Starting phenix.real_space_refine on Wed Jun 11 09:24:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsf_32756/06_2025/7wsf_32756.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsf_32756/06_2025/7wsf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsf_32756/06_2025/7wsf_32756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsf_32756/06_2025/7wsf_32756.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsf_32756/06_2025/7wsf_32756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsf_32756/06_2025/7wsf_32756.cif" } resolution = 2.87 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= 0.053 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.33, per 1000 atoms: 0.74 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: 1.70 Conformation dependent library (CDL) restraints added in 934.0 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: 0.87 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: 1.95 Time building geometry restraints manager: 2.04 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.050 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 (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: -0.12 (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 TRP 0.011 0.001 TRP A 162 HIS 0.003 0.001 HIS A 240 PHE 0.008 0.001 PHE A 522 TYR 0.014 0.001 TYR A 384 ARG 0.002 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.24418 ( 331) hydrogen bonds : angle 8.42667 ( 951) metal coordination : bond 0.00468 ( 2) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.80209 ( 10) covalent geometry : bond 0.00266 ( 7371) covalent geometry : angle 0.43965 (10002) *********************** 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 : 0.742 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: 0.7012 (ptp90) REVERT: A 634 TRP cc_start: 0.2653 (OUTLIER) cc_final: 0.1487 (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: 1.3325 time to fit residues: 241.6697 Evaluate side-chains 88 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 73 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 387 GLN A 637 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.113736 restraints weight = 9229.688| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.96 r_work: 0.3185 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2172 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= 0.146 Angle : 0.532 7.313 10012 Z= 0.278 Chirality : 0.042 0.132 1034 Planarity : 0.004 0.038 1293 Dihedral : 4.726 49.288 980 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.22 % Allowed : 13.02 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.49 (0.27), residues: 875 helix: 0.57 (0.25), residues: 419 sheet: 1.26 (0.64), residues: 61 loop : 0.05 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 164 HIS 0.005 0.001 HIS A 240 PHE 0.021 0.001 PHE A 680 TYR 0.017 0.001 TYR A 384 ARG 0.004 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.05732 ( 331) hydrogen bonds : angle 5.63143 ( 951) metal coordination : bond 0.00352 ( 2) SS BOND : bond 0.00276 ( 5) SS BOND : angle 1.77633 ( 10) covalent geometry : bond 0.00325 ( 7371) covalent geometry : angle 0.52978 (10002) *********************** 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 116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.734 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 136 ASN cc_start: 0.5364 (OUTLIER) cc_final: 0.5159 (m-40) REVERT: A 145 PRO cc_start: 0.8439 (Cg_endo) cc_final: 0.8114 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: A 362 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6824 (mmtt) REVERT: A 634 TRP cc_start: 0.2367 (OUTLIER) cc_final: 0.1441 (m100) REVERT: A 681 ASN cc_start: 0.6771 (m-40) cc_final: 0.6258 (m-40) REVERT: B 324 PRO cc_start: 0.7704 (Cg_endo) cc_final: 0.7503 (Cg_exo) REVERT: B 341 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: B 395 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.7989 (ttp80) REVERT: B 439 LYS cc_start: 0.8542 (mttp) cc_final: 0.8306 (mttt) outliers start: 26 outliers final: 8 residues processed: 112 average time/residue: 1.4303 time to fit residues: 168.6012 Evaluate side-chains 98 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 136 ASN 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 Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 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 = 0.3818 r_free = 0.3818 target = 0.151700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117948 restraints weight = 9135.605| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.89 r_work: 0.3259 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7378 Z= 0.105 Angle : 0.468 6.064 10012 Z= 0.243 Chirality : 0.040 0.129 1034 Planarity : 0.004 0.037 1293 Dihedral : 4.348 50.036 978 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.19 % Allowed : 14.95 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.80 (0.28), residues: 875 helix: 0.90 (0.25), residues: 422 sheet: 0.90 (0.66), residues: 55 loop : 0.23 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 164 HIS 0.003 0.001 HIS A 240 PHE 0.014 0.001 PHE A 680 TYR 0.015 0.001 TYR A 384 ARG 0.004 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 331) hydrogen bonds : angle 5.08069 ( 951) metal coordination : bond 0.00086 ( 2) SS BOND : bond 0.00272 ( 5) SS BOND : angle 0.89850 ( 10) covalent geometry : bond 0.00214 ( 7371) covalent geometry : angle 0.46785 (10002) *********************** 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 