Starting phenix.real_space_refine on Sun Apr 27 19:49:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wlr_37629/04_2025/8wlr_37629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wlr_37629/04_2025/8wlr_37629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wlr_37629/04_2025/8wlr_37629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wlr_37629/04_2025/8wlr_37629.map" model { file = "/net/cci-nas-00/data/ceres_data/8wlr_37629/04_2025/8wlr_37629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wlr_37629/04_2025/8wlr_37629.cif" } resolution = 3.12 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= 0.001 sd= 0.043 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 Zn 1 6.06 5 S 37 5.16 5 C 4107 2.51 5 N 1063 2.21 5 O 1223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6431 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4873 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.45, per 1000 atoms: 1.31 Number of scatterers: 6431 At special positions: 0 Unit cell: (85, 84.15, 118.15, 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) Zn 1 29.99 S 37 16.00 O 1223 8.00 N 1063 7.00 C 4107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 56.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 21 through 53 removed outlier: 3.623A pdb=" N LYS A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP A 39 " --> pdb=" O HIS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 82 removed outlier: 3.788A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.945A pdb=" N GLN A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.851A pdb=" N ALA A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.225A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.728A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 250 removed outlier: 4.001A pdb=" N THR A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.197A pdb=" N ASP A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.544A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.908A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.720A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.604A pdb=" N ARG A 393 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 4.009A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.651A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.909A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.699A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.873A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.865A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 600 removed outlier: 3.510A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.609A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.642A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.705A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.987A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.183A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 281 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 2.31 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: 2065 1.34 - 1.46: 1587 1.46 - 1.58: 2898 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6608 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.66e+00 bond pdb=" CA ASP A 216 " pdb=" CB ASP A 216 " ideal model delta sigma weight residual 1.535 1.557 -0.023 1.93e-02 2.68e+03 1.36e+00 bond pdb=" CB ASP A 216 " pdb=" CG ASP A 216 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.27e+00 bond pdb=" C ASP A 36 " pdb=" O ASP A 36 " ideal model delta sigma weight residual 1.237 1.249 -0.013 1.19e-02 7.06e+03 1.17e+00 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.15e+00 ... (remaining 6603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 8732 1.35 - 2.70: 185 2.70 - 4.05: 42 4.05 - 5.40: 12 5.40 - 6.75: 2 Bond angle restraints: 8973 Sorted by residual: angle pdb=" C ALA A 384 " pdb=" N TYR A 385 " pdb=" CA TYR A 385 " ideal model delta sigma weight residual 122.65 117.89 4.76 1.66e+00 3.63e-01 8.22e+00 angle pdb=" N ASN B 343 " pdb=" CA ASN B 343 " pdb=" C ASN B 343 " ideal model delta sigma weight residual 108.49 104.37 4.12 1.65e+00 3.67e-01 6.23e+00 angle pdb=" CA TYR A 385 " pdb=" CB TYR A 385 " pdb=" CG TYR A 385 " ideal model delta sigma weight residual 113.90 118.38 -4.48 1.80e+00 3.09e-01 6.19e+00 angle pdb=" CA ASP A 216 " pdb=" CB ASP A 216 " pdb=" CG ASP A 216 " ideal model delta sigma weight residual 112.60 114.82 -2.22 1.00e+00 1.00e+00 4.92e+00 angle pdb=" CB MET A 249 " pdb=" CG MET A 249 " pdb=" SD MET A 249 " ideal model delta sigma weight residual 112.70 119.22 -6.52 3.00e+00 1.11e-01 4.73e+00 ... (remaining 8968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 3369 16.89 - 33.79: 408 33.79 - 50.68: 112 50.68 - 67.57: 