Starting phenix.real_space_refine on Fri Dec 27 19:46:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7met_23803/12_2024/7met_23803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7met_23803/12_2024/7met_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_23803/12_2024/7met_23803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7met_23803/12_2024/7met_23803.map" model { file = "/net/cci-nas-00/data/ceres_data/7met_23803/12_2024/7met_23803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7met_23803/12_2024/7met_23803.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'ARG:plan': 16, 'TYR:plan': 9, 'ASN:plan1': 14, 'HIS:plan': 9, 'PHE:plan': 7, 'GLU:plan': 15, 'ASP:plan': 19} 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: {'GLN:plan1': 21, 'HIS:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 13, 'ASP:plan': 18, 'PHE:plan': 7, 'GLU:plan': 15, 'ARG:plan': 16} 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: 4.45, per 1000 atoms: 0.68 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: 1.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.80 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: 1.94 Time building geometry restraints manager: 2.07 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: 0.000 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: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.820 ------------------------------------------------------------------------------- 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= 0.270 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 : 8.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), 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 TRP 0.010 0.001 TRP A 262 HIS 0.002 0.000 HIS A 199 PHE 0.011 0.001 PHE A 71 TYR 0.017 0.001 TYR B 110 ARG 0.015 0.001 ARG A 160 *********************** 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 : 0.631 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: 0.1671 time to fit residues: 41.7628 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 : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 40.0000 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6596 Z= 0.273 Angle : 0.638 9.152 9033 Z= 0.336 Chirality : 0.044 0.164 1132 Planarity : 0.004 0.073 1185 Dihedral : 4.810 36.105 1093 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.13 % Favored : 94.27 % Rotamer: Outliers : 2.39 % Allowed : 20.76 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 1013 helix: 1.54 (0.20), residues: 651 sheet: 0.78 (0.95), residues: 34 loop : -1.50 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 19 HIS 0.004 0.001 HIS A 199 PHE 0.013 0.002 PHE A 214 TYR 0.019 0.002 TYR B 18 ARG 0.007 0.001 ARG A 160 *********************** 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 199 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8823 (t0) cc_final: 0.8462 (t0) REVERT: A 101 LYS cc_start: 0.8685 (tttm) cc_final: 0.8193 (tttm) REVERT: A 127 GLU cc_start: 0.7801 (tp30) cc_final: 0.7486 (tp30) REVERT: A 194 MET cc_start: 0.7476 (tpt) cc_final: 0.7268 (tpt) REVERT: B 47 ILE cc_start: 0.7350 (mm) cc_final: 0.7097 (mm) REVERT: B 72 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7788 (ptp-170) REVERT: B 90 LEU cc_start: 0.8252 (tp) cc_final: 0.8013 (tp) outliers start: 10 outliers final: 8 residues processed: 193 average time/residue: 0.1700 time to fit residues: 44.4126 Evaluate side-chains 187 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 50 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 50.0000 chunk 99 optimal weight: 50.0000 chunk 81 optimal weight: 50.0000 chunk 31 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.0050 overall best weight: 1.4400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6596 Z= 0.165 Angle : 0.559 8.620 9033 Z= 0.291 Chirality : 0.042 0.163 1132 Planarity : 0.004 0.057 1185 Dihedral : 4.524 37.615 1093 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.54 % Favored : 94.87 % Rotamer: Outliers : 2.39 % Allowed : 26.01 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 1013 helix: 1.70 (0.21), residues: 652 sheet: 0.77 (0.92), residues: 34 loop : -1.41 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 19 HIS 0.002 0.001 HIS A 199 PHE 0.011 0.001 PHE A 214 TYR 0.014 0.001 TYR B 18 ARG 0.003 0.000 ARG B 304 *********************** 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: 10 poor density : 187 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8659 (t0) cc_final: 0.8299 (t0) REVERT: A 101 LYS cc_start: 0.8707 (tttm) cc_final: 0.8180 (tttm) REVERT: A 127 GLU cc_start: 0.7660 (tp30) cc_final: 0.7299 (tp30) REVERT: A 194 MET cc_start: 0.7285 (tpt) cc_final: 0.6826 (tpt) REVERT: A 314 GLU cc_start: 0.8652 (pp20) cc_final: 0.8402 (pp20) REVERT: B 47 ILE cc_start: 0.7435 (mm) cc_final: 0.7226 (mm) REVERT: B 72 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7871 (ptm160) REVERT: B 113 ASN cc_start: 0.8128 (m-40) cc_final: 0.7922 (m110) REVERT: B 121 LYS cc_start: 0.7799 (ttmm) cc_final: 0.7222 (ttmm) outliers start: 10 outliers final: 7 residues processed: 190 average time/residue: 0.1712 time to fit residues: 43.7993 Evaluate side-chains 187 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASN 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 Chi-restraints excluded: chain B residue 279 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 40.