Starting phenix.real_space_refine on Tue Mar 3 22:13:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zvt_14986/03_2026/7zvt_14986.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zvt_14986/03_2026/7zvt_14986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zvt_14986/03_2026/7zvt_14986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zvt_14986/03_2026/7zvt_14986.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zvt_14986/03_2026/7zvt_14986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zvt_14986/03_2026/7zvt_14986.map" } resolution = 2.74 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 40 5.16 5 C 5549 2.51 5 N 1489 2.21 5 O 1728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3957 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 464} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 4236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4236 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.14, per 1000 atoms: 0.24 Number of scatterers: 8842 At special positions: 0 Unit cell: (94.25, 86.45, 132.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 36 15.00 O 1728 8.00 N 1489 7.00 C 5549 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: 0.60 Conformation dependent library (CDL) restraints added in 224.3 milliseconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 38.7% alpha, 21.3% beta 10 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.782A pdb=" N PHE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 50 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 77 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 123 through 136 Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.520A pdb=" N VAL A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.810A pdb=" N LYS A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.627A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 495 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 87 through 96 Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 146 through 157 Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.743A pdb=" N ILE B 197 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'B' and resid 218 through 223 removed outlier: 4.232A pdb=" N ASP B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.820A pdb=" N ARG B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 466 through 470 removed outlier: 4.048A pdb=" N LYS B 469 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 470 " --> pdb=" O ASP B 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 466 through 470' Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 484 through 500 removed outlier: 4.048A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.553A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.523A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 6.472A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU A 107 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU A 83 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 82 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ARG A 35 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ARG A 165 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 37 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N MET A 167 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 39 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE A 169 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 41 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N PHE A 199 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU A 168 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.622A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR A 401 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU A 345 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 304 removed outlier: 3.851A pdb=" N LYS A 299 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 294 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR B 295 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA7, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.491A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA B 8 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA B 55 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 10 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL B 57 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU B 12 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE B 59 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N MET B 14 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA B 9 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLU B 133 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 11 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE B 135 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 13 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N TYR B 225 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.641A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU B 268 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N ASN B 