Starting phenix.real_space_refine on Thu Mar 13 14:31:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zvt_14986/03_2025/7zvt_14986.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zvt_14986/03_2025/7zvt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zvt_14986/03_2025/7zvt_14986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zvt_14986/03_2025/7zvt_14986.map" model { file = "/net/cci-nas-00/data/ceres_data/7zvt_14986/03_2025/7zvt_14986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zvt_14986/03_2025/7zvt_14986.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'ARG:plan': 1, 'ASP: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: 7.05, per 1000 atoms: 0.80 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: 2.37 Conformation dependent library (CDL) restraints added in 943.1 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: 3.18 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: 3.04 Time building geometry restraints manager: 2.79 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: 57.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.860 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.480 ------------------------------------------------------------------------------- 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= 0.261 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (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 TRP 0.002 0.000 TRP B 247 HIS 0.004 0.001 HIS A 163 PHE 0.010 0.001 PHE B 409 TYR 0.008 0.001 TYR A 88 ARG 0.012 0.000 ARG B 141 *********************** 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 : 0.789 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: 1.2190 time to fit residues: 143.7000 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 : 1.019 ------------------------------------------------------------------------------- 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 87 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.108711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.069125 restraints weight = 13897.646| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.84 r_work: 0.2741 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.0706 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= 0.206 Angle : 0.517 9.682 12378 Z= 0.267 Chirality : 0.040 0.143 1388 Planarity : 0.004 0.048 1478 Dihedral : 17.349 165.349 1497 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.27), residues: 1012 helix: 2.12 (0.28), residues: 344 sheet: 0.53 (0.41), residues: 155 loop : 0.54 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.003 0.000 HIS B 511 PHE 0.016 0.001 PHE B 409 TYR 0.007 0.001 TYR A 103 ARG 0.012 0.000 ARG A 252 *********************** 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 120 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 1.020 Fit side-chains REVERT: A 92 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8447 (mtmp) REVERT: A 212 ASP cc_start: 0.8517 (t70) cc_final: 0.8034 (t0) REVERT: A 294 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8424 (pm20) REVERT: A 421 ASP cc_start: 0.8114 (t0) cc_final: 0.7881 (t0) REVERT: A 448 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7817 (p90) REVERT: B 53 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: B 243 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7367 (p90) REVERT: B 330 GLN cc_start: 0.9155 (tp40) cc_final: 0.8895 (tm-30) REVERT: B 434 MET cc_start: 0.8803 (tpt) cc_final: 0.8537 (tpt) outliers start: 29 outliers final: 7 residues processed: 113 average time/residue: 1.3851 time to fit residues: 166.3710 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 : 1.007 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.0770 chunk 68 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 48 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.110450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.071898 restraints weight = 13980.755| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.79 r_work: 0.2748 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9078 Z= 0.151 Angle : 0.491 9.210 12378 Z= 0.253 Chirality : 0.039 0.163 1388 Planarity : 0.003 0.036 1478 Dihedral : 17.132 165.194 1472 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.92 % Allowed : 21.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (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 TRP 0.003 0.000 TRP B 247 HIS 0.002 0.000 HIS B 511 PHE 0.013 0.001 PHE B 409 TYR 0.012 0.001 TYR A 88 ARG 0.006 0.000 ARG A 218 *********************** 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 125 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 0.940 Fit side-chains REVERT: A 92 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8446 (mtmp) REVERT: A 212 ASP cc_start: 0.8489 (t70) cc_final: 0.7976 (t0) REVERT: A 252 ARG cc_start: 0.7957 (mmm-85) cc_final: 0.7733 (mtp-110) REVERT: A 294 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8458 (pm20) REVERT: A 391 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8660 (tp30) REVERT: B 53 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: B 243 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7288 (p90) REVERT: B 330 GLN cc_start: 0.9169 (tp40) cc_final: 0.8912 (tm-30) REVERT: B 434 MET cc_start: 0.8756 (tpt) cc_final: 0.8477 (tpt) outliers start: 36 outliers final: 6 residues processed: 116 average time/residue: 1.2798 time to fit residues: 158.2275 Evaluate side-chains 95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.110056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.071436 restraints weight = 13852.466| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.78 r_work: 0.2731 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9078 Z= 0.189 Angle : 0.516 9.243 12378 Z= 0.262 Chirality : 0.040 0.152 1388 Planarity : 0.003 0.036 1478 Dihedral : 17.074 165.647 1465 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.81 % Allowed : 20.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 1012 helix: 2.26 (0.28), residues: 345 sheet: 0.34 (0.41), residues: 157 loop : 0.47 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 247 HIS 0.003 0.000 HIS B 511 PHE 0.013 0.001 PHE B 409 TYR 0.014 0.001 TYR A 88 ARG 0.006 0.000 ARG B 141 *********************** 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: 35 poor density : 88 time to evaluate : 0.943 Fit side-chains REVERT: A 92 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8453 (mtmp) REVERT: A 212 ASP cc_start: 0.8519 (t70) cc_final: 0.8014 (t0) REVERT: A 294 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8436 (pm20) REVERT: A 391 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8671 (tp30) REVERT: A 448 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7918 (p90) REVERT: B 53 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: B 243 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7282 (p90) REVERT: B 330 GLN cc_start: 0.9177 (tp40) cc_final: 0.8958 (tm-30) REVERT: B 434 MET cc_start: 0.8790 (tpt) cc_final: 0.8533 (tpt) outliers start: 35 outliers final: 8 residues processed: 109 average time/residue: 1.2878 time to fit residues: 149.6621 Evaluate side-chains 98 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 51 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 80 HIS B 432 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.072379 restraints weight = 13849.687| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.78 r_work: 0.2758 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9078 Z= 0.149 Angle : 0.505 8.893 12378 Z= 0.257 Chirality : 0.039 0.153 1388 Planarity : 0.003 0.037 1478 Dihedral : 16.948 165.553 1463 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.27), residues: 1012 helix: 2.31 (0.28), residues: 345 sheet: 0.34 (0.43), residues: 147 loop : 0.46 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 247 HIS 0.002 0.000 HIS B 511 PHE 0.012 0.001 PHE B 409 TYR 0.017 0.001 TYR A 88 ARG 0.007 0.000 ARG B 141 *********************** 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 118 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.913 Fit side-chains REVERT: A 92 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8440 (mtmp) REVERT: A 212 ASP cc_start: 0.8526 (t70) cc_final: 0.7998 (t0) REVERT: A 294 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8466 (pm20) REVERT: B 53 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: B 243 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.7256 (p90) REVERT: B 330 GLN cc_start: 0.9176 (tp40) cc_final: 0.8949 (tm-30) REVERT: B 434 MET cc_start: 0.8759 (tpt) cc_final: 0.8514 (tpt) outliers start: 29 outliers final: 8 residues processed: 107 average time/residue: 1.3038 time to fit residues: 148.8229 Evaluate side-chains 97 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 134 MET Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 157 VAL 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 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 0.0970 chunk 63 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.109344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.071153 restraints weight = 13751.882| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.72 r_work: 0.2728 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9078 Z= 0.224 Angle : 0.533 9.401 12378 Z= 0.269 Chirality : 0.040 0.149 1388 Planarity : 0.003 0.057 1478 Dihedral : 16.997 165.998 1463 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.92 % Allowed : 21.87 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 1012 helix: 2.35 (0.28), residues: 345 sheet: 0.17 (0.41), residues: 154 loop : 0.46 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 247 HIS 0.003 0.001 HIS B 511 PHE 0.013 0.001 PHE B 409 TYR 0.015 0.001 TYR A 88 ARG 0.016 0.000 ARG A 252 *********************** 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 127 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.951 Fit side-chains REVERT: A 50 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8429 (mp0) REVERT: A 92 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8403 (mtmp) REVERT: A 212 ASP cc_start: 0.8524 (t70) cc_final: 0.7999 (t0) REVERT: A 294 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8451 (pm20) REVERT: A 391 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8657 (tp30) REVERT: B 53 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: B 141 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7400 (ttp80) REVERT: B 243 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7279 (p90) REVERT: B 330 GLN cc_start: 0.9173 (tp40) cc_final: 0.8935 (tm-30) REVERT: B 434 MET cc_start: 0.8823 (tpt) cc_final: 0.8591 (tpt) outliers start: 36 outliers final: 11 residues processed: 111 average time/residue: 1.2870 time to fit residues: 153.0012 Evaluate side-chains 105 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 157 VAL 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.109964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.071452 restraints weight = 13919.475| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.77 r_work: 0.2736 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 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 0.034 9078 Z= 0.185 Angle : 0.525 9.663 12378 Z= 0.266 Chirality : 0.040 0.148 1388 Planarity : 0.003 0.036 1478 Dihedral : 16.952 165.534 1463 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.60 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 1012 helix: 2.34 (0.28), residues: 345 sheet: 0.26 (0.43), residues: 145 loop : 0.42 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 247 HIS 0.003 0.000 HIS B 511 PHE 0.012 0.001 PHE B 409 TYR 0.016 0.001 TYR A 88 ARG 0.006 0.000 ARG B 141 *********************** 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 121 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 1.046 Fit side-chains REVERT: A 50 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: A 92 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8401 (mtmp) REVERT: A 212 ASP cc_start: 0.8527 (t70) cc_final: 0.8028 (t0) REVERT: A 252 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7681 (ttp-110) REVERT: A 294 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: A 391 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8668 (tp30) REVERT: A 448 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8096 (p90) REVERT: B 53 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: B 243 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.7533 (p90) REVERT: B 330 GLN cc_start: 0.9178 (tp40) cc_final: 0.8936 (tm-30) REVERT: B 434 MET cc_start: 0.8797 (tpt) cc_final: 0.8576 (tpt) outliers start: 32 outliers final: 12 residues processed: 106 average time/residue: 1.3457 time to fit residues: 151.7008 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 : 0.929 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 LEU 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 213 ILE 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 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 97 optimal weight: 0.0060 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.110402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.072332 restraints weight = 14020.663| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.75 r_work: 0.2751 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1341 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= 0.173 Angle : 0.536 11.457 12378 Z= 0.269 Chirality : 0.039 0.148 1388 Planarity : 0.003 0.054 1478 Dihedral : 16.889 165.792 1462 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.61 % Allowed : 23.72 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 1012 helix: 2.37 (0.28), residues: 345 sheet: 0.24 (0.43), residues: 145 loop : 0.41 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 247 HIS 0.002 0.000 HIS B 511 PHE 0.017 0.001 PHE B 183 TYR 0.012 0.001 TYR A 88 ARG 0.010 0.000 ARG B 141 *********************** 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 117 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: A 92 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8402 (mtmp) REVERT: A 163 HIS cc_start: 0.7494 (m90) cc_final: 0.6440 (m170) REVERT: A 212 ASP cc_start: 0.8507 (t70) cc_final: 0.7988 (t0) REVERT: A 294 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8446 (pm20) REVERT: A 335 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8374 (mm-30) REVERT: A 391 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8668 (tp30) REVERT: B 44 ARG cc_start: 0.8671 (ttt90) cc_final: 0.8359 (tpp80) REVERT: B 53 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: B 65 ASP cc_start: 0.8060 (t0) cc_final: 0.7743 (t0) REVERT: B 243 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7595 (p90) REVERT: B 330 GLN cc_start: 0.9146 (tp40) cc_final: 0.8921 (tm-30) REVERT: B 434 MET cc_start: 0.8809 (tpt) cc_final: 0.8588 (tpt) outliers start: 24 outliers final: 10 residues processed: 107 average time/residue: 1.3864 time to fit residues: 157.7647 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 : 1.439 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 157 VAL 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 391 GLU 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 25 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 