Starting phenix.real_space_refine on Wed Sep 17 10:10:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oi8_70510/09_2025/9oi8_70510.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oi8_70510/09_2025/9oi8_70510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oi8_70510/09_2025/9oi8_70510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oi8_70510/09_2025/9oi8_70510.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oi8_70510/09_2025/9oi8_70510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oi8_70510/09_2025/9oi8_70510.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 1.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4939 2.51 5 N 1344 2.21 5 O 1403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7719 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3240 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 17, 'TRANS': 416} Chain breaks: 2 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 4, 'ASP:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2556 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 315} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 861 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1037 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain breaks: 1 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'GA3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.98, per 1000 atoms: 0.26 Number of scatterers: 7719 At special positions: 0 Unit cell: (77.0679, 97.3935, 119.413, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1403 8.00 N 1344 7.00 C 4939 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: 0.61 Conformation dependent library (CDL) restraints added in 337.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1934 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 55.7% alpha, 13.7% 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 44 through 51 Processing helix chain 'A' and resid 58 through 76 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.808A pdb=" N LEU A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.671A pdb=" N LEU A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 252 removed outlier: 3.807A pdb=" N ALA A 240 " --> pdb=" O ASN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 275 removed outlier: 4.390A pdb=" N LYS A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 300 through 316 Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.686A pdb=" N LEU A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.911A pdb=" N GLU A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 461 through 479 removed outlier: 3.554A pdb=" N ARG A 465 " --> pdb=" O VAL A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 504 Processing helix chain 'A' and resid 517 through 527 Processing helix chain 'A' and resid 536 through 550 removed outlier: 3.607A pdb=" N PHE A 540 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 removed outlier: 3.779A pdb=" N VAL B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 16' Processing helix chain 'B' and resid 17 through 34 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 94 through 99 removed outlier: 4.036A pdb=" N GLU B 98 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 removed outlier: 3.721A pdb=" N LEU B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 Processing helix chain 'B' and resid 191 through 206 removed outlier: 3.899A pdb=" N ASN B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.749A pdb=" N ARG B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.976A pdb=" N GLN B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 342 removed outlier: 4.623A pdb=" N HIS B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 59 through 67 removed outlier: 3.678A pdb=" N GLN C 67 " --> pdb=" O HIS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 removed outlier: 3.897A pdb=" N TRP C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 98 Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.680A pdb=" N SER C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 121 through 140 removed outlier: 3.896A pdb=" N LEU C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 26 through 35 Processing helix chain 'D' and resid 48 through 71 Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 94 through 109 removed outlier: 4.053A pdb=" N LEU D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 129 through 138 removed outlier: 3.814A pdb=" N ARG D 134 " --> pdb=" O PRO D 130 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 155 through 160 removed outlier: 3.844A pdb=" N PHE D 159 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU D 160 " --> pdb=" O GLN D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 160' Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211 removed outlier: 5.586A pdb=" N SER B 65 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG B 82 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASP B 67 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 80 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU B 69 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER B 78 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL B 108 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA B 188 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU B 110 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP B 190 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE B 112 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 213 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN B 214 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL B 284 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 216 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ALA B 286 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER B 281 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N MET B 312 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 283 " --> pdb=" O MET B 312 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU B 314 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 285 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 393 removed outlier: 6.485A pdb=" N VAL A 323 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR A 356 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 325 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 358 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP A 327 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A 415 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR A 449 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 417 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N VAL A 451 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER A 419 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N GLN A 453 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 393 removed outlier: 6.485A pdb=" N VAL A 323 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR A 356 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 325 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 358 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP A 327 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A 415 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR A 449 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 417 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N VAL A 451 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER A 419 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N GLN A 453 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TRP A 569 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 15 through 19 removed outlier: 3.825A pdb=" N VAL D 42 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 9 " --> pdb=" O VAL D 42 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1260 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: 0.81 Time building geometry restraints manager: 0.78 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: 1385 1.32 - 1.45: 2003 1.45 - 1.57: 4452 1.57 - 1.70: 1 1.70 - 1.82: 50 Bond restraints: 7891 Sorted by residual: bond pdb=" CA SER A 479 " pdb=" C SER A 479 " ideal model delta sigma weight residual 1.518 1.582 -0.064 4.01e-02 6.22e+02 2.57e+00 bond pdb=" CA VAL A 504 " pdb=" C VAL A 504 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.27e-02 6.20e+03 1.70e+00 bond pdb=" CB GLN C 87 " pdb=" CG GLN C 87 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB ASP B 38 " pdb=" CG ASP B 38 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.33e+00 bond pdb=" CG ARG C 91 " pdb=" CD ARG C 91 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 ... (remaining 7886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 10409 2.11 - 4.22: 285 4.22 - 6.34: 58 6.34 - 8.45: 13 8.45 - 10.56: 3 Bond angle restraints: 10768 Sorted by residual: angle pdb=" CA GLN C 87 " pdb=" CB GLN C 87 " pdb=" CG GLN C 87 " ideal model delta sigma weight residual 114.10 122.08 -7.98 2.00e+00 2.50e-01 1.59e+01 angle pdb=" CA VAL A 504 " pdb=" CB VAL A 504 " pdb=" CG1 VAL A 504 " ideal model delta sigma weight residual 110.40 116.87 -6.47 1.70e+00 3.46e-01 1.45e+01 angle pdb=" CA ILE B 105 " pdb=" CB ILE B 105 " pdb=" CG1 ILE B 105 " ideal model delta sigma weight