359 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 9.936A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG B 394 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL B 342 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA B 396 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE B 340 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 465 347 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2733 1.34 - 1.46: 1590 1.46 - 1.58: 4624 1.58 - 1.70: 64 1.70 - 1.82: 67 Bond restraints: 9078 Sorted by residual: bond pdb=" O14 IHP B 801 " pdb=" P4 IHP B 801 " ideal model delta sigma weight residual 1.671 1.604 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O12 IHP B 801 " pdb=" P2 IHP B 801 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" O16 IHP B 801 " pdb=" P6 IHP B 801 " ideal model delta sigma weight residual 1.672 1.614 0.058 2.00e-02 2.50e+03 8.33e+00 bond pdb=" O15 IHP B 801 " pdb=" P5 IHP B 801 " ideal model delta sigma weight residual 1.675 1.618 0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" C5 IHP B 801 " pdb=" O15 IHP B 801 " ideal model delta sigma weight residual 1.389 1.440 -0.051 2.00e-02 2.50e+03 6.60e+00 ... (remaining 9073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 12244 2.36 - 4.72: 107 4.72 - 7.08: 23 7.08 - 9.44: 2 9.44 - 11.80: 2 Bond angle restraints: 12378 Sorted by residual: angle pdb=" CB MET A 161 " pdb=" CG MET A 161 " pdb=" SD MET A 161 " ideal model delta sigma weight residual 112.70 124.50 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CB GLN B 330 " pdb=" CG GLN B 330 " pdb=" CD GLN B 330 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.70e+00 3.46e-01 1.24e+01 angle pdb=" CB LYS B 442 " pdb=" CG LYS B 442 " pdb=" CD LYS B 442 " ideal model delta sigma weight residual 111.30 118.57 -7.27 2.30e+00 1.89e-01 9.98e+00 angle pdb=" CA GLN B 330 " pdb=" CB GLN B 330 " pdb=" CG GLN B 330 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.86e+00 angle pdb=" CA GLU B 329 " pdb=" CB GLU B 329 " pdb=" CG GLU B 329 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.60e+00 ... (remaining 12373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.85: 5171 32.85 - 65.70: 345 65.70 - 98.55: 12 98.55 - 131.40: 0 131.40 - 164.25: 1 Dihedral angle restraints: 5529 sinusoidal: 2533 harmonic: 2996 Sorted by residual: dihedral pdb=" C4' DT C 8 " pdb=" C3' DT C 8 " pdb=" O3' DT C 8 " pdb=" P DA C 9 " ideal model delta sinusoidal sigma weight residual 220.00 55.75 164.25 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CB GLU A 524 " pdb=" CG GLU A 524 " pdb=" CD GLU A 524 " pdb=" OE1 GLU A 524 " ideal model delta sinusoidal sigma weight residual 0.00 -89.03 89.03 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 49 " pdb=" CG GLU B 49 " pdb=" CD GLU B 49 " pdb=" OE1 GLU B 49 " ideal model delta sinusoidal sigma weight residual 0.00 86.91 -86.91 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 5526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1143 0.050 - 0.100: 193 0.100 - 0.150: 48 0.150 - 0.201: 3 0.201 - 0.251: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" C1 IHP B 801 " pdb=" C2 IHP B 801 " pdb=" C6 IHP B 801 " pdb=" O11 IHP B 801 " both_signs ideal model delta sigma weight residual False 2.32 2.57 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C3 IHP B 801 " pdb=" C2 IHP B 801 " pdb=" C4 IHP B 801 " pdb=" O13 IHP B 801 " both_signs ideal model delta sigma weight residual False -2.34 -2.54 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CG LEU A 147 " pdb=" CB LEU A 147 " pdb=" CD1 LEU A 147 " pdb=" CD2 LEU A 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 1385 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 329 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" CD GLU B 329 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU B 329 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 329 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 189 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO B 190 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 190 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 190 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 141 " 0.095 9.50e-02 1.11e+02 4.32e-02 1.63e+00 pdb=" NE ARG B 141 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 141 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 141 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 141 " -0.001 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 579 2.73 - 3.28: 8499 3.28 - 3.82: 14823 3.82 - 4.36: 17962 4.36 - 4.90: 30299 Nonbonded interactions: 72162 Sorted by model distance: nonbonded pdb=" N GLU A 450 " pdb=" OE1 GLU A 450 " model vdw 2.192 3.120 nonbonded pdb=" N GLN A 126 " pdb=" OE1 GLN A 126 " model vdw 2.219 3.120 nonbonded pdb=" N GLN A 158 " pdb=" OE1 GLN A 158 " model vdw 2.227 3.120 nonbonded pdb=" N GLU A 240 " pdb=" OE1 GLU A 240 " model vdw 2.270 3.120 nonbonded pdb=" O ILE B 118 " pdb=" OG1 THR B 122 " model vdw 2.279 3.040 ... (remaining 