Starting phenix.real_space_refine on Fri Sep 11 11:18:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zwa_14995/09_2026/7zwa_14995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zwa_14995/09_2026/7zwa_14995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zwa_14995/09_2026/7zwa_14995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zwa_14995/09_2026/7zwa_14995.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zwa_14995/09_2026/7zwa_14995.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zwa_14995/09_2026/7zwa_14995.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zwa_14995/09_2026/7zwa_14995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zwa_14995/09_2026/7zwa_14995.cif" } resolution = 2.8 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 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 32 5.49 5 S 42 5.16 5 C 5678 2.51 5 N 1532 2.21 5 O 1754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9038 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4009 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 27, 'TRANS': 475} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4222 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 502} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 165 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 3, 'TRANS': 19} Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 304 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "E" 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.13, per 1000 atoms: 0.24 Number of scatterers: 9038 At special positions: 0 Unit cell: (92.95, 87.75, 141.7, 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 42 16.00 P 32 15.00 O 1754 8.00 N 1532 7.00 C 5678 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: 0.92 Conformation dependent library (CDL) restraints added in 321.7 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 37.5% alpha, 20.9% beta 6 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.801A pdb=" N GLU A 50 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 78 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.974A pdb=" N GLY A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 removed outlier: 4.074A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.613A pdb=" N GLY A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 238 through 244 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 Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.586A pdb=" N LYS A 443 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 496 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 123 removed outlier: 4.041A pdb=" N ILE B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 198 through 217 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.755A pdb=" N LEU B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 233 No H-bonds generated for 'chain 'B' and resid 232 through 233' Processing helix chain 'B' and resid 234 through 238 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 332 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 447 through 461 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 484 through 500 removed outlier: 4.013A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 526 through 537 removed outlier: 3.555A pdb=" N LEU B 530 " --> pdb=" O SER B 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.902A pdb=" N ARG A 35 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS A 164 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N SER A 37 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 166 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 39 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU A 168 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 41 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THR A 170 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASP A 43 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N PHE A 199 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.752A 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: 3.689A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR A 401 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 5.676A 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: 3.797A pdb=" N PHE A 303 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 290 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 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 removed outlier: 6.652A pdb=" N GLU A 419 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.339A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 