26 67.57 - 84.46: 7 Dihedral angle restraints: 3922 sinusoidal: 1598 harmonic: 2324 Sorted by residual: dihedral pdb=" CG ARG A 340 " pdb=" CD ARG A 340 " pdb=" NE ARG A 340 " pdb=" CZ ARG A 340 " ideal model delta sinusoidal sigma weight residual -180.00 -136.27 -43.73 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CA PHE B 342 " pdb=" C PHE B 342 " pdb=" N ASN B 343 " pdb=" CA ASN B 343 " ideal model delta harmonic sigma weight residual -180.00 -164.41 -15.59 0 5.00e+00 4.00e-02 9.72e+00 dihedral pdb=" CA ASP A 368 " pdb=" CB ASP A 368 " pdb=" CG ASP A 368 " pdb=" OD1 ASP A 368 " ideal model delta sinusoidal sigma weight residual -30.00 -83.30 53.30 1 2.00e+01 2.50e-03 9.66e+00 ... (remaining 3919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 735 0.049 - 0.097: 170 0.097 - 0.146: 33 0.146 - 0.195: 0 0.195 - 0.243: 1 Chirality restraints: 939 Sorted by residual: chirality pdb=" CA ASN B 343 " pdb=" N ASN B 343 " pdb=" C ASN B 343 " pdb=" CB ASN B 343 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C5 NAG B1301 " pdb=" C4 NAG B1301 " pdb=" C6 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.41 -2.55 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 936 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 146 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO B 521 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 522 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C GLN A 522 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN A 522 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 523 " 0.010 2.00e-02 2.50e+03 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1629 2.79 - 3.32: 5642 3.32 - 3.85: 10164 3.85 - 4.37: 12323 4.37 - 4.90: 21611 Nonbonded interactions: 51369 Sorted by model distance: nonbonded pdb=" OE1 GLU A 435 " pdb=" OH TYR A 540 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.267 3.040 nonbonded pdb=" OD1 ASN B 343 " pdb=" N2 NAG B1301 " model vdw 2.299 3.120 nonbonded pdb=" O SER B 438 " pdb=" OG SER B 438 " model vdw 2.315 3.040 nonbonded pdb=" N PRO A 425 " pdb=" CG PRO A 425 " model vdw 2.315 2.816 ... (remaining 51364 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 31.740 Find NCS groups from input model: 0.100 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:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 0.033 6617 Z= 0.142 Angle : 0.545 7.281 8988 Z= 0.292 Chirality : 0.042 0.243 939 Planarity : 0.004 0.055 1159 Dihedral : 16.120 84.462 2416 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.14 % Allowed : 19.36 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.29), residues: 788 helix: 0.57 (0.27), residues: 363 sheet: 1.24 (0.79), residues: 49 loop : -0.42 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 566 HIS 0.004 0.001 HIS A 265 PHE 0.011 0.001 PHE A 369 TYR 0.023 0.001 TYR A 385 ARG 0.002 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.01407 ( 1) link_NAG-ASN : angle 6.12021 ( 3) hydrogen bonds : bond 0.18303 ( 281) hydrogen bonds : angle 5.96780 ( 792) metal coordination : bond 0.00081 ( 2) SS BOND : bond 0.00203 ( 6) SS BOND : angle 0.81412 ( 12) covalent geometry : bond 0.00309 ( 6608) covalent geometry : angle 0.53344 ( 8973) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.855 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2788 time to fit residues: 30.9563 Evaluate side-chains 76 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.0470 chunk 32 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.0030 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.3688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 77 GLN A 97 GLN A 102 GLN A 122 ASN A 137 ASN A 374 HIS A 493 HIS A 531 GLN B 414 GLN B 450 ASN B 501 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.098097 restraints weight = 9074.757| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.41 r_work: 0.3026 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.181 6617 Z= 0.133 Angle : 0.479 5.720 8988 Z= 0.255 Chirality : 0.040 0.125 939 Planarity : 0.004 0.059 1159 Dihedral : 4.065 23.529 890 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.16 % Allowed : 17.34 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.30), residues: 788 helix: 0.79 (0.28), residues: 372 sheet: 1.17 (0.76), residues: 51 loop : -0.22 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 566 HIS 0.004 0.001 HIS A 265 PHE 0.009 0.001 PHE A 327 TYR 0.016 0.001 TYR B 369 ARG 0.001 0.000 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.01233 ( 1) link_NAG-ASN : angle 2.59152 ( 3) hydrogen bonds : bond 0.05411 ( 281) hydrogen bonds : angle 4.41609 ( 792) metal coordination : bond 0.12797 ( 2) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.52681 ( 12) covalent geometry : bond 0.00231 ( 6608) covalent geometry : angle 0.47707 ( 8973) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.723 Fit side-chains REVERT: B 498 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7158 (mp10) outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 0.2024 time to fit residues: 23.6760 Evaluate side-chains 78 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 0.0040 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095465 restraints weight = 9157.963| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.32 r_work: 0.3004 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6617 Z= 0.123 Angle : 0.473 5.244 8988 Z= 0.251 Chirality : 0.041 0.126 939 Planarity : 0.004 0.059 1159 Dihedral : 3.962 18.073 890 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.59 % Allowed : 16.76 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 788 helix: 1.00 (0.28), residues: 370 sheet: 1.10 (0.76), residues: 51 loop : -0.20 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 566 HIS 0.004 0.001 HIS A 265 PHE 0.012 0.001 PHE A 327 TYR 0.016 0.001 TYR A 385 ARG 0.001 0.000 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00027 ( 1) link_NAG-ASN : angle 1.66109 ( 3) hydrogen bonds : bond 0.05292 ( 281) hydrogen bonds : angle 4.20780 ( 792) metal coordination : bond 0.00666 ( 2) SS BOND : bond 0.00218 ( 6) SS BOND : angle 0.67445 ( 12) covalent geometry : bond 0.00278 ( 6608) covalent geometry : angle 0.47181 ( 8973) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.714 Fit side-chains REVERT: A 536 GLU cc_start: 0.8325 (pm20) cc_final: 0.8005 (mp0) outliers start: 11 outliers final: 6 residues processed: 89 average time/residue: 0.2016 time to fit residues: 23.9000 Evaluate side-chains 82 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 0.0870 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 90 GLN B 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.097422 restraints weight = 9356.254| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.43 r_work: 0.3009 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6617 Z= 0.130 Angle : 0.489 7.472 8988 Z= 0.256 Chirality : 0.041 0.137 939 Planarity : 0.004 0.058 1159 Dihedral : 3.947 16.782 890 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.30 % Allowed : 17.77 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.30), residues: 788 helix: 0.99 (0.28), residues: 373 sheet: 1.07 (0.76), residues: 51 loop : -0.16 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.019 0.001 TYR B 369 ARG 0.001 0.000 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00028 ( 1) link_NAG-ASN : angle 1.76461 ( 3) hydrogen bonds : bond 0.05104 ( 281) hydrogen bonds : angle 4.12730 ( 792) metal coordination : bond 0.00270 ( 2) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.75582 ( 12) covalent geometry : bond 0.00301 ( 6608) covalent geometry : angle 0.48776 ( 8973) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.704 Fit side-chains REVERT: A 305 LYS cc_start: 0.8392 (tttm) cc_final: 0.7960 (mptt) REVERT: A 536 GLU cc_start: 0.8318 (pm20) cc_final: 0.8021 (mp0) REVERT: B 498 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.7205 (mp10) outliers start: 9 outliers final: 7 residues processed: 86 average time/residue: 0.2158 time to fit residues: 23.9611 Evaluate side-chains 87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.0040 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097297 restraints weight = 9222.246| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.41 r_work: 0.3010 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6617 Z= 0.125 Angle : 0.482 6.560 8988 Z= 0.251 Chirality : 0.041 0.127 939 Planarity : 0.004 0.058 1159 Dihedral : 3.922 16.121 890 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.59 % Allowed : 17.92 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.30), residues: 788 helix: 1.04 (0.28), residues: 374 sheet: 1.13 (0.76), residues: 51 loop : -0.16 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.004 0.001 HIS A 265 PHE 0.010 0.001 PHE A 327 TYR 0.016 0.001 TYR A 385 ARG 0.001 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00002 ( 1) link_NAG-ASN : angle 1.84574 ( 3) hydrogen bonds : bond 0.04936 ( 281) hydrogen bonds : angle 4.07511 ( 792) metal coordination : bond 0.00251 ( 2) SS BOND : bond 0.00202 ( 6) SS BOND : angle 0.71674 ( 12) covalent geometry : bond 0.00288 ( 6608) covalent geometry : angle 0.48086 ( 8973) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.711 Fit side-chains REVERT: A 305 LYS cc_start: 0.8374 (tttm) cc_final: 0.7953 (mptt) REVERT: A 536 GLU cc_start: 0.8350 (pm20) cc_final: 0.8103 (mp0) REVERT: B 498 