72157 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 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 0.067 9078 Z= 0.182 Angle : 0.573 11.803 12378 Z= 0.276 Chirality : 0.041 0.251 1388 Planarity : 0.003 0.043 1478 Dihedral : 19.189 164.252 3577 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.94 % Allowed : 24.81 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.27), residues: 1012 helix: 2.04 (0.29), residues: 343 sheet: 0.69 (0.42), residues: 161 loop : 0.55 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 141 TYR 0.008 0.001 TYR A 88 PHE 0.010 0.001 PHE B 409 TRP 0.002 0.000 TRP B 247 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9078) covalent geometry : angle 0.57263 (12378) hydrogen bonds : bond 0.15152 ( 371) hydrogen bonds : angle 6.46656 ( 1023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.344 Fit side-chains REVERT: A 448 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7537 (p90) outliers start: 27 outliers final: 20 residues processed: 110 average time/residue: 0.5693 time to fit residues: 67.0118 Evaluate side-chains 106 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 472 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.108882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.069939 restraints weight = 13974.010| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.79 r_work: 0.2754 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9078 Z= 0.130 Angle : 0.511 9.588 12378 Z= 0.264 Chirality : 0.040 0.143 1388 Planarity : 0.004 0.050 1478 Dihedral : 17.318 165.350 1497 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.16 % Allowed : 22.31 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.27), residues: 1012 helix: 2.14 (0.28), residues: 344 sheet: 0.54 (0.42), residues: 155 loop : 0.55 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 252 TYR 0.007 0.001 TYR A 88 PHE 0.015 0.001 PHE B 409 TRP 0.006 0.001 TRP B 247 HIS 0.002 0.000 HIS B 511 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9078) covalent geometry : angle 0.51088 (12378) hydrogen bonds : bond 0.04299 ( 371) hydrogen bonds : angle 5.09466 ( 1023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.348 Fit side-chains REVERT: A 92 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8440 (mtmp) REVERT: A 134 MET cc_start: 0.9177 (ppp) cc_final: 0.8859 (ppp) REVERT: A 294 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8423 (pm20) REVERT: A 421 ASP cc_start: 0.8101 (t0) cc_final: 0.7878 (t0) REVERT: A 448 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7781 (p90) REVERT: B 53 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: B 243 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7336 (p90) REVERT: B 330 GLN cc_start: 0.9164 (tp40) cc_final: 0.8911 (tm-30) REVERT: B 434 MET cc_start: 0.8783 (tpt) cc_final: 0.8506 (tpt) outliers start: 29 outliers final: 7 residues processed: 111 average time/residue: 0.6749 time to fit residues: 79.3123 Evaluate side-chains 92 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 125 GLN A 132 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS A 232 HIS B 432 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.109104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.070105 restraints weight = 14033.779| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.82 r_work: 0.2782 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9078 Z= 0.128 Angle : 0.499 9.276 12378 Z= 0.257 Chirality : 0.040 0.165 1388 Planarity : 0.003 0.035 1478 Dihedral : 17.179 165.242 1472 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.81 % Allowed : 21.87 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.27), residues: 1012 helix: 2.21 (0.28), residues: 345 sheet: 0.45 (0.41), residues: 155 loop : 0.50 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 218 TYR 0.013 0.001 TYR A 88 PHE 0.014 0.001 PHE B 409 TRP 0.003 0.000 TRP B 247 HIS 0.003 0.000 HIS B 511 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9078) covalent geometry : angle 0.49915 (12378) hydrogen bonds : bond 0.03766 ( 371) hydrogen bonds : angle 4.79719 ( 1023) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.227 Fit side-chains REVERT: A 92 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8478 (mtmp) REVERT: A 212 ASP cc_start: 0.8502 (t70) cc_final: 0.8009 (t0) REVERT: A 252 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7769 (mtp-110) REVERT: A 294 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: A 391 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8647 (tp30) REVERT: B 53 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: B 243 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.7308 (p90) REVERT: B 330 GLN cc_start: 0.9175 (tp40) cc_final: 0.8919 (tm-30) REVERT: B 434 MET cc_start: 0.8796 (tpt) cc_final: 0.8539 (tpt) outliers start: 35 outliers final: 7 residues processed: 112 average time/residue: 0.5995 time to fit residues: 71.4992 Evaluate side-chains 96 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 310 