residual 110.40 116.81 -6.41 1.70e+00 3.46e-01 1.42e+01 angle pdb=" N ASN A 310 " pdb=" CA ASN A 310 " pdb=" CB ASN A 310 " ideal model delta sigma weight residual 110.12 115.52 -5.40 1.47e+00 4.63e-01 1.35e+01 angle pdb=" CB GLN C 87 " pdb=" CG GLN C 87 " pdb=" CD GLN C 87 " ideal model delta sigma weight residual 112.60 118.42 -5.82 1.70e+00 3.46e-01 1.17e+01 ... (remaining 10763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 4130 16.92 - 33.84: 428 33.84 - 50.76: 148 50.76 - 67.68: 19 67.68 - 84.60: 8 Dihedral angle restraints: 4733 sinusoidal: 1749 harmonic: 2984 Sorted by residual: dihedral pdb=" CA ASP B 128 " pdb=" CB ASP B 128 " pdb=" CG ASP B 128 " pdb=" OD1 ASP B 128 " ideal model delta sinusoidal sigma weight residual -30.00 -87.72 57.72 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP B 180 " pdb=" CB ASP B 180 " pdb=" CG ASP B 180 " pdb=" OD1 ASP B 180 " ideal model delta sinusoidal sigma weight residual -30.00 -84.46 54.46 1 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA LYS D 140 " pdb=" C LYS D 140 " pdb=" N ASN D 141 " pdb=" CA ASN D 141 " ideal model delta harmonic sigma weight residual 180.00 164.25 15.75 0 5.00e+00 4.00e-02 9.92e+00 ... (remaining 4730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 912 0.048 - 0.095: 248 0.095 - 0.143: 74 0.143 - 0.190: 12 0.190 - 0.238: 2 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CB ILE B 291 " pdb=" CA ILE B 291 " pdb=" CG1 ILE B 291 " pdb=" CG2 ILE B 291 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU A 269 " pdb=" CB LEU A 269 " pdb=" CD1 LEU A 269 " pdb=" CD2 LEU A 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB THR A 71 " pdb=" CA THR A 71 " pdb=" OG1 THR A 71 " pdb=" CG2 THR A 71 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 1245 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 260 " -0.046 5.00e-02 4.00e+02 7.04e-02 7.94e+00 pdb=" N PRO B 261 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 87 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C GLN C 87 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN C 87 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN C 88 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 387 " -0.012 2.00e-02 2.50e+03 1.92e-02 6.47e+00 pdb=" CG PHE A 387 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 387 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 387 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 387 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 387 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 387 " -0.000 2.00e-02 2.50e+03 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 2951 2.89 - 3.39: 7520 3.39 - 3.89: 12462 3.89 - 4.40: 13488 4.40 - 4.90: 23087 Nonbonded interactions: 59508 Sorted by model distance: nonbonded pdb=" O VAL B 241 " pdb=" OD1 ASP B 245 " model vdw 2.382 3.040 nonbonded pdb=" O HIS A 306 " pdb=" OD1 ASN A 310 " model vdw 2.416 3.040 nonbonded pdb=" O ASN D 141 " pdb=" OD1 ASN D 141 " model vdw 2.431 3.040 nonbonded pdb=" O GLN C 87 " pdb=" OE1 GLN C 87 " model vdw 2.436 3.040 nonbonded pdb=" O THR C 65 " pdb=" OD1 ASP C 68 " model vdw 2.500 3.040 ... (remaining 59503 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.610 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 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 0.064 7891 Z= 0.174 Angle : 0.870 10.561 10768 Z= 0.471 Chirality : 0.049 0.238 1248 Planarity : 0.007 0.070 1384 Dihedral : 15.712 84.595 2799 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.74 % Allowed : 27.50 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: -1.82 (0.24), residues: 1013 helix: -0.09 (0.21), residues: 539 sheet: -1.24 (0.50), residues: 99 loop : -2.86 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 259 TYR 0.016 0.002 TYR B 81 PHE 0.043 0.002 PHE A 387 TRP 0.025 0.002 TRP B 294 HIS 0.008 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7891) covalent geometry : angle 0.87029 (10768) hydrogen bonds : bond 0.12707 ( 413) hydrogen bonds : angle 5.65694 ( 1260) *********************** 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 238 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.6906 (ttm) cc_final: 0.6266 (mpt) REVERT: A 441 LYS cc_start: 0.7577 (tttt) cc_final: 0.7297 (tmmt) REVERT: A 488 ASP cc_start: 0.7496 (m-30) cc_final: 0.6126 (m-30) REVERT: A 547 LEU cc_start: 0.8414 (mm) cc_final: 0.8109 (mm) REVERT: A 566 MET cc_start: 0.7919 (mpp) cc_final: 0.7671 (mpt) REVERT: B 70 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7083 (pp) REVERT: C 106 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8035 (mp) REVERT: D 12 ASP cc_start: 0.5978 (t0) cc_final: 0.5333 (m-30) REVERT: D 62 HIS cc_start: 0.8259 (m-70) cc_final: 0.8032 (m-70) REVERT: D 93 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7644 (mp) REVERT: D 123 ASP cc_start: 0.8590 (m-30) cc_final: 0.8370 (m-30) outliers start: 36 outliers final: 8 residues processed: 227 average time/residue: 0.4097 time to fit residues: 100.2355 Evaluate side-chains 137 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 93 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 223 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN A 562 ASN ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.125295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.104077 restraints weight = 16896.008| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 4.13 r_work: 0.3751 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7891 Z= 0.137 Angle : 0.715 12.396 10768 Z= 0.351 Chirality : 0.044 0.372 1248 Planarity : 0.005 0.048 1384 Dihedral : 5.187 51.416 1196 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.53 % Allowed : 26.97 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: -0.08 (0.26), residues: 1013 helix: 1.35 (0.23), residues: 544 sheet: -0.32 (0.53), residues: 95 loop : -2.17 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 55 TYR 0.018 0.002 TYR A 264 PHE 0.015 0.002 PHE B 330 TRP 0.009 0.001 TRP A 99 HIS 0.007 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7891) covalent geometry : angle 0.71492 (10768) hydrogen bonds : bond 0.04197 ( 413) hydrogen bonds : angle 4.16422 ( 1260) *********************** 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 174 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8039 (pp20) REVERT: A 72 MET cc_start: 0.5414 (ttm) cc_final: 0.4976 (mpt) REVERT: A 297 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7980 (tm-30) REVERT: A 400 LEU cc_start: 0.8786 (mt) cc_final: 0.8521 (mm) REVERT: A 441 LYS cc_start: 0.7282 (tttt) cc_final: 0.6945 (tmmt) REVERT: A 491 MET cc_start: 0.6888 (tpp) cc_final: 0.6566 (tpp) REVERT: A 492 SER cc_start: 0.7507 (OUTLIER) cc_final: 0.7066 (p) REVERT: A 566 MET cc_start: 0.7600 (mpp) cc_final: 0.7072 (mpt) REVERT: B 70 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.6884 (pt) REVERT: B 300 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8654 (mp0) REVERT: D 12 ASP cc_start: 0.6046 (t0) cc_final: 0.5630 (m-30) REVERT: D 62 HIS cc_start: 0.8831 (m-70) cc_final: 0.8535 (m-70) outliers start: 42 outliers final: 13 residues processed: 164 average time/residue: 0.3473 time to fit residues: 62.2425 Evaluate side-chains 136 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 93 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 331 ASN C 79 HIS ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.123616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.102442 restraints weight = 16822.347| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 4.07 r_work: 0.3704 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7891 Z= 0.118 Angle : 0.617 12.106 10768 Z= 0.301 Chirality : 0.041 0.260 1248 Planarity : 0.004 0.043 1384 Dihedral : 4.696 53.154 1186 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.87 % Allowed : 26.45 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.36 (0.26), residues: 1013 helix: 1.62 (0.23), residues: 543 sheet: 0.26 (0.54), residues: 97 loop : -1.94 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 55 TYR 0.013 0.001 TYR A 264 PHE 0.010 0.001 PHE B 238 TRP 0.013 0.001 TRP A 99 HIS 0.006 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7891) covalent geometry : angle 0.61746 (10768) hydrogen bonds : bond 0.03709 ( 413) hydrogen bonds : angle 3.83066 ( 1260) *********************** 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 170 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8130 (pp20) REVERT: A 72 MET cc_start: 0.5563 (ttm) cc_final: 0.5084 (mpt) REVERT: A 239 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8321 (tm) REVERT: A 297 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7780 (tm-30) REVERT: A 400 LEU cc_start: 0.8740 (mt) cc_final: 0.8368 (mm) REVERT: A 401 ASP cc_start: 0.8427 (m-30) cc_final: 0.7886 (t0) REVERT: A 441 LYS cc_start: 0.7573 (tttt) cc_final: 0.7209 (tmmt) REVERT: A 491 MET cc_start: 0.7152 (tpp) cc_final: 0.6686 (tpp) REVERT: A 566 MET cc_start: 0.7609 (mpp) cc_final: 0.7139 (mpt) REVERT: B 70 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.6869 (pt) REVERT: B 230 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7283 (pp20) REVERT: B 277 SER cc_start: 0.8295 (t) cc_final: 0.7942 (p) REVERT: B 300 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8740 (mp0) REVERT: D 12 ASP cc_start: 0.6195 (t0) cc_final: 0.5815 (m-30) REVERT: D 62 HIS cc_start: 0.8810 (m-70) cc_final: 0.8505 (m-70) outliers start: 37 outliers final: 20 residues processed: 159 average time/residue: 0.3836 time to fit residues: 66.2493 Evaluate side-chains 144 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 159 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 33 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 331 ASN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.125535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.104393 restraints weight = 17093.849| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 4.03 r_work: 0.3692 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7891 Z= 0.112 Angle : 0.612 12.133 10768 Z= 0.299 Chirality : 0.040 0.140 1248 Planarity : 0.004 0.042 1384 Dihedral : 4.723 53.510 1186 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 6.71 % Allowed : 26.58 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.53 (0.26), residues: 1013 helix: 1.69 (0.22), residues: 546 sheet: 0.31 (0.52), residues: 101 loop : -1.77 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 70 TYR 0.012 0.001 TYR A 264 PHE 0.024 0.001 PHE A 304 TRP 0.015 0.001 TRP A 99 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7891) covalent geometry : angle 0.61169 (10768) hydrogen bonds : bond 0.03547 ( 413) hydrogen bonds : angle 3.73091 ( 1260) *********************** 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 183 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7010 (mm) REVERT: A 67 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: A 72 MET cc_start: 0.5538 (ttm) cc_final: 0.5146 (mpt) REVERT: A 297 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7954 (tm-30) REVERT: A 441 LYS cc_start: 0.7631 (tttt) cc_final: 0.7321 (tmmt) REVERT: A 491 MET cc_start: 0.7327 (tpp) cc_final: 0.6853 (tpp) REVERT: B 68 VAL cc_start: 0.7934 (t) cc_final: 0.7623 (p) REVERT: B 277 SER cc_start: 0.8316 (t) cc_final: 0.7963 (p) REVERT: B 300 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8742 (mp0) REVERT: D 12 ASP cc_start: 0.5932 (t0) cc_final: 0.5727 (m-30) REVERT: D 62 HIS cc_start: 0.8836 (m-70) cc_final: 0.8527 (m-70) REVERT: D 114 LEU cc_start: 0.8536 (mm) cc_final: 0.8239 (pp) outliers start: 51 outliers final: 24 residues processed: 168 average time/residue: 0.3382 time to fit residues: 62.4159 Evaluate side-chains 147 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 159 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 34 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 331 ASN D 27 GLN D 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.121545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.100383 restraints weight = 17115.181| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 4.10 r_work: 0.3700 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7891 Z= 0.114 Angle : 0.612 12.292 10768 Z= 0.298 Chirality : 0.041 0.155 1248 Planarity : 0.004 0.041 1384 Dihedral : 4.442 54.359 1184 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.53 % Allowed : 27.63 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.60 (0.26), residues: 1013 helix: 1.68 (0.22), residues: 545 sheet: 0.53 (0.48), residues: 113 loop : -1.76 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 35 TYR 0.012 0.001 TYR A 264 PHE 0.024 0.001 PHE A 304 TRP 0.014 0.001 TRP A 99 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7891) covalent geometry : angle 0.61231 (10768) hydrogen bonds : bond 0.03550 ( 413) hydrogen bonds : angle 3.72666 ( 1260) *********************** 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 165 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7019 (mm) REVERT: A 67 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8171 (pp20) REVERT: A 72 MET cc_start: 0.5686 (ttm) cc_final: 0.5187 (mpt) REVERT: A 297 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 401 ASP cc_start: 0.8474 (m-30) cc_final: 0.7573 (t70) REVERT: A 441 LYS cc_start: 0.7570 (tttt) cc_final: 0.7226 (tmmt) REVERT: A 491 MET cc_start: 0.7253 (tpp) cc_final: 0.6780 (tpp) REVERT: A 566 MET cc_start: 0.7519 (mpp) cc_final: 0.7130 (mpt) REVERT: B 68 VAL cc_start: 0.8006 (t) cc_final: 0.7682 (p) REVERT: B 277 SER cc_start: 0.8344 (t) cc_final: 0.7966 (p) REVERT: B 300 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8692 (mp0) REVERT: D 12 ASP cc_start: 0.5917 (t0) cc_final: 0.5707 (m-30) REVERT: D 62 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8524 (m-70) REVERT: D 99 PHE cc_start: 0.8866 (m-10) cc_final: 0.8484 (t80) REVERT: D 100 GLU cc_start: 0.9163 (mp0) cc_final: 0.8590 (mm-30) outliers start: 42 outliers final: 26 residues processed: 151 average time/residue: 0.3523 time to fit residues: 58.2413 Evaluate side-chains 149 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 62 HIS Chi-restraints excluded: chain D residue 93 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.122805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.101560 restraints weight = 17048.505| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 4.03 r_work: 0.3678 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7891 Z= 0.117 Angle : 0.625 13.311 10768 Z= 0.302 Chirality : 0.040 0.152 1248 Planarity : 0.004 0.041 1384 Dihedral : 4.463 55.132 1184 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.26 % Allowed : 28.03 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.66 (0.26), residues: 1013 helix: 1.70 (0.22), residues: 545 sheet: 0.68 (0.49), residues: 113 loop : -1.71 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 70 TYR 0.014 0.001 TYR A 301 PHE 0.026 0.001 PHE A 304 TRP 0.013 0.001 TRP A 99 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7891) covalent geometry : angle 0.62478 (10768) hydrogen bonds : bond 0.03453 ( 413) hydrogen bonds : angle 3.74156 ( 1260) *********************** 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 163 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7031 (mm) REVERT: A 67 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8191 (pp20) REVERT: A 72 MET cc_start: 0.5779 (ttm) cc_final: 0.5271 (mpt) REVERT: A 297 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7833 (tm-30) REVERT: A 401 ASP cc_start: 0.8558 (m-30) cc_final: 0.7646 (t70) REVERT: A 441 LYS cc_start: 0.7653 (tttt) cc_final: 0.7293 (tmmt) REVERT: A 491 MET cc_start: 0.7317 (tpp) cc_final: 0.6340 (tpp) REVERT: A 566 MET cc_start: 0.7579 (mpp) cc_final: 0.7212 (mpt) REVERT: B 68 VAL cc_start: 0.8021 (t) cc_final: 0.7764 (p) REVERT: B 277 SER cc_start: 0.8339 (t) cc_final: 0.7993 (p) REVERT: B 300 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8724 (mp0) REVERT: D 57 GLU cc_start: 0.8679 (pt0) cc_final: 0.8461 (pt0) REVERT: D 62 HIS cc_start: 0.8841 (OUTLIER) cc_final: 0.8511 (m-70) REVERT: D 99 PHE cc_start: 0.8845 (m-10) cc_final: 0.8468 (t80) REVERT: D 100 GLU cc_start: 0.9108 (mp0) cc_final: 0.8600 (mm-30) outliers start: 40 outliers final: 27 residues processed: 148 average time/residue: 0.4275 time to fit residues: 68.6404 Evaluate side-chains 143 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 62 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 0.0570 chunk 71 optimal weight: 0.7980 chunk 89 optimal weight: 0.0170 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.123943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.102387 restraints weight = 16981.081| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 4.03 r_work: 0.3705 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7891 Z= 0.112 Angle : 0.634 14.986 10768 Z= 0.306 Chirality : 0.040 0.160 1248 Planarity : 0.004 0.041 1384 Dihedral : 4.411 57.329 1183 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.74 % Allowed : 29.08 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.79 (0.26), residues: 1013 helix: 1.78 (0.22), residues: 546 sheet: 0.79 (0.49), residues: 113 loop : -1.65 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 70 TYR 0.012 0.001 TYR A 301 PHE 0.027 0.001 PHE A 304 TRP 0.013 0.001 TRP A 99 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7891) covalent geometry : angle 0.63410 (10768) hydrogen bonds : bond 0.03325 ( 413) hydrogen bonds : angle 3.67414 ( 1260) *********************** 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 161 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7006 (mm) REVERT: A 67 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8175 (pp20) REVERT: A 72 MET cc_start: 0.5880 (ttm) cc_final: 0.5337 (mpt) REVERT: A 297 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7924 (tm-30) REVERT: A 401 ASP cc_start: 0.8575 (m-30) cc_final: 0.7674 (t70) REVERT: A 441 LYS cc_start: 0.7621 (tttt) cc_final: 0.7267 (tmmt) REVERT: A 491 MET cc_start: 0.7346 (tpp) cc_final: 0.6377 (tpp) REVERT: A 566 MET cc_start: 0.7576 (mpp) cc_final: 0.7199 (mpt) REVERT: B 47 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: B 68 VAL cc_start: 0.7924 (t) cc_final: 0.7683 (p) REVERT: B 277 SER cc_start: 0.8303 (t) cc_final: 0.7983 (p) REVERT: B 300 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8711 (mp0) REVERT: C 126 LYS cc_start: 0.7129 (mmmm) cc_final: 0.6891 (mptm) REVERT: D 5 LYS cc_start: 0.7831 (mppt) cc_final: 0.6758 (tptt) REVERT: D 62 HIS cc_start: 0.8880 (OUTLIER) cc_final: 0.8612 (m-70) REVERT: D 99 PHE cc_start: 0.8845 (m-10) cc_final: 0.8445 (t80) REVERT: D 100 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8671 (mm-30) REVERT: D 138 ASN cc_start: 0.5809 (m-40) cc_final: 0.5581 (t0) outliers start: 36 outliers final: 26 residues processed: 147 average time/residue: 0.4003 time to fit residues: 64.0970 Evaluate side-chains 150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 62 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 0.0980 chunk 70 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 0.0000 chunk 69 optimal weight: 0.1980 chunk 68 optimal weight: 0.0270 overall best weight: 0.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 310 ASN A 331 ASN D 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.125585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.104104 restraints weight = 16832.111| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 4.02 r_work: 0.3763 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7891 Z= 0.108 Angle : 0.633 14.783 10768 Z= 0.305 Chirality : 0.041 0.286 1248 Planarity : 0.004 0.044 1384 Dihedral : 4.345 58.993 1183 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.47 % Allowed : 30.39 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.94 (0.26), residues: 1013 helix: 1.83 (0.22), residues: 547 sheet: 1.02 (0.48), residues: 111 loop : -1.51 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 70 TYR 0.013 0.001 TYR A 301 PHE 0.028 0.001 PHE A 304 TRP 0.015 0.001 TRP A 99 HIS 0.004 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7891) covalent geometry : angle 0.63316 (10768) hydrogen bonds : bond 0.03001 ( 413) hydrogen bonds : angle 3.63051 ( 1260) *********************** 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 159 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6980 (mm) REVERT: A 67 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8152 (pp20) REVERT: A 72 MET cc_start: 0.5808 (ttm) cc_final: 0.5252 (mpt) REVERT: A 297 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 401 ASP cc_start: 0.8593 (m-30) cc_final: 0.7743 (t70) REVERT: A 441 LYS cc_start: 0.7501 (tttt) cc_final: 0.7153 (tmmt) REVERT: A 566 MET cc_start: 0.7530 (mpp) cc_final: 0.6986 (mpt) REVERT: B 47 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: B 68 VAL cc_start: 0.7774 (t) cc_final: 0.7535 (p) REVERT: B 277 SER cc_start: 0.8319 (t) cc_final: 0.7959 (p) REVERT: B 300 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8646 (mp0) REVERT: D 5 LYS cc_start: 0.7969 (mppt) cc_final: 0.6973 (tptt) REVERT: D 62 HIS cc_start: 0.8876 (OUTLIER) cc_final: 0.8548 (m-70) REVERT: D 93 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8069 (mp) REVERT: D 99 PHE cc_start: 0.8860 (m-10) cc_final: 0.8419 (t80) REVERT: D 100 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8664 (mm-30) REVERT: D 126 LYS cc_start: 0.6300 (tppp) cc_final: 0.5842 (tppt) outliers start: 34 outliers final: 18 residues processed: 145 average time/residue: 0.4131 time to fit residues: 65.0883 Evaluate side-chains 143 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 62 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 310 ASN A 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.117991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.096704 restraints weight = 17450.636| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.97 r_work: 0.3607 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7891 Z= 0.183 Angle : 0.714 16.929 10768 Z= 0.351 Chirality : 0.044 0.208 1248 Planarity : 0.005 0.044 1384 Dihedral : 4.742 59.086 1183 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.00 % Allowed : 29.47 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.62 (0.26), residues: 1013 helix: 1.52 (0.22), residues: 549 sheet: 0.63 (0.50), residues: 105 loop : -1.43 (0.28), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 346 TYR 0.018 0.002 TYR A 473 PHE 0.022 0.002 PHE A 304 TRP 0.016 0.002 TRP A 521 HIS 0.006 0.002 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 7891) covalent geometry : angle 0.71440 (10768) hydrogen bonds : bond 0.04394 ( 413) hydrogen bonds : angle 3.92116 ( 1260) *********************** 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 164 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8193 (pp20) REVERT: A 72 MET cc_start: 0.5795 (ttm) cc_final: 0.5238 (mpt) REVERT: A 297 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8024 (tm-30) REVERT: A 401 ASP cc_start: 0.8638 (m-30) cc_final: 0.7769 (t70) REVERT: A 441 LYS cc_start: 0.7596 (tttt) cc_final: 0.7228 (tmmt) REVERT: A 491 MET cc_start: 0.7185 (tpp) cc_final: 0.6982 (tpp) REVERT: B 277 SER cc_start: 0.8375 (t) cc_final: 0.8023 (p) REVERT: B 300 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8667 (mp0) REVERT: C 102 ARG cc_start: 0.5173 (mtt180) cc_final: 0.4073 (mmt180) REVERT: D 5 LYS cc_start: 0.8044 (mppt) cc_final: 0.6961 (tptt) REVERT: D 6 ILE cc_start: 0.2801 (mm) cc_final: 0.2580 (mp) REVERT: D 93 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8296 (mp) REVERT: D 99 PHE cc_start: 0.8911 (m-10) cc_final: 0.8464 (t80) REVERT: D 100 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8681 (mm-30) outliers start: 38 outliers final: 23 residues processed: 152 average time/residue: 0.4287 time to fit residues: 70.8541 Evaluate side-chains 141 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 310 ASN A 331 ASN C 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.118483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.097581 restraints weight = 17228.508| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.99 r_work: 0.3620 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7891 Z= 0.142 Angle : 0.691 15.824 10768 Z= 0.334 Chirality : 0.042 0.224 1248 Planarity : 0.004 0.047 1384 Dihedral : 4.646 57.537 1183 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.08 % Allowed : 31.45 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.81 (0.26), residues: 1013 helix: 1.65 (0.22), residues: 548 sheet: 0.86 (0.48), residues: 115 loop : -1.41 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 51 TYR 0.012 0.001 TYR B 81 PHE 0.027 0.002 PHE A 304 TRP 0.013 0.001 TRP D 157 HIS 0.004 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7891) covalent geometry : angle 0.69138 (10768) hydrogen bonds : bond 0.03905 ( 413) hydrogen bonds : angle 3.85337 ( 1260) ********************** 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 152 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8176 (pp20) REVERT: A 72 MET cc_start: 0.6033 (ttm) cc_final: 0.5430 (mpt) REVERT: A 297 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8081 (tm-30) REVERT: A 320 LYS cc_start: 0.5923 (OUTLIER) cc_final: 0.5656 (mttp) REVERT: A 401 ASP cc_start: 0.8682 (m-30) cc_final: 0.7849 (t70) REVERT: A 441 LYS cc_start: 0.7670 (tttt) cc_final: 0.7299 (tmmt) REVERT: A 566 MET cc_start: 0.7483 (mpp) cc_final: 0.7197 (mpt) REVERT: B 277 SER cc_start: 0.8363 (t) cc_final: 0.8045 (p) REVERT: B 300 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8713 (mp0) REVERT: C 102 ARG cc_start: 0.5332 (mtt180) cc_final: 0.4534 (mtp180) REVERT: D 5 LYS cc_start: 0.8036 (mppt) cc_final: 0.6960 (tptt) REVERT: D 6 ILE cc_start: 0.2851 (mm) cc_final: 0.2571 (mp) REVERT: D 93 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8239 (mp) REVERT: D 99 PHE cc_start: 0.8846 (m-10) cc_final: 0.8436 (t80) REVERT: D 100 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8624 (mm-30) REVERT: D 126 LYS cc_start: 0.6470 (tppp) cc_final: 0.6204 (tppt) outliers start: 31 outliers final: 20 residues processed: 138 average time/residue: 0.3887 time to fit residues: 58.6856 Evaluate side-chains 144 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 310 ASN A 331 ASN C 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.118945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.097564 restraints weight = 17197.717| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 4.04 r_work: 0.3644 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7891 Z= 0.129 Angle : 0.682 16.011 10768 Z= 0.328 Chirality : 0.042 0.202 1248 Planarity : 0.004 0.047 1384 Dihedral : 4.570 57.384 1183 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.34 % Allowed : 31.05 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.89 (0.26), residues: 1013 helix: 1.67 (0.22), residues: 549 sheet: 0.92 (0.48), residues: 115 loop : -1.30 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 51 TYR 0.013 0.001 TYR A 301 PHE 0.027 0.002 PHE A 304 TRP 0.011 0.001 TRP D 157 HIS 0.005 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7891) covalent geometry : angle 0.68224 (10768) hydrogen bonds : bond 0.03744 ( 413) hydrogen bonds : angle 3.83501 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2832.05 seconds wall clock time: 49 minutes 5.81 seconds (2945.81 seconds total)