6.287A 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 253 removed outlier: 3.554A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU B 268 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N ASN B 359 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 390 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE B 345 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 392 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.676A 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 466 367 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2463 1.33 - 1.45: 1551 1.45 - 1.57: 5139 1.57 - 1.69: 60 1.69 - 1.81: 70 Bond restraints: 9283 Sorted by residual: bond pdb=" O3 PO4 A 701 " pdb=" P PO4 A 701 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" O4 PO4 A 701 " pdb=" P PO4 A 701 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" O2 PO4 A 701 " pdb=" P PO4 A 701 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" O1 PO4 A 701 " pdb=" P PO4 A 701 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" C3' DT E 4 " pdb=" C2' DT E 4 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.97e+00 ... (remaining 9278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 12242 1.37 - 2.73: 357 2.73 - 4.10: 48 4.10 - 5.47: 12 5.47 - 6.84: 1 Bond angle restraints: 12660 Sorted by residual: angle pdb=" N3 DT D 3 " pdb=" C4 DT D 3 " pdb=" O4 DT D 3 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT D 15 " pdb=" C4 DT D 15 " pdb=" O4 DT D 15 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT E 14 " pdb=" C4 DT E 14 " pdb=" O4 DT E 14 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT E 2 " pdb=" C4 DT E 2 " pdb=" O4 DT E 2 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (remaining 12655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 5407 35.58 - 71.16: 204 71.16 - 106.74: 9 106.74 - 142.32: 0 142.32 - 177.90: 1 Dihedral angle restraints: 5621 sinusoidal: 2533 harmonic: 3088 Sorted by residual: dihedral pdb=" C4' DT E 4 " pdb=" C3' DT E 4 " pdb=" O3' DT E 4 " pdb=" P DC E 5 " ideal model delta sinusoidal sigma weight residual 220.00 42.10 177.90 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ASP B 398 " pdb=" CB ASP B 398 " pdb=" CG ASP B 398 " pdb=" OD1 ASP B 398 " ideal model delta sinusoidal sigma weight residual -30.00 -88.85 58.85 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP B 72 " pdb=" C ASP B 72 " pdb=" N GLN B 73 " pdb=" CA GLN B 73 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 816 0.029 - 0.057: 369 0.057 - 0.086: 134 0.086 - 0.114: 87 0.114 - 0.143: 13 Chirality restraints: 1419 Sorted by residual: chirality pdb=" C3' DT E 4 " pdb=" C4' DT E 4 " pdb=" O3' DT E 4 " pdb=" C2' DT E 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA GLU B 216 " pdb=" N GLU B 216 " pdb=" C GLU B 216 " pdb=" CB GLU B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE B 24 " pdb=" N ILE B 24 " pdb=" C ILE B 24 " pdb=" CB ILE B 24 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 1416 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 126 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C GLN A 126 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 126 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 127 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 211 " 0.013 2.00e-02 2.50e+03 1.39e-02 3.37e+00 pdb=" CG PHE A 211 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 211 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 211 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 211 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 211 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 211 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 518 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO B 519 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 519 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 519 " 0.018 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1188 2.76 - 3.29: 8601 3.29 - 3.83: 15153 3.83 - 4.36: 17888 4.36 - 4.90: 30091 Nonbonded interactions: 72921 Sorted by model distance: nonbonded pdb=" OH TYR A 409 " pdb=" OE1 GLN B 269 " model vdw 2.220 3.040 nonbonded pdb=" ND2 ASN A 171 " pdb=" O LYS A 206 " model vdw 2.237 3.120 nonbonded pdb=" OG SER A 78 " pdb=" OD2 ASP A 81 " model vdw 2.245 3.040 nonbonded pdb=" OE1 GLU B 223 " pdb=" OH TYR B 225 " model vdw 2.247 3.040 nonbonded pdb=" O ILE B 118 " pdb=" OG1 THR B 122 " model vdw 2.254 3.040 ... (remaining 72916 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: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.770 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:8.