Starting phenix.real_space_refine on Sat Sep 12 00:52:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wsf_32756/09_2026/7wsf_32756.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsf_32756/09_2026/7wsf_32756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wsf_32756/09_2026/7wsf_32756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsf_32756/09_2026/7wsf_32756.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wsf_32756/09_2026/7wsf_32756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsf_32756/09_2026/7wsf_32756.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wsf_32756/09_2026/7wsf_32756.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wsf_32756/09_2026/7wsf_32756.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6717 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 C 4590 2.51 5 N 1192 2.21 5 O 1349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 7170 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5677 Classifications: {'peptide': 693} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 659} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1492 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 173} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.25 Number of scatterers: 7170 At special positions: 0 Unit cell: (72.252, 94.998, 140.49, 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 38 16.00 O 1349 8.00 N 1192 7.00 C 4590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " 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 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 519.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 373 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 377 " 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 55.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.614A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.667A pdb=" N SER A 106 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.700A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.600A pdb=" N ILE A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 193 removed outlier: 4.091A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 217 through 251 removed outlier: 3.877A pdb=" N ILE A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Proline residue: A 234 - end of helix Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.546A pdb=" N ASN A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.554A pdb=" N PHE A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.703A pdb=" N TRP A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 384 removed outlier: 3.618A pdb=" N HIS A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.625A pdb=" N GLY A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.640A pdb=" N GLN A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.872A pdb=" N THR A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.519A pdb=" N CYS A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.576A pdb=" N GLY A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 removed outlier: 3.739A pdb=" N ILE A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 removed outlier: 3.589A pdb=" N PHE A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'A' and resid 638 through 657 removed outlier: 4.259A pdb=" N PHE A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 643 " --> pdb=" O MET A 639 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 706 removed outlier: 3.596A pdb=" N SER A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 352 through 358 removed outlier: 3.890A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 358' Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.012A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.501A pdb=" N GLN B 492 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262 removed outlier: 5.840A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 351 removed outlier: 6.502A pdb=" N ASP A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 617 through 620 removed outlier: 6.987A pdb=" N SER A 679 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 674 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 617 through 620 removed outlier: 12.867A pdb=" N PHE A 682 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N ILE A 693 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL A 684 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N SER A 691 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 686 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.504A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 439 through 441 335 hydrogen bonds defined for protein. 