final: 15 residues processed: 194 average time/residue: 0.0661 time to fit residues: 17.4411 Evaluate side-chains 195 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 40.0000 chunk 52 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 78 optimal weight: 40.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.208089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.174073 restraints weight = 9560.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.175236 restraints weight = 5681.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.175643 restraints weight = 4143.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175817 restraints weight = 2597.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.176118 restraints weight = 2434.267| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6596 Z= 0.141 Angle : 0.624 9.852 9033 Z= 0.320 Chirality : 0.044 0.202 1132 Planarity : 0.003 0.058 1185 Dihedral : 4.634 34.237 1093 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.84 % Favored : 94.57 % Rotamer: Outliers : 4.77 % Allowed : 34.84 % Favored : 60.38 % 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: 0.99 (0.27), residues: 1013 helix: 1.62 (0.21), residues: 655 sheet: 0.77 (0.89), residues: 34 loop : -1.40 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.013 0.002 TYR A 156 PHE 0.010 0.001 PHE A 214 TRP 0.023 0.002 TRP A 262 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6596) covalent geometry : angle 0.62401 ( 9033) hydrogen bonds : bond 0.03557 ( 476) hydrogen bonds : angle 4.24153 ( 1413) =============================================================================== Job complete usr+sys time: 962.60 seconds wall clock time: 17 minutes 14.36 seconds (1034.36 seconds total)