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6596 Z= 0.168 Angle : 0.558 7.441 9033 Z= 0.287 Chirality : 0.042 0.168 1132 Planarity : 0.003 0.058 1185 Dihedral : 4.510 39.267 1093 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.54 % Favored : 94.87 % Rotamer: Outliers : 5.49 % Allowed : 24.34 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1013 helix: 1.81 (0.20), residues: 651 sheet: 0.69 (0.90), residues: 34 loop : -1.39 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 262 HIS 0.002 0.001 HIS A 199 PHE 0.011 0.001 PHE A 214 TYR 0.016 0.002 TYR A 281 ARG 0.003 0.000 ARG B 304 *********************** 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 206 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8623 (t0) cc_final: 0.8260 (t0) REVERT: A 101 LYS cc_start: 0.8736 (tttm) cc_final: 0.8158 (tttm) REVERT: A 127 GLU cc_start: 0.7490 (tp30) cc_final: 0.7188 (tp30) REVERT: A 194 MET cc_start: 0.7253 (tpt) cc_final: 0.7031 (tpt) REVERT: B 41 LYS cc_start: 0.8685 (mmmt) cc_final: 0.8112 (mmtt) REVERT: B 47 ILE cc_start: 0.7410 (mm) cc_final: 0.7207 (mm) REVERT: B 72 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7866 (ptm160) REVERT: B 121 LYS cc_start: 0.7789 (ttmm) cc_final: 0.7250 (ttmm) REVERT: B 311 SER cc_start: 0.7676 (OUTLIER) cc_final: 0.7405 (p) outliers start: 23 outliers final: 15 residues processed: 193 average time/residue: 0.1784 time to fit residues: 46.0321 Evaluate side-chains 193 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU 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 A residue 289 SER Chi-restraints excluded: chain B residue 25 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 114 SER Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 279 VAL 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 55 optimal weight: 30.0000 chunk 1 optimal weight: 0.0970 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 50.0000 overall best weight: 2.7584 ------------------------------------------------------------------------------- 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 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1998 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= 0.230 Angle : 0.604 9.853 9033 Z= 0.315 Chirality : 0.044 0.176 1132 Planarity : 0.004 0.058 1185 Dihedral : 4.657 37.910 1093 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.13 % Favored : 94.27 % Rotamer: Outliers : 5.49 % Allowed : 28.16 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 1013 helix: 1.67 (0.20), residues: 655 sheet: 0.65 (0.89), residues: 34 loop : -1.44 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.004 0.001 HIS A 199 PHE 0.012 0.001 PHE A 214 TYR 0.018 0.002 TYR A 281 ARG 0.003 0.000 ARG B 304 *********************** 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: 23 poor density : 180 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8729 (t0) cc_final: 0.8392 (t0) REVERT: A 101 LYS cc_start: 0.8747 (tttm) cc_final: 0.8179 (tttm) REVERT: A 127 GLU cc_start: 0.7826 (tp30) cc_final: 0.7465 (tp30) REVERT: B 41 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8256 (mmtt) REVERT: B 72 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7872 (ptm160) REVERT: B 121 LYS cc_start: 0.7879 (ttmm) cc_final: 0.7345 (ttmm) outliers start: 23 outliers final: 17 residues processed: 189 average time/residue: 0.1784 time to fit residues: 45.0018 Evaluate side-chains 194 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 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 246 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 25 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 114 SER Chi-restraints excluded: chain B residue 134 SER 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 87 optimal weight: 0.0470 chunk 19 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 81 optimal weight: 50.0000 chunk 45 optimal weight: 50.0000 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 50.0000 chunk 51 optimal weight: 50.0000 chunk 94 optimal weight: 20.0000 overall best weight: 1.