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 27 optimal weight: 0.0010 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 132 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.071160 restraints weight = 14028.404| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.77 r_work: 0.2728 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9078 Z= 0.128 Angle : 0.514 9.392 12378 Z= 0.260 Chirality : 0.040 0.153 1388 Planarity : 0.003 0.035 1478 Dihedral : 17.094 165.578 1465 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.92 % Allowed : 20.57 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.27), residues: 1012 helix: 2.26 (0.28), residues: 345 sheet: 0.35 (0.41), residues: 155 loop : 0.47 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 141 TYR 0.014 0.001 TYR A 88 PHE 0.013 0.001 PHE B 409 TRP 0.003 0.000 TRP B 247 HIS 0.003 0.000 HIS B 511 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9078) covalent geometry : angle 0.51395 (12378) hydrogen bonds : bond 0.03606 ( 371) hydrogen bonds : angle 4.70080 ( 1023) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.382 Fit side-chains REVERT: A 212 ASP cc_start: 0.8510 (t70) cc_final: 0.8015 (t0) REVERT: A 294 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (pm20) REVERT: A 391 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8668 (tp30) REVERT: A 448 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7930 (p90) REVERT: B 53 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: B 243 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7259 (p90) REVERT: B 330 GLN cc_start: 0.9173 (tp40) cc_final: 0.8954 (tm-30) REVERT: B 434 MET cc_start: 0.8793 (tpt) cc_final: 0.8560 (tpt) outliers start: 36 outliers final: 7 residues processed: 109 average time/residue: 0.5972 time to fit residues: 69.3338 Evaluate side-chains 95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 310 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 125 GLN A 132 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.069416 restraints weight = 13797.851| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.71 r_work: 0.2693 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9078 Z= 0.191 Angle : 0.544 10.065 12378 Z= 0.276 Chirality : 0.041 0.152 1388 Planarity : 0.003 0.034 1478 Dihedral : 17.139 165.592 1463 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.13 % Allowed : 21.11 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.27), residues: 1012 helix: 2.23 (0.28), residues: 345 sheet: 0.25 (0.41), residues: 155 loop : 0.43 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 252 TYR 0.016 0.001 TYR A 88 PHE 0.014 0.001 PHE B 409 TRP 0.003 0.001 TRP B 247 HIS 0.006 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 9078) covalent geometry : angle 0.54389 (12378) hydrogen bonds : bond 0.03964 ( 371) hydrogen bonds : angle 4.67479 ( 1023) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 0.378 Fit side-chains REVERT: A 92 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8411 (mtmp) REVERT: A 212 ASP cc_start: 0.8526 (t70) cc_final: 0.8031 (t0) REVERT: A 294 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8456 (pm20) REVERT: A 391 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8652 (tp30) REVERT: A 448 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8133 (p90) REVERT: B 53 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: B 243 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7300 (p90) REVERT: B 330 GLN cc_start: 0.9189 (tp40) cc_final: 0.8943 (tm-30) REVERT: B 434 MET cc_start: 0.8844 (tpt) cc_final: 0.8620 (tpt) outliers start: 38 outliers final: 12 residues processed: 111 average time/residue: 0.6754 time to fit residues: 79.5919 Evaluate side-chains 104 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 54 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.109172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.070635 restraints weight = 13820.777| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.75 r_work: 0.2718 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9078 Z= 0.130 Angle : 0.538 9.556 12378 Z= 0.271 Chirality : 0.040 0.149 1388 Planarity : 0.004 0.068 1478 Dihedral : 17.055 165.003 1463 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.59 % Allowed : 22.31 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.27), residues: 1012 helix: 2.27 (0.28), residues: 345 sheet: 0.20 (0.41), residues: 155 loop : 0.45 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 252 TYR 0.015 0.001 TYR A 88 PHE 0.013 0.001 PHE B 409 TRP 0.004 0.000 TRP B 247 HIS 0.002 0.000 HIS B 511 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9078) covalent geometry : angle 0.53774 (12378) hydrogen bonds : bond 0.03520 ( 371) hydrogen bonds : angle 4.61863 ( 1023) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.362 Fit side-chains REVERT: A 50 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8448 (mp0) REVERT: A 92 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8427 (mtmp) REVERT: A 212 ASP