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.003 0.059 9283 Z= 0.224 Angle : 0.549 6.835 12660 Z= 0.363 Chirality : 0.042 0.143 1419 Planarity : 0.003 0.032 1523 Dihedral : 16.751 177.899 3611 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 1047 helix: 1.93 (0.29), residues: 336 sheet: 0.39 (0.41), residues: 164 loop : -0.21 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 271 TYR 0.010 0.001 TYR A 103 PHE 0.032 0.001 PHE A 211 TRP 0.004 0.001 TRP B 247 HIS 0.002 0.000 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.22 ( 9283) covalent geometry : angle 0.54880 / 0.36 (12660) hydrogen bonds : bond 0.15424 / 10.56 ( 383) hydrogen bonds : angle 6.18194 / 4.37 ( 1055) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.345 Fit side-chains REVERT: A 128 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8299 (pm20) REVERT: A 129 LYS cc_start: 0.9077 (mppt) cc_final: 0.8755 (mptt) REVERT: A 216 PHE cc_start: 0.8415 (t80) cc_final: 0.8174 (t80) REVERT: A 265 LYS cc_start: 0.8929 (pttp) cc_final: 0.8656 (pptt) REVERT: C 184 SER cc_start: 0.9008 (t) cc_final: 0.8794 (t) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.6874 time to fit residues: 100.2988 Evaluate side-chains 91 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS A 304 ASN B 269 GLN B 312 GLN B 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.070840 restraints weight = 15467.125| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.13 r_work: 0.2650 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9283 Z= 0.165 Angle : 0.577 7.250 12660 Z= 0.304 Chirality : 0.043 0.263 1419 Planarity : 0.004 0.032 1523 Dihedral : 17.809 178.409 1467 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.28 % Allowed : 9.85 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.26), residues: 1047 helix: 2.02 (0.29), residues: 336 sheet: 0.13 (0.39), residues: 164 loop : -0.12 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 315 TYR 0.010 0.001 TYR A 409 PHE 0.013 0.001 PHE B 107 TRP 0.005 0.001 TRP B 247 HIS 0.004 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 9283) covalent geometry : angle 0.57688 / 0.30 (12660) hydrogen bonds : bond 0.04094 / 2.80 ( 383) hydrogen bonds : angle 4.86827 / 3.49 ( 1055) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8384 (mtp) REVERT: A 99 PHE cc_start: 0.7644 (m-10) cc_final: 0.7436 (m-10) REVERT: A 265 LYS cc_start: 0.9066 (pttp) cc_final: 0.8798 (pptt) REVERT: B 270 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8686 (tt0) REVERT: C 184 SER cc_start: 0.8975 (t) cc_final: 0.8763 (t) outliers start: 12 outliers final: 4 residues processed: 110 average time/residue: 0.6109 time to fit residues: 71.8268 Evaluate side-chains 102 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 270 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 432 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.070534 restraints weight = 15212.274| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.11 r_work: 0.2626 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9283 Z= 0.155 Angle : 0.539 6.547 12660 Z= 0.286 Chirality : 0.042 0.283 1419 Planarity : 0.004 0.035 1523 Dihedral : 17.870 179.424 1467 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.61 % Allowed : 11.67 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.26), residues: 1047 helix: 2.06 (0.29), residues: 336 sheet: 0.01 (0.39), residues: 164 loop : -0.11 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 290 TYR 0.014 0.001 TYR A 289 PHE 0.022 0.001 PHE A 216 TRP 0.004 0.001 TRP B 247 HIS 0.003 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9283) covalent geometry : angle 0.53919 / 0.29 (12660) hydrogen bonds : bond 0.03796 / 2.59 ( 383) hydrogen bonds : angle 4.68393 / 3.35 ( 1055) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.395 Fit side-chains REVERT: A 48 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8340 (mtp) REVERT: A 99 PHE cc_start: 0.7762 (m-10) cc_final: 0.7480 (m-80) REVERT: A 128 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8353 (pm20) REVERT: A 129 LYS cc_start: 0.9168 (mppt) cc_final: 0.8883 (mptt) REVERT: B 270 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: B 282 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8984 (mmmm) REVERT: B 328 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.9171 (tt0) REVERT: C 184 SER cc_start: 0.8977 (t) cc_final: 0.8768 (t) outliers start: 15 