0.0570 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.108642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.070443 restraints weight = 13858.200| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.71 r_work: 0.2712 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9078 Z= 0.265 Angle : 0.568 11.704 12378 Z= 0.285 Chirality : 0.040 0.151 1388 Planarity : 0.004 0.055 1478 Dihedral : 16.970 166.071 1462 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.18 % Allowed : 24.16 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 1012 helix: 2.33 (0.28), residues: 345 sheet: 0.13 (0.41), residues: 154 loop : 0.44 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.008 0.001 HIS A 163 PHE 0.013 0.001 PHE B 409 TYR 0.013 0.001 TYR A 88 ARG 0.013 0.000 ARG A 218 *********************** 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 114 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.915 Fit side-chains REVERT: A 50 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8407 (mp0) REVERT: A 92 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8410 (mtmp) REVERT: A 212 ASP cc_start: 0.8486 (t70) cc_final: 0.7978 (t0) REVERT: A 294 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: A 391 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8661 (tp30) REVERT: A 421 ASP cc_start: 0.8246 (t0) cc_final: 0.8007 (t0) REVERT: A 448 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8217 (p90) REVERT: B 44 ARG cc_start: 0.8728 (ttt90) cc_final: 0.8408 (tpp80) REVERT: B 53 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: B 65 ASP cc_start: 0.8124 (t0) cc_final: 0.7786 (t0) REVERT: B 243 HIS cc_start: 0.7948 (OUTLIER) cc_final: 0.7562 (p90) REVERT: B 330 GLN cc_start: 0.9151 (tp40) cc_final: 0.8929 (tm-30) REVERT: B 434 MET cc_start: 0.8804 (tpt) cc_final: 0.8537 (tpt) outliers start: 20 outliers final: 10 residues processed: 108 average time/residue: 1.5775 time to fit residues: 180.3422 Evaluate side-chains 108 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 2.038 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 157 VAL 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 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 69 optimal weight: 0.3980 chunk 37 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 0.0370 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.110574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.072684 restraints weight = 13913.684| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.73 r_work: 0.2757 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9078 Z= 0.172 Angle : 0.565 12.726 12378 Z= 0.282 Chirality : 0.039 0.147 1388 Planarity : 0.004 0.079 1478 Dihedral : 16.847 165.164 1462 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.96 % Allowed : 24.81 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 1012 helix: 2.34 (0.28), residues: 345 sheet: 0.23 (0.42), residues: 145 loop : 0.39 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 247 HIS 0.002 0.000 HIS B 511 PHE 0.016 0.001 PHE B 183 TYR 0.014 0.001 TYR A 88 ARG 0.021 0.001 ARG A 252 ********************** 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 112 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.992 Fit side-chains REVERT: A 50 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: A 92 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8392 (mtmp) REVERT: A 134 MET cc_start: 0.8940 (ppp) cc_final: 0.8539 (ppp) REVERT: A 294 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: A 421 ASP cc_start: 0.8220 (t0) cc_final: 0.7989 (t0) REVERT: B 44 ARG cc_start: 0.8665 (ttt90) cc_final: 0.8293 (tpp80) REVERT: B 53 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: B 65 ASP cc_start: 0.8131 (t0) cc_final: 0.7795 (t0) REVERT: B 243 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7663 (p90) outliers start: 18 outliers final: 8 residues processed: 105 average time/residue: 1.3392 time to fit residues: 149.6889 Evaluate side-chains 106 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 157 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 42 optimal weight: 0.0770 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.9740 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.109546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.071060 restraints weight = 13895.355| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.76 r_work: 0.2724 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9078 Z= 0.235 Angle : 0.604 12.248 12378 Z= 0.298 Chirality : 0.040 0.151 1388 Planarity : 0.003 0.056 1478 Dihedral : 16.888 166.104 1462 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.74 % Allowed : 25.46 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 1012 helix: 2.34 (0.28), residues: 345 sheet: 0.18 (0.42), residues: 145 loop : 0.40 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 247 HIS 0.003 0.000 HIS B 511 PHE 0.012 0.001 PHE B 409 TYR 0.013 0.001 TYR A 88 ARG 0.013 0.000 ARG A 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6377.06 seconds wall clock time: 111 minutes 53.19 seconds (6713.19 seconds total)