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6596 Z= 0.181 Angle : 0.583 9.325 9033 Z= 0.302 Chirality : 0.043 0.181 1132 Planarity : 0.003 0.058 1185 Dihedral : 4.575 36.751 1093 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.54 % Favored : 94.87 % Rotamer: Outliers : 5.49 % Allowed : 30.79 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 1013 helix: 1.70 (0.20), residues: 653 sheet: 0.66 (0.89), residues: 34 loop : -1.40 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 262 HIS 0.003 0.001 HIS A 199 PHE 0.010 0.001 PHE A 214 TYR 0.016 0.002 TYR A 281 ARG 0.003 0.000 ARG B 304 *********************** 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 200 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8670 (t0) cc_final: 0.8332 (t0) REVERT: A 101 LYS cc_start: 0.8746 (tttm) cc_final: 0.8156 (tttm) REVERT: A 103 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5420 (pp) REVERT: A 127 GLU cc_start: 0.7649 (tp30) cc_final: 0.7161 (tp30) REVERT: B 16 LYS cc_start: 0.8956 (pttt) cc_final: 0.8569 (pptt) REVERT: B 41 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8214 (mmtt) REVERT: B 72 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7880 (ptm160) outliers start: 23 outliers final: 15 residues processed: 188 average time/residue: 0.1725 time to fit residues: 43.5910 Evaluate side-chains 190 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain B residue 25 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 114 SER Chi-restraints excluded: chain B residue 134 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 40.0000 chunk 97 optimal weight: 30.0000 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 50.0000 chunk 58 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 6596 Z= 0.292 Angle : 0.645 8.170 9033 Z= 0.344 Chirality : 0.046 0.265 1132 Planarity : 0.004 0.058 1185 Dihedral : 4.977 37.619 1093 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.53 % Favored : 93.88 % Rotamer: Outliers : 5.49 % Allowed : 32.70 % Favored : 61.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1013 helix: 1.44 (0.20), residues: 645 sheet: 0.62 (0.88), residues: 34 loop : -1.61 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 262 HIS 0.005 0.001 HIS A 199 PHE 0.015 0.001 PHE A 214 TYR 0.019 0.002 TYR A 281 ARG 0.004 0.000 ARG B 304 *********************** 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 196 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8857 (t0) cc_final: 0.8534 (t0) REVERT: A 52 ASN cc_start: 0.7405 (m-40) cc_final: 0.7158 (m110) REVERT: A 101 LYS cc_start: 0.8750 (tttm) cc_final: 0.8185 (tttm) REVERT: A 103 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5712 (pp) REVERT: A 127 GLU cc_start: 0.7890 (tp30) cc_final: 0.7264 (tp30) REVERT: A 304 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.8093 (tpp-160) REVERT: B 72 ARG cc_start: 0.8345 (ttm170) cc_final: 0.7968 (ptm160) REVERT: B 121 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7525 (ttmm) REVERT: B 123 MET cc_start: 0.8653 (mtm) cc_final: 0.8351 (ttm) REVERT: B 140 ILE cc_start: 0.9144 (tp) cc_final: 0.8922 (tp) outliers start: 23 outliers final: 21 residues processed: 187 average time/residue: 0.1626 time to fit residues: 41.0824 Evaluate side-chains 195 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 240 ILE 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 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 87 SER Chi-restraints excluded: chain B residue 114 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 30.0000 chunk 9 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6596 Z= 0.273 Angle : 0.628 7.804 9033 Z= 0.337 Chirality : 0.045 0.188 1132 Planarity : 0.004 0.057 1185 Dihedral : 4.965 35.962 1093 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.03 % Favored : 94.37 % Rotamer: Outliers : 5.73 % Allowed : 32.46 % Favored : 61.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1013 helix: 1.29 (0.20), residues: 649 sheet: 0.52 (0.86), residues: 34 loop : -1.58 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 262 HIS 0.005 0.001 HIS A 199 PHE 0.013 0.001 PHE A 214 TYR 0.021 0.002 TYR A 281 ARG 0.003 0.000 ARG B 304 *********************** 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: 24 poor density : 174 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8818 (t0) cc_final: 0.8479 (t0) REVERT: A 101 LYS cc_start: 0.8752 (tttm) cc_final: 0.8206 (tttm) REVERT: A 103 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5339 (pp) REVERT: A 127 GLU cc_start: 0.7800 (tp30) cc_final: 0.7406 (tp30) REVERT: A 304 ARG cc_start: 0.8324 (tpp-160) cc_final: 0.8101 (tpp-160) REVERT: B 41 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8406 (mmtt) REVERT: B 72 ARG cc_start: 0.8352 (ttm170) cc_final: 0.7938 (ptm160) REVERT: B 121 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7621 (ttmm) REVERT: B 140 ILE cc_start: 0.9133 (tp) cc_final: 0.8919 (tp) REVERT: B 287 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8463 (mt) outliers start: 24 outliers final: 21 residues processed: 186 average time/residue: 0.1669 time to fit residues: 41.7647 Evaluate side-chains 195 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 194 MET 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 87 SER Chi-restraints excluded: chain B residue 114 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.1980 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 0.0470 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 50.0000 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6596 Z= 0.175 Angle : 0.601 12.893 9033 Z= 