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7300 (mp10) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.2107 time to fit residues: 24.4819 Evaluate side-chains 88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098642 restraints weight = 9179.607| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.42 r_work: 0.3031 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6617 Z= 0.103 Angle : 0.464 7.024 8988 Z= 0.241 Chirality : 0.040 0.125 939 Planarity : 0.004 0.057 1159 Dihedral : 3.767 15.624 890 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.45 % Allowed : 18.35 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.30), residues: 788 helix: 1.15 (0.28), residues: 374 sheet: 1.18 (0.76), residues: 51 loop : -0.11 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.003 0.001 HIS A 265 PHE 0.008 0.001 PHE A 327 TYR 0.018 0.001 TYR B 369 ARG 0.001 0.000 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 1.69729 ( 3) hydrogen bonds : bond 0.04445 ( 281) hydrogen bonds : angle 3.98120 ( 792) metal coordination : bond 0.00159 ( 2) SS BOND : bond 0.00164 ( 6) SS BOND : angle 0.55105 ( 12) covalent geometry : bond 0.00228 ( 6608) covalent geometry : angle 0.46322 ( 8973) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.728 Fit side-chains REVERT: A 305 LYS cc_start: 0.8371 (tttm) cc_final: 0.8002 (mptt) REVERT: A 536 GLU cc_start: 0.8346 (pm20) cc_final: 0.8076 (mp0) REVERT: B 498 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.7129 (mp10) outliers start: 10 outliers final: 6 residues processed: 87 average time/residue: 0.2200 time to fit residues: 24.8226 Evaluate side-chains 81 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.0040 chunk 67 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.096976 restraints weight = 9222.469| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.43 r_work: 0.3016 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6617 Z= 0.127 Angle : 0.492 6.426 8988 Z= 0.253 Chirality : 0.041 0.128 939 Planarity : 0.004 0.057 1159 Dihedral : 3.834 15.895 890 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.73 % Allowed : 17.77 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.30), residues: 788 helix: 1.13 (0.28), residues: 374 sheet: 1.18 (0.76), residues: 51 loop : -0.12 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.017 0.001 TYR A 613 ARG 0.001 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00038 ( 1) link_NAG-ASN : angle 1.91332 ( 3) hydrogen bonds : bond 0.04886 ( 281) hydrogen bonds : angle 3.99775 ( 792) metal coordination : bond 0.00260 ( 2) SS BOND : bond 0.00219 ( 6) SS BOND : angle 0.70955 ( 12) covalent geometry : bond 0.00294 ( 6608) covalent geometry : angle 0.49058 ( 8973) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.828 Fit side-chains REVERT: A 305 LYS cc_start: 0.8415 (tttm) cc_final: 0.8039 (mptt) REVERT: A 536 GLU cc_start: 0.8389 (pm20) cc_final: 0.8132 (mp0) REVERT: B 498 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: B 518 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8259 (mt) outliers start: 12 outliers final: 7 residues processed: 86 average time/residue: 0.2281 time to fit residues: 25.4130 Evaluate side-chains 85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 25 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098956 restraints weight = 9202.832| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.44 r_work: 0.3045 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6617 Z= 0.101 Angle : 0.467 6.570 8988 Z= 0.240 Chirality : 0.040 0.126 939 Planarity : 0.004 0.058 1159 Dihedral : 3.716 15.998 890 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.59 % Allowed : 17.63 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.30), residues: 788 helix: 1.25 (0.28), residues: 374 sheet: 1.25 (0.76), residues: 51 loop : -0.07 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.003 0.001 HIS A 265 PHE 0.009 0.001 PHE A 603 TYR 0.019 0.001 TYR B 369 ARG 0.001 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 1) link_NAG-ASN : angle 1.69507 ( 3) hydrogen bonds : bond 0.04332 ( 281) hydrogen bonds : angle 3.93412 ( 792) metal coordination : bond 0.00160 ( 2) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.52155 ( 12) covalent geometry : bond 0.00222 ( 6608) covalent geometry : angle 0.46640 ( 8973) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.813 Fit side-chains REVERT: A 305 LYS cc_start: 0.8366 (tttm) cc_final: 0.8008 (mptt) REVERT: A 497 TYR cc_start: 0.8240 (m-80) cc_final: 0.7976 (m-80) REVERT: A 536 GLU cc_start: 0.8368 (pm20) cc_final: 0.8124 (mp0) REVERT: B 498 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.7180 (mp10) outliers start: 11 outliers final: 9 