cc_start: 0.8523 (t70) cc_final: 0.8019 (t0) REVERT: A 279 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8954 (tttm) REVERT: A 294 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: A 391 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8448 (tp30) REVERT: A 448 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8116 (p90) REVERT: B 53 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: B 141 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7403 (ttp80) REVERT: B 243 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7280 (p90) REVERT: B 330 GLN cc_start: 0.9179 (tp40) cc_final: 0.8947 (tm-30) outliers start: 33 outliers final: 10 residues processed: 112 average time/residue: 0.6497 time to fit residues: 77.2606 Evaluate side-chains 104 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 125 GLN A 132 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.109199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.070528 restraints weight = 13928.579| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.77 r_work: 0.2717 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9078 Z= 0.138 Angle : 0.539 9.876 12378 Z= 0.272 Chirality : 0.040 0.148 1388 Planarity : 0.003 0.035 1478 Dihedral : 17.019 165.352 1463 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.48 % Allowed : 22.96 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.27), residues: 1012 helix: 2.30 (0.28), residues: 345 sheet: 0.14 (0.41), residues: 154 loop : 0.42 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 141 TYR 0.015 0.001 TYR A 88 PHE 0.013 0.001 PHE B 409 TRP 0.004 0.000 TRP B 247 HIS 0.003 0.000 HIS B 511 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9078) covalent geometry : angle 0.53862 (12378) hydrogen bonds : bond 0.03532 ( 371) hydrogen bonds : angle 4.58267 ( 1023) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.351 Fit side-chains REVERT: A 50 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: A 163 HIS cc_start: 0.7510 (m90) cc_final: 0.6391 (m170) REVERT: A 212 ASP cc_start: 0.8521 (t70) cc_final: 0.8032 (t0) REVERT: A 279 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8949 (tttm) REVERT: A 294 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8461 (pm20) REVERT: A 332 GLU cc_start: 0.8857 (mp0) cc_final: 0.8649 (pm20) REVERT: A 391 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8656 (tp30) REVERT: A 448 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8120 (p90) REVERT: B 44 ARG cc_start: 0.8748 (ttt90) cc_final: 0.8407 (tpp80) REVERT: B 53 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: B 243 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7488 (p90) REVERT: B 330 GLN cc_start: 0.9184 (tp40) cc_final: 0.8950 (tm-30) REVERT: B 434 MET cc_start: 0.8806 (tpt) cc_final: 0.8534 (tpt) outliers start: 32 outliers final: 12 residues processed: 109 average time/residue: 0.6843 time to fit residues: 79.0955 Evaluate side-chains 106 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 72 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 89 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.071318 restraints weight = 13819.476| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.76 r_work: 0.2730 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9078 Z= 0.122 Angle : 0.533 10.982 12378 Z= 0.269 Chirality : 0.039 0.147 1388 Planarity : 0.003 0.045 1478 Dihedral : 16.960 165.339 1463 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.83 % Allowed : 23.83 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.27), residues: 1012 helix: 2.31 (0.28), residues: 345 sheet: 0.24 (0.43), residues: 145 loop : 0.37 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 141 TYR 0.019 0.001 TYR A 88 PHE 0.012 0.001 PHE B 409 TRP 0.004 0.000 TRP B 247 HIS 0.002 0.000 HIS B 511 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9078) covalent geometry : angle 0.53272 (12378) hydrogen bonds : bond 0.03378 ( 371) hydrogen bonds : angle 4.54031 ( 1023) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.241 Fit side-chains REVERT: A 50 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: A 212 ASP cc_start: 0.8513 (t70) cc_final: 0.8017 (t0) REVERT: A 279 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8927 (tttm) REVERT: A 294 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: A 332 GLU cc_start: 0.8855 (mp0) cc_final: 0.8637 (pm20) REVERT: A 391 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8456 (tp30) REVERT: A 421 ASP cc_start: 0.8230 (t0) cc_final: 0.7996 (t0) REVERT: A 448 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8155 (p90) REVERT: B 44 ARG cc_start: 0.8726 (ttt90) cc_final: 0.8394 (tpp80) REVERT: B 53 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: B 243 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7568 (p90) REVERT: B 330 GLN cc_start: 0.9156 (tp40) cc_final: 0.8933 (tm-30) REVERT: B 434 MET cc_start: 0.8811 (tpt) cc_final: 0.8546 (tpt) outliers start: 26 outliers final: 9 residues processed: 105 average time/residue: 