outliers final: 5 residues processed: 110 average time/residue: 0.5518 time to fit residues: 65.2108 Evaluate side-chains 105 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 37 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 GLN B 104 GLN B 432 GLN B 440 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.071532 restraints weight = 15570.014| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.15 r_work: 0.2663 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9283 Z= 0.114 Angle : 0.520 6.961 12660 Z= 0.275 Chirality : 0.041 0.265 1419 Planarity : 0.003 0.029 1523 Dihedral : 17.827 178.299 1467 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.50 % Allowed : 13.49 % Favored : 85.01 % 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: 0.85 (0.26), residues: 1047 helix: 1.99 (0.29), residues: 342 sheet: 0.22 (0.41), residues: 149 loop : -0.21 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 502 TYR 0.010 0.001 TYR A 289 PHE 0.012 0.001 PHE B 18 TRP 0.004 0.001 TRP B 247 HIS 0.002 0.000 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 9283) covalent geometry : angle 0.52008 / 0.28 (12660) hydrogen bonds : bond 0.03436 / 2.34 ( 383) hydrogen bonds : angle 4.57343 / 3.27 ( 1055) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8241 (mtp) REVERT: A 99 PHE cc_start: 0.7860 (m-10) cc_final: 0.7609 (m-80) REVERT: A 128 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8163 (pm20) REVERT: B 242 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7524 (ttm-80) REVERT: B 328 GLU cc_start: 0.9430 (OUTLIER) cc_final: 0.9201 (tt0) outliers start: 14 outliers final: 6 residues processed: 114 average time/residue: 0.5713 time to fit residues: 69.7617 Evaluate side-chains 103 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 0.0970 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 0.0050 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 0.0670 chunk 6 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.3330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 432 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.110566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.071846 restraints weight = 15319.800| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.10 r_work: 0.2685 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9283 Z= 0.109 Angle : 0.538 7.561 12660 Z= 0.285 Chirality : 0.041 0.256 1419 Planarity : 0.003 0.029 1523 Dihedral : 17.814 178.040 1467 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.28 % Allowed : 15.42 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1047 helix: 1.99 (0.29), residues: 342 sheet: 0.20 (0.41), residues: 149 loop : -0.19 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 502 TYR 0.009 0.001 TYR A 289 PHE 0.011 0.001 PHE B 18 TRP 0.003 0.000 TRP B 247 HIS 0.002 0.000 HIS B 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9283) covalent geometry : angle 0.53842 / 0.28 (12660) hydrogen bonds : bond 0.03278 / 2.22 ( 383) hydrogen bonds : angle 4.48419 / 3.20 ( 1055) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.385 Fit side-chains REVERT: A 48 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8242 (mtp) REVERT: A 128 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8156 (pm20) REVERT: A 129 LYS cc_start: 0.9189 (mppt) cc_final: 0.8795 (mptt) REVERT: A 135 MET cc_start: 0.8811 (mtm) cc_final: 0.8128 (mtm) REVERT: A 265 LYS cc_start: 0.9207 (ptmm) cc_final: 0.8715 (pptt) REVERT: B 242 ARG cc_start: 0.7959 (mtp85) cc_final: 0.7543 (ttm-80) outliers start: 12 outliers final: 7 residues processed: 110 average time/residue: 0.5329 time to fit residues: 63.1279 Evaluate side-chains 104 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 94 optimal weight: 0.0060 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 312 GLN B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.071069 restraints weight = 15334.498| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.11 r_work: 0.2661 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9283 Z= 0.130 Angle : 0.549 9.015 12660 Z= 0.285 Chirality : 0.042 0.268 1419 Planarity : 0.003 0.030 1523 Dihedral : 17.837 178.367 1467 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.46 % Allowed : 15.31 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1047 helix: 2.13 (0.29), residues: 335 sheet: 0.14 (0.41), residues: 155 loop : -0.11 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 502 TYR 0.008 0.001 TYR A 141 PHE 0.027 0.001 PHE A 216 TRP 0.003 0.001 TRP B 247 HIS 0.004 0.001 HIS B 