118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.873 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 89 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7441 (tt0) REVERT: A 145 PRO cc_start: 0.8431 (Cg_endo) cc_final: 0.8117 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: A 362 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6943 (mmtt) REVERT: A 533 LYS cc_start: 0.8606 (mmmm) cc_final: 0.8368 (mmtt) REVERT: A 596 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: A 634 TRP cc_start: 0.2410 (OUTLIER) cc_final: 0.1474 (m100) REVERT: B 341 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7497 (mt-10) outliers start: 18 outliers final: 4 residues processed: 115 average time/residue: 1.2295 time to fit residues: 149.5923 Evaluate side-chains 90 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 362 LYS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 596 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.147926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113446 restraints weight = 9426.502| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.94 r_work: 0.3184 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7378 Z= 0.152 Angle : 0.497 5.676 10012 Z= 0.257 Chirality : 0.041 0.129 1034 Planarity : 0.004 0.055 1293 Dihedral : 4.417 48.875 978 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.45 % Allowed : 15.59 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.80 (0.28), residues: 875 helix: 0.93 (0.25), residues: 424 sheet: 0.97 (0.64), residues: 61 loop : 0.16 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 164 HIS 0.005 0.001 HIS A 240 PHE 0.013 0.001 PHE B 364 TYR 0.019 0.001 TYR A 384 ARG 0.007 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04771 ( 331) hydrogen bonds : angle 5.06004 ( 951) metal coordination : bond 0.00094 ( 2) SS BOND : bond 0.00217 ( 5) SS BOND : angle 0.89790 ( 10) covalent geometry : bond 0.00353 ( 7371) covalent geometry : angle 0.49660 (10002) *********************** 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 102 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.897 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 89 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7341 (tp40) REVERT: A 145 PRO cc_start: 0.8483 (Cg_endo) cc_final: 0.8192 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: A 362 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7040 (mmtt) REVERT: A 533 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8375 (mmtt) REVERT: A 634 TRP cc_start: 0.2427 (OUTLIER) cc_final: 0.1387 (m100) REVERT: B 341 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7543 (mt-10) outliers start: 20 outliers final: 6 residues processed: 98 average time/residue: 1.5974 time to fit residues: 166.1494 Evaluate side-chains 88 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 404 VAL 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 61 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 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 = 0.3773 r_free = 0.3773 target = 0.148914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114392 restraints weight = 9330.501| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.96 r_work: 0.3195 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7378 Z= 0.117 Angle : 0.472 6.950 10012 Z= 0.245 Chirality : 0.040 0.131 1034 Planarity : 0.004 0.045 1293 Dihedral : 4.346 48.921 978 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.19 % Allowed : 15.85 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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 (0.28), residues: 875 helix: 1.10 (0.26), residues: 423 sheet: 0.82 (0.62), residues: 61 loop : 0.14 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 PHE 0.012 0.001 PHE B 364 TYR 0.017 0.001 TYR A 384 ARG 0.004 0.000 ARG B 395 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 331) hydrogen bonds : angle 4.91983 ( 951) metal coordination : bond 0.00090 ( 2) SS BOND : bond 0.00159 ( 5) SS BOND : angle 1.10212 ( 10) covalent geometry : bond 0.00260 ( 7371) covalent geometry : angle 0.47118 (10002) *********************** 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 107 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.818 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 145 PRO cc_start: 0.8454 (Cg_endo) cc_final: 0.8176 (Cg_exo) REVERT: A 155 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: A 362 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7131 (mmtt) REVERT: A 634 TRP cc_start: 0.2449 (OUTLIER) cc_final: 0.1358 (m100) REVERT: A 703 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6660 (pt) REVERT: B 341 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7483 (mt-10) outliers start: 18 outliers final: 8 residues processed: 105 average time/residue: 1.3851 time to fit residues: 153.5570 Evaluate side-chains 97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 362 LYS Chi-restraints excluded: chain A residue 435 ILE 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 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 66 optimal weight: 7.9990 chunk 19 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 84 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 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 = 0.3778 r_free = 0.3778 target = 0.149424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115158 restraints weight = 9383.884| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.96 r_work: 0.3209 