951 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: 1.06 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2301 1.34 - 1.46: 1884 1.46 - 1.58: 3124 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 7371 Sorted by residual: bond pdb=" N PRO A 424 " pdb=" CA PRO A 424 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 6.81e-01 bond pdb=" C PRO A 424 " pdb=" O PRO A 424 " ideal model delta sigma weight residual 1.246 1.239 0.006 8.50e-03 1.38e+04 5.22e-01 bond pdb=" CB PRO B 470 " pdb=" CG PRO B 470 " ideal model delta sigma weight residual 1.506 1.482 0.024 3.90e-02 6.57e+02 3.74e-01 bond pdb=" CG PRO A 499 " pdb=" CD PRO A 499 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.56e-01 bond pdb=" C SER B 461 " pdb=" O SER B 461 " ideal model delta sigma weight residual 1.244 1.236 0.008 1.41e-02 5.03e+03 3.33e-01 ... (remaining 7366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 9865 1.42 - 2.83: 104 2.83 - 4.25: 25 4.25 - 5.67: 7 5.67 - 7.09: 1 Bond angle restraints: 10002 Sorted by residual: angle pdb=" CA LEU A 583 " pdb=" CB LEU A 583 " pdb=" CG LEU A 583 " ideal model delta sigma weight residual 116.30 123.39 -7.09 3.50e+00 8.16e-02 4.10e+00 angle pdb=" N GLU A 494 " pdb=" CA GLU A 494 " pdb=" C GLU A 494 " ideal model delta sigma weight residual 110.80 114.49 -3.69 2.13e+00 2.20e-01 3.01e+00 angle pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 109.34 112.94 -3.60 2.08e+00 2.31e-01 3.00e+00 angle pdb=" CA TYR A 384 " pdb=" CB TYR A 384 " pdb=" CG TYR A 384 " ideal model delta sigma weight residual 113.90 116.45 -2.55 1.80e+00 3.09e-01 2.00e+00 angle pdb=" N ASP A 493 " pdb=" CA ASP A 493 " pdb=" C ASP A 493 " ideal model delta sigma weight residual 107.48 110.64 -3.16 2.29e+00 1.91e-01 1.90e+00 ... (remaining 9997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4146 17.99 - 35.99: 187 35.99 - 53.98: 33 53.98 - 71.97: 12 71.97 - 89.96: 3 Dihedral angle restraints: 4381 sinusoidal: 1788 harmonic: 2593 Sorted by residual: dihedral pdb=" CA ASP A 493 " pdb=" C ASP A 493 " pdb=" N GLU A 494 " pdb=" CA GLU A 494 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA CYS A 343 " pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 360 " ideal model delta sinusoidal sigma weight residual 79.00 19.07 59.93 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA PRO A 135 " pdb=" C PRO A 135 " pdb=" N ASN A 136 " pdb=" CA ASN A 136 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 4378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 555 0.026 - 0.052: 309 0.052 - 0.078: 99 0.078 - 0.104: 57 0.104 - 0.130: 14 Chirality restraints: 1034 Sorted by residual: chirality pdb=" CA ILE A 694 " pdb=" N ILE A 694 " pdb=" C ILE A 694 " pdb=" CB ILE A 694 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA VAL A 208 " pdb=" N VAL A 208 " pdb=" C VAL A 208 " pdb=" CB VAL A 208 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL B 369 " pdb=" N VAL B 369 " pdb=" C VAL B 369 " pdb=" CB VAL B 369 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 1031 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 387 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 388 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 144 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 145 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 581 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO A 582 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " 0.016 5.00e-02 4.00e+02 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 60 2.59 - 3.17: 5886 3.17 - 3.75: 11309 3.75 - 4.32: 16500 4.32 - 4.90: 26677 Nonbonded interactions: 60432 Sorted by model distance: nonbonded pdb=" OE2 GLU A 401 " pdb="ZN ZN A 801 " model vdw 2.016 2.230 nonbonded pdb=" OG SER B 336 " pdb=" O LYS B 439 " model vdw 2.158 3.040 nonbonded pdb=" OD2 ASP B 393 " pdb=" OH TYR B 481 " model vdw 2.220 3.040 nonbonded pdb=" O VAL A 432 " pdb=" ND2 ASN A 436 " model vdw 2.233 3.120 nonbonded pdb=" OH TYR B 356 " pdb=" OD1 ASN B 375 " model vdw 2.239 3.040 ... (remaining 60427 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: 4.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.180 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 0.028 7378 Z= 0.114 Angle : 0.440 7.085 10012 Z= 0.222 Chirality : 0.039 0.130 1034 Planarity : 0.003 0.035 1293 Dihedral : 11.232 89.963 2702 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.87 % Allowed : 7.09 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.12 (0.27), residues: 875 helix: -0.14 (0.24), residues: 422 sheet: 1.68 (0.65), residues: 60 loop : -0.12 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.014 0.001 TYR A 384 PHE 0.008 0.001 PHE A 522 TRP 0.011 0.001 TRP A 162 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 7371) covalent geometry : angle 0.43965 / 0.22 (10002) SS BOND : bond 0.00222 / 0.12 ( 5) SS BOND : angle 0.80209 / 0.45 ( 10) hydrogen bonds : bond 0.24418 / 16.26 ( 331) hydrogen bonds : angle 8.42667 / 6.07 ( 951) metal coordination : bond 0.00468 / 0.24 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.315 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 35 GLU cc_start: 0.8173 (tt0) cc_final: 0.7551 (tp30) REVERT: A 362 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6956 (mmtt) REVERT: A 596 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7553 (mm-30) REVERT: A 599 ARG cc_start: 0.7290 (mtm110) cc_final: 0.7013 (ptp90) REVERT: A 634 TRP cc_start: 0.2653 (OUTLIER) cc_final: 0.1488 (m100) REVERT: B 324 PRO cc_start: 0.7678 (Cg_endo) cc_final: 0.7474 (Cg_exo) REVERT: B 395 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7058 (ttp80) REVERT: B 425 THR cc_start: 0.8914 (p) cc_final: 0.8627 (p) outliers start: 31 outliers final: 2 residues processed: 173 average time/residue: 0.6109 time to fit residues: 110.8768 Evaluate side-chains 89 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.0270 chunk 74 optimal weight: 6.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 298 ASN A 387 GLN A 521 GLN A 637 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116199 restraints weight = 9169.159| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.94 r_work: 0.3237 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7378 Z= 0.131 Angle : 0.524 7.263 10012 Z= 0.274 Chirality : 0.041 0.133 1034 Planarity : 0.004 0.037 1293 Dihedral : 4.715 49.602 980 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.09 % Allowed : 12.37 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.51 (0.27), residues: 875 helix: 0.60 (0.25), residues: 417 sheet: 1.23 (0.64), residues: 61 loop : 0.07 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.017 0.001 TYR A 384 PHE 0.021 0.001 PHE A 680 TRP 0.012 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7371) covalent geometry : angle 0.52165 / 0.27 (10002) SS BOND : bond 0.00234 / 0.12 ( 5) SS BOND : angle 1.56919 / 0.99 ( 10) hydrogen bonds : bond 0.05319 / 3.64 ( 331) hydrogen bonds : angle 5.56988 / 3.95 ( 951) metal coordination : bond 0.00353 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.277 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 89 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7426 (tp40) REVERT: A 145 PRO cc_start: 0.8443 (Cg_endo) cc_final: 0.8112 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: A 362 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6833 (mmtt) REVERT: A 634 TRP cc_start: 0.2404 (OUTLIER) cc_final: 0.1477 (m100) REVERT: A 681 ASN cc_start: 0.6905 (m-40) cc_final: 0.6359 (m-40) REVERT: B 341 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7518 (mt-10) outliers start: 25 outliers final: 5 residues processed: 114 average time/residue: 0.5807 time to fit residues: 69.8461 Evaluate side-chains 99 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain B residue 341 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 59 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 521 GLN B 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.145110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110394 restraints weight = 9329.400| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.96 r_work: 0.3136 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7378 Z= 0.232 Angle : 0.567 6.824 10012 Z= 0.294 Chirality : 0.045 0.131 1034 Planarity : 0.005 0.052 1293 Dihedral : 4.730 48.754 978 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.45 % Allowed : 15.46 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.47 (0.27), residues: 875 helix: 0.57 (0.25), residues: 423 sheet: 0.94 (0.68), residues: 55 loop : 0.10 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.020 0.002 TYR A 384 PHE 0.015 0.002 PHE A 32 TRP 0.013 0.002 TRP A 477 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 ( 7371) covalent geometry : angle 0.56542 / 0.29 (10002) SS BOND : bond 0.00320 / 0.16 ( 5) SS BOND : angle 1.35207 / 0.82 ( 10) hydrogen bonds : bond 0.05595 / 3.83 ( 331) hydrogen bonds : angle 5.41535 / 3.82 ( 951) metal coordination : bond 0.00185 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 93 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8828 (mp) REVERT: A 145 PRO cc_start: 0.8473 (Cg_endo) cc_final: 0.8176 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: A 362 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7049 (mmtt) REVERT: A 533 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8349 (mmtt) REVERT: A 634 TRP cc_start: 0.2505 (OUTLIER) cc_final: 0.1330 (m100) REVERT: B 341 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: B 395 ARG cc_start: 0.8357 (ptm-80) cc_final: 0.8138 (ptm-80) outliers start: 19 outliers final: 7 residues processed: 104 average time/residue: 0.6052 time to fit residues: 66.3511 Evaluate side-chains 98 