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9283) covalent geometry : angle 0.54940 / 0.29 (12660) hydrogen bonds : bond 0.03368 / 2.27 ( 383) hydrogen bonds : angle 4.46729 / 3.19 ( 1055) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8265 (mtp) REVERT: A 99 PHE cc_start: 0.8025 (m-80) cc_final: 0.7429 (m-80) REVERT: A 128 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8197 (pm20) REVERT: A 201 ASP cc_start: 0.8368 (m-30) cc_final: 0.8075 (m-30) REVERT: A 265 LYS cc_start: 0.9202 (ptmm) cc_final: 0.8720 (pptt) REVERT: B 242 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7582 (ttm-80) REVERT: B 328 GLU cc_start: 0.9451 (OUTLIER) cc_final: 0.9172 (tt0) outliers start: 23 outliers final: 10 residues processed: 112 average time/residue: 0.5203 time to fit residues: 62.8528 Evaluate side-chains 109 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 382 HIS B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.069787 restraints weight = 15427.948| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.11 r_work: 0.2626 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9283 Z= 0.170 Angle : 0.571 8.935 12660 Z= 0.296 Chirality : 0.042 0.291 1419 Planarity : 0.003 0.030 1523 Dihedral : 17.903 179.195 1467 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.57 % Allowed : 16.49 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 1047 helix: 2.12 (0.29), residues: 335 sheet: 0.01 (0.39), residues: 164 loop : -0.08 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 502 TYR 0.007 0.001 TYR A 88 PHE 0.016 0.001 PHE C 190 TRP 0.003 0.001 TRP A 148 HIS 0.003 0.001 HIS B 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 9283) covalent geometry : angle 0.57057 / 0.30 (12660) hydrogen bonds : bond 0.03588 / 2.41 ( 383) hydrogen bonds : angle 4.50286 / 3.21 ( 1055) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8313 (mtp) REVERT: A 99 PHE cc_start: 0.8029 (m-80) cc_final: 0.7472 (m-10) REVERT: A 128 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8204 (pm20) REVERT: A 201 ASP cc_start: 0.8371 (m-30) cc_final: 0.8054 (m-30) REVERT: A 265 LYS cc_start: 0.9198 (ptmm) cc_final: 0.8716 (pptt) REVERT: B 242 ARG cc_start: 0.8021 (mtp85) cc_final: 0.7621 (ttm-80) REVERT: B 328 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9214 (tt0) outliers start: 24 outliers final: 12 residues processed: 114 average time/residue: 0.5125 time to fit residues: 63.0689 Evaluate side-chains 114 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.070070 restraints weight = 15341.242| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.09 r_work: 0.2639 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9283 Z= 0.154 Angle : 0.571 12.112 12660 Z= 0.296 Chirality : 0.042 0.289 1419 Planarity : 0.003 0.031 1523 Dihedral : 17.893 178.857 1467 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.25 % Allowed : 16.92 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 1047 helix: 2.09 (0.29), residues: 335 sheet: 0.21 (0.41), residues: 149 loop : -0.12 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 502 TYR 0.008 0.001 TYR A 141 PHE 0.031 0.001 PHE A 216 TRP 0.003 0.001 TRP B 247 HIS 0.003 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 9283) covalent geometry : angle 0.57128 / 0.30 (12660) hydrogen bonds : bond 0.03536 / 2.37 ( 383) hydrogen bonds : angle 4.50947 / 3.21 ( 1055) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8315 (mtp) REVERT: A 99 PHE cc_start: 0.8014 (m-80) cc_final: 0.7413 (m-10) REVERT: A 128 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8188 (pm20) REVERT: A 201 ASP cc_start: 0.8399 (m-30) cc_final: 0.8091 (m-30) REVERT: A 265 LYS cc_start: 0.9194 (ptmm) cc_final: 0.8716 (pptt) REVERT: B 242 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7628 (ttm-80) REVERT: B 328 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9196 (tt0) outliers start: 21 outliers final: 11 residues processed: 110 average time/residue: 0.4587 time to fit residues: 54.6401 Evaluate side-chains 107 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 0.7980 chunk 39 optimal weight: 0.0770 chunk 98 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.072332 restraints weight = 15264.775| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.10 r_work: 0.2669 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9283 Z= 0.118 Angle : 0.567 10.533 12660 Z= 0.294 Chirality : 0.041 0.271 1419 Planarity : 0.003 0.031 1523 Dihedral : 17.876 178.265 1467 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.50 % Allowed : 