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2952 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= 0.106 Angle : 0.463 7.588 10012 Z= 0.239 Chirality : 0.040 0.131 1034 Planarity : 0.004 0.040 1293 Dihedral : 4.270 48.306 978 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.58 % Allowed : 15.21 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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 (0.28), residues: 875 helix: 1.20 (0.26), residues: 424 sheet: 0.78 (0.65), residues: 55 loop : 0.20 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 164 HIS 0.003 0.001 HIS A 240 PHE 0.010 0.001 PHE A 522 TYR 0.016 0.001 TYR A 384 ARG 0.007 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 331) hydrogen bonds : angle 4.83628 ( 951) metal coordination : bond 0.00043 ( 2) SS BOND : bond 0.00171 ( 5) SS BOND : angle 0.98979 ( 10) covalent geometry : bond 0.00232 ( 7371) covalent geometry : angle 0.46177 (10002) *********************** 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 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.343 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 57 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: A 155 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: A 362 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7174 (mmtt) REVERT: A 581 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7925 (mppt) REVERT: A 634 TRP cc_start: 0.2530 (OUTLIER) cc_final: 0.1400 (m100) REVERT: B 341 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7473 (mt-10) outliers start: 21 outliers final: 8 residues processed: 105 average time/residue: 1.9574 time to fit residues: 216.8144 Evaluate side-chains 94 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 400 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP 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 0 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 0.0070 chunk 69 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113156 restraints weight = 9116.281| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.95 r_work: 0.3200 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7378 Z= 0.114 Angle : 0.470 8.012 10012 Z= 0.242 Chirality : 0.040 0.131 1034 Planarity : 0.004 0.058 1293 Dihedral : 4.264 48.157 978 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.45 % Allowed : 15.34 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.06 (0.28), residues: 875 helix: 1.24 (0.26), residues: 423 sheet: 0.83 (0.66), residues: 55 loop : 0.22 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 PHE 0.011 0.001 PHE A 522 TYR 0.017 0.001 TYR A 384 ARG 0.003 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 331) hydrogen bonds : angle 4.83085 ( 951) metal coordination : bond 0.00067 ( 2) SS BOND : bond 0.00160 ( 5) SS BOND : angle 0.89235 ( 10) covalent geometry : bond 0.00256 ( 7371) covalent geometry : angle 0.46955 (10002) *********************** 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 109 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.737 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 57 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7845 (pm20) REVERT: A 155 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: A 362 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7252 (mmtt) REVERT: A 581 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7897 (mppt) REVERT: A 634 TRP cc_start: 0.2583 (OUTLIER) cc_final: 0.1455 (m100) REVERT: B 341 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7472 (mt-10) outliers start: 20 outliers final: 10 residues processed: 104 average time/residue: 1.2796 time to fit residues: 140.4373 Evaluate side-chains 104 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 0.0270 chunk 19 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 0.0070 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3821 r_free = 0.3821 target = 0.151810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118190 restraints weight = 9097.913| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.88 r_work: 0.3273 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7378 Z= 0.096 Angle : 0.460 8.538 10012 Z= 0.236 Chirality : 0.039 0.131 1034 Planarity : 0.004 0.057 1293 Dihedral : 4.181 47.731 978 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.58 % Allowed : 15.34 % 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 (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: 1.14 (0.28), residues: 875 helix: 1.38 (0.26), residues: 416 sheet: 0.87 (0.66), residues: 55 loop : 0.19 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 164 HIS 0.002 0.001 HIS A 240 PHE 0.010 0.001 PHE A 522 TYR 0.015 0.001 TYR A 384 ARG 0.004 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 331) hydrogen bonds : angle 4.73474 ( 951) metal coordination : bond 0.00040 ( 2) SS BOND : bond 0.00134 ( 5) SS BOND : angle 0.73905 ( 10) covalent geometry : bond 0.00201 ( 7371) covalent geometry : angle 0.45918 (10002) *********************** 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 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.816 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 155 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: A 339 ARG cc_start: 0.8493 (mtm180) cc_final: 0.7964 (mtm110) REVERT: A 362 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7317 (mmtt) REVERT: A 634 TRP cc_start: 0.2648 (OUTLIER) cc_final: 0.1537 (m100) REVERT: A 681 ASN cc_start: 0.6598 (m-40) cc_final: 0.6284 (m110) REVERT: B 341 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: B 342 ARG cc_start: 0.8865 (ttm170) cc_final: 0.8644 (ttm170) outliers start: 21 outliers final: 6 residues processed: 107 average time/residue: 1.2198 time to fit residues: 138.1530 Evaluate side-chains 96 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 375 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3770 r_free = 0.3770 target = 0.148626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114134 restraints weight = 9451.176| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.97 r_work: 0.3197 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7378 Z= 0.130 Angle : 0.496 9.102 10012 Z= 0.252 Chirality : 0.041 0.134 1034 Planarity : 0.004 0.057 1293 Dihedral : 4.257 47.229 978 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.42 % Allowed : 16.75 % 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 (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: 1.10 (0.28), residues: 875 helix: 1.35 (0.26), residues: 417 sheet: 0.84 (0.67), residues: 55 loop : 0.18 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 PHE 0.012 0.001 PHE A 32 TYR 0.018 0.001 TYR A 384 ARG 0.004 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 331) hydrogen bonds : angle 4.78163 ( 951) metal coordination : bond 0.00093 ( 2) SS BOND : bond 0.00175 ( 5) SS BOND : angle 0.87401 ( 10) covalent geometry : bond 0.00303 ( 7371) covalent geometry : angle 0.49538 (10002) *********************** 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 94 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.866 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 155 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: A 362 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7386 (mmtt) REVERT: A 634 TRP cc_start: 0.2761 (OUTLIER) cc_final: 0.1553 (m100) REVERT: A 681 ASN cc_start: 0.6615 (m-40) cc_final: 0.6315 (m110) REVERT: B 341 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7490 (mt-10) outliers start: 12 outliers final: 7 residues processed: 92 average time/residue: 1.2730 time to fit residues: 123.7855 Evaluate side-chains 92 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 LYS 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 602 PRO 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 84 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3765 r_free = 0.3765 target = 0.148313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113924 restraints weight = 9527.347| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.95 r_work: 0.3190 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7378 Z= 0.129 Angle : 0.498 9.070 10012 Z= 0.253 Chirality : 0.041 0.136 1034 Planarity : 0.004 0.058 1293 Dihedral : 4.286 45.723 978 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.42 % Allowed : 16.75 % 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 (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: 1.08 (0.28), residues: 875 helix: 1.30 (0.26), residues: 421 sheet: 0.88 (0.63), residues: 61 loop : 0.16 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 PHE 0.011 0.001 PHE A 32 TYR 0.018 0.001 TYR A 384 ARG 0.008 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 331) hydrogen bonds : angle 4.80653 ( 951) metal coordination : bond 0.00072 ( 2) SS BOND : bond 0.00172 ( 5) SS BOND : angle 0.94674 ( 10) covalent geometry : bond 0.00298 ( 7371) covalent geometry : angle 0.49754 (10002) ********************** 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 95 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.750 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 155 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 362 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7457 (mmtt) REVERT: A 407 MET cc_start: 0.9189 (mmt) cc_final: 0.8576 (mmt) REVERT: A 634 TRP cc_start: 0.2814 (OUTLIER) cc_final: 0.1574 (m100) outliers start: 12 outliers final: 6 residues processed: 93 average time/residue: 1.2556 time to fit residues: 123.1448 Evaluate side-chains 91 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 155 GLU 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 602 PRO Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 72 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.149324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114969 restraints weight = 9322.712| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.95 r_work: 0.3197 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7378 Z= 0.115 Angle : 0.489 9.091 10012 Z= 0.249 Chirality : 0.040 0.134 1034 Planarity : 0.004 0.058 1293 Dihedral : 4.243 45.574 978 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.29 % Allowed : 17.14 % 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 (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: 1.12 (0.28), residues: 875 helix: 1.33 (0.26), residues: 421 sheet: 0.80 (0.67), residues: 55 loop : 0.23 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 164 HIS 0.003 0.001 HIS A 240 PHE 0.012 0.001 PHE B 361 TYR 0.017 0.001 TYR A 384 ARG 0.006 0.000 ARG B 395 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 331) hydrogen bonds : angle 4.75221 ( 951) metal coordination : bond 0.00053 ( 2) SS BOND : bond 0.00151 ( 5) SS BOND : angle 0.85288 ( 10) covalent geometry : bond 0.00259 ( 7371) covalent geometry : angle 0.48871 (10002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6681.51 seconds wall clock time: 118 minutes 24.19 seconds (7104.19 seconds total)