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 40 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112616 restraints weight = 9394.223| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.96 r_work: 0.3165 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7378 Z= 0.138 Angle : 0.498 6.289 10012 Z= 0.258 Chirality : 0.041 0.131 1034 Planarity : 0.004 0.042 1293 Dihedral : 4.563 48.157 977 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.19 % Allowed : 16.24 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.66 (0.28), residues: 875 helix: 0.80 (0.25), residues: 424 sheet: 0.84 (0.67), residues: 55 loop : 0.12 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.017 0.001 TYR A 384 PHE 0.014 0.001 PHE B 361 TRP 0.013 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7371) covalent geometry : angle 0.49692 / 0.26 (10002) SS BOND : bond 0.00239 / 0.12 ( 5) SS BOND : angle 0.99378 / 0.58 ( 10) hydrogen bonds : bond 0.04772 / 3.28 ( 331) hydrogen bonds : angle 5.15259 / 3.63 ( 951) metal coordination : bond 0.00105 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7444 (tp40) REVERT: A 93 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8807 (mp) REVERT: A 145 PRO cc_start: 0.8490 (Cg_endo) cc_final: 0.8199 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: A 362 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7059 (mmtt) REVERT: A 533 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8378 (mmtt) REVERT: A 634 TRP cc_start: 0.2461 (OUTLIER) cc_final: 0.1333 (m100) REVERT: B 341 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7546 (mt-10) outliers start: 17 outliers final: 4 residues processed: 105 average time/residue: 0.6293 time to fit residues: 69.5621 Evaluate side-chains 92 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 ASN B 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112650 restraints weight = 9360.431| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.97 r_work: 0.3171 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7378 Z= 0.135 Angle : 0.486 6.328 10012 Z= 0.252 Chirality : 0.041 0.131 1034 Planarity : 0.004 0.039 1293 Dihedral : 4.492 48.058 977 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.45 % Allowed : 15.72 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.73 (0.28), residues: 875 helix: 0.96 (0.25), residues: 423 sheet: 0.75 (0.62), residues: 61 loop : 0.04 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.017 0.001 TYR A 384 PHE 0.013 0.001 PHE B 361 TRP 0.012 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7371) covalent geometry : angle 0.48493 / 0.25 (10002) SS BOND : bond 0.00207 / 0.10 ( 5) SS BOND : angle 1.27931 / 0.73 ( 10) hydrogen bonds : bond 0.04591 / 3.16 ( 331) hydrogen bonds : angle 5.01860 / 3.52 ( 951) metal coordination : bond 0.00090 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7440 (tp40) REVERT: A 145 PRO cc_start: 0.8498 (Cg_endo) cc_final: 0.8210 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 362 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7266 (mmtt) REVERT: A 533 LYS cc_start: 0.8613 (mmmm) cc_final: 0.8388 (mmtt) REVERT: A 634 TRP cc_start: 0.2601 (OUTLIER) cc_final: 0.1460 (m100) REVERT: A 681 ASN cc_start: 0.6633 (m-40) cc_final: 0.6335 (m110) REVERT: A 703 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6677 (pt) REVERT: B 341 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7546 (mt-10) outliers start: 19 outliers final: 7 residues processed: 107 average time/residue: 0.5641 time to fit residues: 63.8060 Evaluate side-chains 97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.0030 chunk 81 optimal weight: 3.9990 chunk 54 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.4346 > 50:) chunk 45 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 71 optimal weight: 6.9990 chunk 64 optimal weight: 0.2980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN B 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.149591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115484 restraints weight = 9382.512| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.97 r_work: 0.3212 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7378 Z= 0.100 Angle : 0.457 7.685 10012 Z= 0.237 Chirality : 0.039 0.133 1034 Planarity : 0.004 0.041 1293 Dihedral : 4.297 47.718 977 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.84 % Allowed : 15.72 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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 (0.28), residues: 875 helix: 1.22 (0.26), residues: 416 sheet: 0.76 (0.66), residues: 55 loop : 0.09 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 305 TYR 0.015 0.001 TYR A 384 PHE 0.012 0.001 PHE B 361 TRP 0.013 0.001 TRP A 164 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 