0.6477 time to fit residues: 72.2100 Evaluate side-chains 106 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 125 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.071063 restraints weight = 13896.257| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.77 r_work: 0.2730 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9078 Z= 0.126 Angle : 0.550 12.170 12378 Z= 0.278 Chirality : 0.039 0.149 1388 Planarity : 0.004 0.068 1478 Dihedral : 16.923 165.510 1462 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.07 % Allowed : 24.59 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.27), residues: 1012 helix: 2.33 (0.28), residues: 345 sheet: 0.21 (0.42), residues: 145 loop : 0.35 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 252 TYR 0.013 0.001 TYR A 88 PHE 0.012 0.001 PHE B 409 TRP 0.004 0.000 TRP B 247 HIS 0.003 0.000 HIS B 511 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9078) covalent geometry : angle 0.54989 (12378) hydrogen bonds : bond 0.03365 ( 371) hydrogen bonds : angle 4.52039 ( 1023) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: A 279 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8932 (tttm) REVERT: A 294 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8462 (pm20) REVERT: A 332 GLU cc_start: 0.8851 (mp0) cc_final: 0.8643 (pm20) REVERT: A 391 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8459 (tp30) REVERT: A 421 ASP cc_start: 0.8238 (t0) cc_final: 0.8004 (t0) REVERT: A 448 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8146 (p90) REVERT: B 44 ARG cc_start: 0.8723 (ttt90) cc_final: 0.8401 (tpp80) REVERT: B 53 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: B 243 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7607 (p90) REVERT: B 330 GLN cc_start: 0.9155 (tp40) cc_final: 0.8932 (tm-30) REVERT: B 434 MET cc_start: 0.8810 (tpt) cc_final: 0.8543 (tpt) outliers start: 19 outliers final: 8 residues processed: 101 average time/residue: 0.6888 time to fit residues: 73.8013 Evaluate side-chains 103 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 102 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.110338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.071914 restraints weight = 13909.374| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.77 r_work: 0.2743 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9078 Z= 0.119 Angle : 0.553 12.492 12378 Z= 0.277 Chirality : 0.039 0.151 1388 Planarity : 0.004 0.065 1478 Dihedral : 16.870 165.546 1462 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.96 % Allowed : 24.92 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.27), residues: 1012 helix: 2.33 (0.28), residues: 345 sheet: 0.21 (0.42), residues: 145 loop : 0.36 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 141 TYR 0.013 0.001 TYR A 88 PHE 0.018 0.001 PHE B 183 TRP 0.004 0.000 TRP B 247 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9078) covalent geometry : angle 0.55278 (12378) hydrogen bonds : bond 0.03267 ( 371) hydrogen bonds : angle 4.46739 ( 1023) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: A 212 ASP cc_start: 0.8526 (t70) cc_final: 0.8040 (t0) REVERT: A 294 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: A 332 GLU cc_start: 0.8855 (mp0) cc_final: 0.8647 (pm20) REVERT: A 391 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8474 (tp30) REVERT: A 421 ASP cc_start: 0.8241 (t0) cc_final: 0.8009 (t0) REVERT: A 448 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8141 (p90) REVERT: B 44 ARG cc_start: 0.8713 (ttt90) cc_final: 0.8318 (tpp80) REVERT: B 53 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: B 243 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7670 (p90) REVERT: B 434 MET cc_start: 0.8807 (tpt) cc_final: 0.8547 (tpt) outliers start: 18 outliers final: 8 residues processed: 102 average time/residue: 0.6849 time to fit residues: 74.0071 Evaluate side-chains 103 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 0.0050 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.071106 restraints weight = 13768.998| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.75 r_work: 0.2734 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9078 Z= 0.136 Angle : 0.573 12.529 12378 Z= 0.287 Chirality : 0.040 0.147 1388 Planarity : 0.004 0.080 1478 Dihedral : 16.873 165.704 1462 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.96 % Allowed : 25.03 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.27), residues: 1012 helix: 2.31 (0.28), residues: 345 sheet: 0.21 (0.42), residues: 145 loop : 0.39 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 252 TYR 0.013 0.001 TYR A 88 PHE 0.012 0.001 PHE B 409 TRP 0.004 0.000 TRP B 247 HIS 0.003 0.000 HIS B 511 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9078) covalent geometry : angle 0.57280 (12378) hydrogen bonds : bond 0.03376 ( 371) hydrogen bonds : angle 4.48038 ( 1023) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2886.58 seconds wall clock time: 49 minutes 53.49 seconds (2993.49 seconds total)