17.88 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1047 helix: 2.08 (0.29), residues: 335 sheet: 0.20 (0.40), residues: 149 loop : -0.10 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 502 TYR 0.010 0.001 TYR A 88 PHE 0.019 0.001 PHE C 190 TRP 0.003 0.000 TRP B 247 HIS 0.003 0.000 HIS B 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9283) covalent geometry : angle 0.56731 / 0.29 (12660) hydrogen bonds : bond 0.03293 / 2.20 ( 383) hydrogen bonds : angle 4.46591 / 3.17 ( 1055) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.376 Fit side-chains REVERT: A 48 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8322 (mtp) REVERT: A 99 PHE cc_start: 0.7965 (m-80) cc_final: 0.7385 (m-10) REVERT: A 128 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8198 (pm20) REVERT: A 129 LYS cc_start: 0.9167 (mppt) cc_final: 0.8861 (mptt) REVERT: A 201 ASP cc_start: 0.8400 (m-30) cc_final: 0.8107 (m-30) REVERT: A 265 LYS cc_start: 0.9187 (ptmm) cc_final: 0.8707 (pptt) REVERT: B 242 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7624 (ttm-80) REVERT: B 328 GLU cc_start: 0.9445 (OUTLIER) cc_final: 0.9155 (tt0) REVERT: B 368 ARG cc_start: 0.8636 (mtm110) cc_final: 0.8423 (mmp80) outliers start: 14 outliers final: 11 residues processed: 112 average time/residue: 0.4939 time to fit residues: 59.7255 Evaluate side-chains 114 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 81 optimal weight: 0.0570 chunk 78 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 104 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 432 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.072132 restraints weight = 15246.240| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.14 r_work: 0.2677 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9283 Z= 0.119 Angle : 0.563 9.765 12660 Z= 0.291 Chirality : 0.042 0.267 1419 Planarity : 0.003 0.032 1523 Dihedral : 17.900 178.409 1467 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.61 % Allowed : 18.09 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.26), residues: 1047 helix: 2.06 (0.28), residues: 335 sheet: 0.25 (0.41), residues: 149 loop : -0.08 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 141 TYR 0.012 0.001 TYR A 361 PHE 0.035 0.001 PHE A 216 TRP 0.003 0.001 TRP B 247 HIS 0.002 0.000 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9283) covalent geometry : angle 0.56285 / 0.29 (12660) hydrogen bonds : bond 0.03279 / 2.19 ( 383) hydrogen bonds : angle 4.46652 / 3.18 ( 1055) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.366 Fit side-chains REVERT: A 48 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8341 (mtp) REVERT: A 99 PHE cc_start: 0.7930 (m-80) cc_final: 0.7364 (m-10) REVERT: A 128 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8201 (pm20) REVERT: A 129 LYS cc_start: 0.9157 (mppt) cc_final: 0.8874 (mptt) REVERT: A 201 ASP cc_start: 0.8412 (m-30) cc_final: 0.8118 (m-30) REVERT: A 265 LYS cc_start: 0.9182 (ptmm) cc_final: 0.8704 (pptt) REVERT: B 148 ASP cc_start: 0.9249 (m-30) cc_final: 0.8907 (p0) REVERT: B 242 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7641 (ttm-80) REVERT: B 328 GLU cc_start: 0.9457 (OUTLIER) cc_final: 0.9164 (tt0) REVERT: B 368 ARG cc_start: 0.8636 (mtm110) cc_final: 0.8423 (mmp80) outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.5125 time to fit residues: 60.1401 Evaluate side-chains 111 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 0.0030 chunk 42 optimal weight: 0.0270 chunk 57 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.071172 restraints weight = 15303.271| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.14 r_work: 0.2656 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9283 Z= 0.148 Angle : 0.587 10.001 12660 Z= 0.301 Chirality : 0.042 0.283 1419 Planarity : 0.003 0.032 1523 Dihedral : 17.887 179.061 1467 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.71 % Allowed : 18.31 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1047 helix: 1.93 (0.28), residues: 342 sheet: 0.27 (0.41), residues: 149 loop : -0.08 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 502 TYR 0.010 0.001 TYR A 361 PHE 0.018 0.001 PHE C 190 TRP 0.003 0.001 TRP B 276 HIS 0.003 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 9283) covalent geometry : angle 0.58692 / 0.30 (12660) hydrogen bonds : bond 0.03399 / 2.27 ( 383) hydrogen bonds : angle 4.48919 / 3.20 ( 1055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2878.72 seconds wall clock time: 50 minutes 13.49 seconds (3013.49 seconds total)