7371) covalent geometry : angle 0.45612 / 0.24 (10002) SS BOND : bond 0.00148 / 0.07 ( 5) SS BOND : angle 0.89656 / 0.51 ( 10) hydrogen bonds : bond 0.04161 / 2.86 ( 331) hydrogen bonds : angle 4.82832 / 3.39 ( 951) metal coordination : bond 0.00048 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.304 Fit side-chains REVERT: A 57 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: A 145 PRO cc_start: 0.8456 (Cg_endo) cc_final: 0.8164 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 293 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8031 (m) REVERT: A 362 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7258 (mmtt) REVERT: A 533 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8395 (mmtm) REVERT: A 634 TRP cc_start: 0.2592 (OUTLIER) cc_final: 0.1430 (m100) REVERT: A 681 ASN cc_start: 0.6540 (m-40) cc_final: 0.6150 (m110) REVERT: A 703 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6651 (pt) REVERT: B 341 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7470 (mt-10) outliers start: 22 outliers final: 8 residues processed: 112 average time/residue: 0.5660 time to fit residues: 67.1160 Evaluate side-chains 102 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.145369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110791 restraints weight = 9435.676| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.97 r_work: 0.3139 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7378 Z= 0.203 Angle : 0.534 7.960 10012 Z= 0.275 Chirality : 0.043 0.136 1034 Planarity : 0.004 0.058 1293 Dihedral : 4.575 46.517 977 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.19 % Allowed : 16.75 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.75 (0.28), residues: 875 helix: 0.98 (0.25), residues: 426 sheet: 0.70 (0.63), residues: 61 loop : 0.05 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 395 TYR 0.021 0.001 TYR A 384 PHE 0.014 0.002 PHE B 361 TRP 0.011 0.001 TRP A 477 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 ( 7371) covalent geometry : angle 0.53293 / 0.27 (10002) SS BOND : bond 0.00258 / 0.13 ( 5) SS BOND : angle 1.26203 / 0.72 ( 10) hydrogen bonds : bond 0.04914 / 3.39 ( 331) hydrogen bonds : angle 5.05131 / 3.55 ( 951) metal coordination : bond 0.00094 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.293 Fit side-chains REVERT: A 57 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: A 145 PRO cc_start: 0.8502 (Cg_endo) cc_final: 0.8221 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: A 362 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7415 (mmtt) REVERT: A 533 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8424 (mmtt) REVERT: A 634 TRP cc_start: 0.2670 (OUTLIER) cc_final: 0.1356 (m100) REVERT: A 703 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6609 (pt) REVERT: B 341 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7568 (mt-10) outliers start: 17 outliers final: 7 residues processed: 96 average time/residue: 0.6173 time to fit residues: 62.5042 Evaluate side-chains 88 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113166 restraints weight = 9414.978| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.96 r_work: 0.3176 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7378 Z= 0.124 Angle : 0.486 8.426 10012 Z= 0.250 Chirality : 0.040 0.133 1034 Planarity : 0.004 0.057 1293 Dihedral : 4.413 45.849 977 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.93 % Allowed : 17.40 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.87 (0.28), residues: 875 helix: 1.10 (0.25), residues: 425 sheet: 0.65 (0.62), residues: 61 loop : 0.11 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.017 0.001 TYR A 384 PHE 0.012 0.001 PHE B 361 TRP 0.013 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 7371) covalent geometry : angle 0.48519 / 0.25 (10002) SS BOND : bond 0.00183 / 0.09 ( 5) SS BOND : angle 1.02578 / 0.58 ( 10) hydrogen bonds : bond 0.04375 / 3.02 ( 331) hydrogen bonds : angle 4.92057 / 3.46 ( 951) metal coordination : bond 0.00068 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.258 Fit side-chains REVERT: A 57 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: A 145 PRO cc_start: 0.8473 (Cg_endo) cc_final: 0.8186 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: A 293 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8062 (m) REVERT: A 362 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7389 (mmtt) REVERT: A 533 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8405 (mmtt) REVERT: A 634 TRP cc_start: 0.2731 (OUTLIER) cc_final: 0.1421 (m100) outliers start: 15 outliers final: 3 residues processed: 94 average time/residue: 0.6073 time to fit residues: 60.2711 Evaluate side-chains 88 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 0.0670 chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113370 restraints weight = 9352.548| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.96 r_work: 0.3182 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7378 Z= 0.123 Angle : 0.483 8.684 10012 Z= 0.249 Chirality : 0.040 0.134 1034 Planarity : 0.004 0.059 1293 Dihedral : 4.368 45.709 977 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.55 % Allowed : 17.78 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.99 (0.28), residues: 875 helix: 1.19 (0.26), residues: 424 sheet: 1.04 (0.73), residues: 44 loop : 0.16 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 395 TYR 0.017 0.001 TYR A 384 PHE 0.012 0.001 PHE B 361 TRP 0.012 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7371) covalent geometry : angle 0.48228 / 0.25 (10002) SS BOND : bond 0.00178 / 0.09 ( 5) SS BOND : angle 0.94126 / 0.53 ( 10) hydrogen bonds : bond 0.04306 / 2.97 ( 331) hydrogen bonds : angle 4.88340 / 3.43 ( 951) metal coordination : bond 0.00072 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 145 PRO cc_start: 0.8468 (Cg_endo) cc_final: 0.8179 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: A 293 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8064 (m) REVERT: A 362 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7408 (mmtt) REVERT: A 634 TRP cc_start: 0.2766 (OUTLIER) cc_final: 0.1463 (m100) REVERT: A 681 ASN cc_start: 0.6572 (m-40) cc_final: 0.6316 (m110) REVERT: B 341 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7499 (mt-10) outliers start: 12 outliers final: 3 residues processed: 93 average time/residue: 0.6167 time to fit residues: 60.6131 Evaluate side-chains 92 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.0000 chunk 13 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114667 restraints weight = 9329.555| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.95 r_work: 0.3198 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7378 Z= 0.108 Angle : 0.482 9.217 10012 Z= 0.245 Chirality : 0.040 0.133 1034 Planarity : 0.004 0.057 1293 Dihedral : 4.272 45.068 977 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.42 % Allowed : 18.43 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.28), residues: 875 helix: 1.31 (0.26), residues: 417 sheet: 0.88 (0.67), residues: 55 loop : 0.08 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 395 TYR 0.015 0.001 TYR A 384 PHE 0.012 0.001 PHE B 361 TRP 0.013 0.001 TRP A 164 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 7371) covalent geometry : angle 0.48205 / 0.24 (10002) SS BOND : bond 0.00167 / 0.08 ( 5) SS BOND : angle 0.80660 / 0.46 ( 10) hydrogen bonds : bond 0.04115 / 2.84 ( 331) hydrogen bonds : angle 4.80260 / 3.38 ( 951) metal coordination : bond 0.00067 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: A 293 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8073 (m) REVERT: A 362 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7436 (mmtt) REVERT: A 634 TRP cc_start: 0.2900 (OUTLIER) cc_final: 0.1602 (m100) REVERT: A 681 ASN cc_start: 0.6513 (m-40) cc_final: 0.6255 (m110) REVERT: B 341 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7476 (mt-10) outliers start: 11 outliers final: 3 residues processed: 96 average time/residue: 0.6358 time to fit residues: 64.3555 Evaluate side-chains 91 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain B residue 341 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 57 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 40 optimal weight: 0.0030 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 74 optimal weight: 0.0000 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 ASN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116975 restraints weight = 9353.158| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.95 r_work: 0.3234 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7378 Z= 0.094 Angle : 0.465 9.245 10012 Z= 0.238 Chirality : 0.039 0.132 1034 Planarity : 0.004 0.056 1293 Dihedral : 4.108 44.979 977 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.16 % Allowed : 18.69 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.28), residues: 875 helix: 1.49 (0.26), residues: 414 sheet: 0.86 (0.62), residues: 61 loop : 0.21 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 66 TYR 0.013 0.001 TYR A 50 PHE 0.011 0.001 PHE B 361 TRP 0.013 0.001 TRP A 164 HIS 0.002 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 7371) covalent geometry : angle 0.46499 / 0.24 (10002) SS BOND : bond 0.00110 / 0.05 ( 5) SS BOND : angle 0.61049 / 0.34 ( 10) hydrogen bonds : bond 0.03842 / 2.66 ( 331) hydrogen bonds : angle 4.67814 / 3.31 ( 951) metal coordination : bond 0.00042 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.96 seconds wall clock time: 49 minutes 27.82 seconds (2967.82 seconds total)