0.310 Chirality : 0.043 0.199 1132 Planarity : 0.003 0.058 1185 Dihedral : 4.698 34.850 1093 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.03 % Favored : 94.37 % Rotamer: Outliers : 5.25 % Allowed : 34.13 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 1013 helix: 1.54 (0.21), residues: 654 sheet: 0.63 (0.87), residues: 34 loop : -1.43 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 262 HIS 0.002 0.001 HIS A 199 PHE 0.009 0.001 PHE A 214 TYR 0.013 0.001 TYR A 281 ARG 0.003 0.000 ARG B 304 *********************** 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 200 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8628 (t0) cc_final: 0.8309 (t0) REVERT: A 47 ILE cc_start: 0.8542 (tt) cc_final: 0.8238 (tt) REVERT: A 101 LYS cc_start: 0.8695 (tttm) cc_final: 0.8132 (tttm) REVERT: A 103 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5076 (pp) REVERT: A 127 GLU cc_start: 0.7560 (tp30) cc_final: 0.7141 (tp30) REVERT: A 169 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7922 (tt) REVERT: A 304 ARG cc_start: 0.8186 (tpp-160) cc_final: 0.7977 (tpp-160) REVERT: B 41 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8166 (mmtt) REVERT: B 72 ARG cc_start: 0.8245 (ttm170) cc_final: 0.7867 (ptm160) REVERT: B 121 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7289 (ttmm) REVERT: B 287 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8369 (mt) outliers start: 22 outliers final: 15 residues processed: 190 average time/residue: 0.1855 time to fit residues: 48.1429 Evaluate side-chains 190 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 169 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 194 MET 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 289 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 25 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 50.0000 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 80 optimal weight: 40.0000 chunk 8 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 49 optimal weight: 50.0000 chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 overall best weight: 3.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 6596 Z= 0.294 Angle : 0.704 16.583 9033 Z= 0.361 Chirality : 0.046 0.204 1132 Planarity : 0.004 0.057 1185 Dihedral : 5.007 36.806 1093 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.23 % Favored : 94.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 1013 helix: 1.34 (0.21), residues: 651 sheet: 0.55 (0.86), residues: 34 loop : -1.56 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 159 HIS 0.004 0.001 HIS A 199 PHE 0.014 0.001 PHE A 214 TYR 0.023 0.002 TYR A 281 ARG 0.003 0.000 ARG B 304 ********************** 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 195 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8839 (t0) cc_final: 0.8505 (t0) REVERT: A 101 LYS cc_start: 0.8767 (tttm) cc_final: 0.8232 (tttm) REVERT: A 103 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5362 (pp) REVERT: A 127 GLU cc_start: 0.7823 (tp30) cc_final: 0.7404 (tp30) REVERT: A 169 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7961 (tt) REVERT: A 304 ARG cc_start: 0.8298 (tpp-160) cc_final: 0.8050 (tpp-160) REVERT: B 72 ARG cc_start: 0.8351 (ttm170) cc_final: 0.7961 (ptm160) REVERT: B 121 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7514 (ttmm) REVERT: B 140 ILE cc_start: 0.9152 (tp) cc_final: 0.8921 (tp) outliers start: 21 outliers final: 17 residues processed: 189 average time/residue: 0.1646 time to fit residues: 42.1194 Evaluate side-chains 189 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 169 LEU Chi-restraints excluded: chain A residue 194 MET 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 A residue 312 VAL Chi-restraints excluded: chain B residue 25 VAL 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 311 SER Chi-restraints excluded: chain B residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.209583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.175531 restraints weight = 9439.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.175586 restraints weight = 5819.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.177174 restraints weight = 4391.868| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6596 Z= 0.182 Angle : 0.659 16.112 9033 Z= 0.327 Chirality : 0.044 0.203 1132 Planarity : 0.003 0.057 1185 Dihedral : 4.679 34.295 1093 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.15 % Favored : 95.26 % Rotamer: Outliers : 4.06 % Allowed : 34.61 % Favored : 61.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.27), residues: 1013 helix: 1.57 (0.21), residues: 652 sheet: 0.61 (0.86), residues: 34 loop : -1.41 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 262 HIS 0.001 0.001 HIS A 199 PHE 0.009 0.001 PHE A 214 TYR 0.012 0.001 TYR A 82 ARG 0.003 0.000 ARG B 304 =============================================================================== Job complete usr+sys time: 1447.72 seconds wall clock time: 27 minutes 10.93 seconds (1630.93 seconds total)