residues processed: 87 average time/residue: 0.2358 time to fit residues: 27.0185 Evaluate side-chains 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 70 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.131563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.097994 restraints weight = 9362.407| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.46 r_work: 0.3017 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6617 Z= 0.113 Angle : 0.485 6.668 8988 Z= 0.248 Chirality : 0.041 0.141 939 Planarity : 0.004 0.057 1159 Dihedral : 3.721 15.738 890 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.73 % Allowed : 18.06 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.30), residues: 788 helix: 1.23 (0.28), residues: 374 sheet: 1.26 (0.76), residues: 51 loop : -0.08 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.003 0.001 HIS A 265 PHE 0.010 0.001 PHE A 327 TYR 0.015 0.001 TYR A 385 ARG 0.001 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00038 ( 1) link_NAG-ASN : angle 1.79247 ( 3) hydrogen bonds : bond 0.04526 ( 281) hydrogen bonds : angle 3.94287 ( 792) metal coordination : bond 0.00204 ( 2) SS BOND : bond 0.00182 ( 6) SS BOND : angle 0.60119 ( 12) covalent geometry : bond 0.00259 ( 6608) covalent geometry : angle 0.48345 ( 8973) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.781 Fit side-chains REVERT: A 305 LYS cc_start: 0.8343 (tttm) cc_final: 0.7980 (mptt) REVERT: A 497 TYR cc_start: 0.8218 (m-80) cc_final: 0.7956 (m-80) REVERT: A 536 GLU cc_start: 0.8395 (pm20) cc_final: 0.8151 (mp0) REVERT: B 498 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: B 518 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8231 (mt) outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 0.2224 time to fit residues: 25.4054 Evaluate side-chains 87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.096573 restraints weight = 9263.741| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.31 r_work: 0.3019 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6617 Z= 0.124 Angle : 0.487 6.706 8988 Z= 0.251 Chirality : 0.041 0.128 939 Planarity : 0.004 0.057 1159 Dihedral : 3.790 16.376 890 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.73 % Allowed : 18.06 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.30), residues: 788 helix: 1.17 (0.28), residues: 375 sheet: 1.25 (0.76), residues: 51 loop : -0.11 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.011 0.001 PHE A 327 TYR 0.020 0.001 TYR B 369 ARG 0.001 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 1.87551 ( 3) hydrogen bonds : bond 0.04764 ( 281) hydrogen bonds : angle 3.95249 ( 792) metal coordination : bond 0.00240 ( 2) SS BOND : bond 0.00202 ( 6) SS BOND : angle 0.66875 ( 12) covalent geometry : bond 0.00287 ( 6608) covalent geometry : angle 0.48525 ( 8973) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.767 Fit side-chains REVERT: A 305 LYS cc_start: 0.8366 (tttm) cc_final: 0.8021 (mptt) REVERT: A 497 TYR cc_start: 0.8251 (m-80) cc_final: 0.8004 (m-80) REVERT: A 536 GLU cc_start: 0.8386 (pm20) cc_final: 0.8150 (mp0) REVERT: A 603 PHE cc_start: 0.7508 (t80) cc_final: 0.7225 (t80) REVERT: B 498 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7209 (mp10) REVERT: B 518 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8245 (mt) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.2281 time to fit residues: 25.7280 Evaluate side-chains 87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 0.3980 chunk 3 optimal weight: 0.0270 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101060 restraints weight = 9302.528| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.37 r_work: 0.3077 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6617 Z= 0.091 Angle : 0.464 6.909 8988 Z= 0.236 Chirality : 0.040 0.131 939 Planarity : 0.004 0.055 1159 Dihedral : 3.566 15.530 890 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.01 % Allowed : 19.22 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.01 (0.30), residues: 788 helix: 1.33 (0.28), residues: 374 sheet: 1.32 (0.77), residues: 51 loop : -0.04 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.003 0.000 HIS A 265 PHE 0.005 0.001 PHE A 327 TYR 0.014 0.001 TYR A 385 ARG 0.001 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 1) link_NAG-ASN : angle 1.53713 ( 3) hydrogen bonds : bond 0.03866 ( 281) hydrogen bonds : angle 3.87817 ( 792) metal coordination : bond 0.00083 ( 2) SS BOND : bond 0.00133 ( 6) SS BOND : angle 0.43333 ( 12) covalent geometry : bond 0.00195 ( 6608) covalent geometry : angle 0.46362 ( 8973) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4383.20 seconds wall clock time: 76 minutes 19.89 seconds (4579.89 seconds total)